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Posted to users@airavata.apache.org by Heejoon Chae <he...@cs.indiana.edu> on 2015/12/16 23:38:34 UTC
Airavata, monitoring thourgh email : parsing error
Hi,
I have succeeded run job with SLURM.
Now, the job monitoring through email causes some errors as bellow.
It seems the Airavata server correctly log in the email account and bring
email list, but it could not parse it correctly.
#################################################################################
[ERROR] [EJM]: Error parsing email message
=====================================>
org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
identify Resource job manager type from address airavata@bhi2.snu.ac.kr
at
org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
at
org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
at
org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
at
org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
at java.lang.Thread.run(Thread.java:745)
[ERROR] FROM: airavata@bhi2.snu.ac.kr
[ERROR] TO: snu.biovlab@gmail.com
[ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
00:00:01, COMPLETED, ExitCode 0
#################################################################################
Thank you,
Heejoon.
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Since the master is undergoing testing, we have been testing against it. But very soon we will get off the master and do the development on master so we should not get constant build issues on master.
Suresh
> On Dec 21, 2015, at 8:34 PM, Supun Nakandala <su...@gmail.com> wrote:
>
> The build should work fine now.
>
> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Unfortunately, the compile fails at certain point,
>
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 7:41.368s
> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
> [INFO] Final Memory: 95M/3073M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-client-samples: Compilation failure: Compilation failure:
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>
> Now it seems building goes correctly!
>
> Thank you!
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Yes. I am using java 1.8
>
> [heechae@biobrainpool airavata]$ which java
> /packages/jdk1.8.0_65/bin/java
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> I hope you are using java 1.8.
>
> Thanks..
> Chathuri
>
> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Supun,
>
> Thank you for fixing that. I updated and do mvn clean install.
> I got some errors like,
>
> INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 7.754s
> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
> [INFO] Final Memory: 36M/1931M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-data-models: Fatal error compiling: invalid target release: 1.8 -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException <http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException>
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the command
> [ERROR] mvn <goals> -rf :airavata-data-models
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> There was an issue in the pom files and I fixed it now. Can you check whether your build is working now
>
> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> I got following as well,
>
> [INFO] Scanning for projects...
> [ERROR] The build could not read 2 projects -> [Help 1]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException <http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException>
> [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException <http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException>
>
> Thanks,
> Heejoon.
>
> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Instead of building only credential store module, could you build from airavata source root. Credential store module depends on airavata-server-configuration and other jars. That should resolve your issue..
>
> Thanks.
> Chathuri
>
> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Chathuri,
>
> Thank you for the explanation.
>
> I cloned the git and tried to compile credential-store with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following errors.
>
>
> ###############################################################################################################
> Downloaded: http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar <http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar> (571 KB at 2.8 KB/sec)
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 3:53.576s
> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
> [INFO] Final Memory: 11M/1931M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project airavata-credential-store: Could not resolve dependencies for project org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The following artifacts could not be resolved: org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots <http://repository.apache.org/snapshots>) -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException <http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException>
> ###############################################################################################################
>
> Any suggestion?
>
> Thanks,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> You need to set up a valid credential store token in the credential store (experiment-catalog database has tables related to credential store). Same credential store token needs to be set in gateway profiles. This token is used when airavata ssh to resource, input staging and all the remote connections with the resource. Credential store token is the identifier for SSH credential object which contains valid SSH keys. Refer this code https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java <https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java>. There are API methods to generate SSH keys as well. You can use any of the two methods.
>
> Thanks..
> Chathuri
>
>
>
> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Suresh,
>
> Thank you for the help. It correctly parses the email.
>
> Now I have another error caused by 'credential token' as below,
>
> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output staging failed, reason: Provided credential store token is not valid. Please provide the correct credential store token
> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed FAILED -> FAILED
> [INFO] Publishing status to rabbitmq...
> [ERROR] GFac Worker throws an exception
> org.apache.airavata.gfac.core.GFacException: Error while staging output data
> at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
> at org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
> at org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
> I actually set 'false' for storing credential in the 'airavata-server.properties' file as bellow
>
> start.credential.store=false
>
> but it seems still they are active.
>
> Thank you,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> Hi Heejoon,
>
> You will need to configure your email within gfac-config.yaml (you will find it in the bin directory).
>
> If you can add your email to:
>
> - jobManagerType: SLURM
> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
> emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
> resourceEmailAddresses:
> - SDSC Admin <slurm@comet-fe3.sdsc.edu <ma...@comet-fe3.sdsc.edu>> # comet
> - slurm@batch1.stampede.tacc.utexas.edu <ma...@batch1.stampede.tacc.utexas.edu> # stampede
> - airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>
>
> Thanks,
> Suresh
>
> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> >
> > Hi, Suresh,
> >
> > I am using one month old version of PGA and Airavata server. Both were recent version at that time.
> >
> > apache-airavata-server-0.16-SNAPSHOT
> >
> > Thank you,
> > Heejoon.
> >
> >
> >
> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> > Hi Heejoon,
> >
> > Are you using Airavata 0.15 or 0.16 for this purpose?
> >
> > Suresh
> >
> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> >>
> >> Hi,
> >>
> >> I have succeeded run job with SLURM.
> >>
> >> Now, the job monitoring through email causes some errors as bellow.
> >>
> >> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
> >>
> >> #################################################################################
> >> [ERROR] [EJM]: Error parsing email message =====================================>
> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
> >> at java.lang.Thread.run(Thread.java:745)
> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> >> [ERROR] TO: snu.biovlab@gmail.com <ma...@gmail.com>
> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
> >> #################################################################################
> >>
> >> Thank you,
> >> Heejoon.
> >
> >
>
>
>
>
>
>
>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
>
>
>
>
>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Thank you!
I can generate credential token from PGA. Now I am facing the same issue
Nachi mentioned.
I have admin role, but don't see registering computing resource which was
previously available.
Heejoon.
On Tue, Jan 5, 2016 at 10:49 PM, Chathuri Wimalasena <ka...@gmail.com>
wrote:
> Hi Heejon,
>
> When you configure credential store, you need to give a symmetric key in
> the configuration file. Please generate a symmetric key as mentioned in
> step 4 in this link.
> https://cwiki.apache.org/confluence/display/AIRAVATA/Credential+Store+Configuration+Guide
> .
>
> Thanks..
> Chathuri
>
> On Mon, Jan 4, 2016 at 9:16 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Good!
>>
>> I am now able to log in PGA with locally deployed Airavata server.
>>
>> Now I can see the menu for creating credential token. I tried to create
>> credential token, but got following errors.
>>
>> I am using default
>> '/usr/local/apache2/htdocs/apache-airavata-server-0.16-SNAPSHOT/bin/airavata.jks'
>> as store.
>>
>>
>> ##########################################################################################################################
>> [ERROR] Error occurred while saving SSH Credentials.
>> org.apache.airavata.credential.store.store.CredentialStoreException:
>> Error encrypting data
>> at
>> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:441)
>> at
>> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:99)
>> at
>> org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:66)
>> at
>> org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:97)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:802)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:786)
>> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>> at
>> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
>> at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>> Caused by: java.security.InvalidKeyException: No installed provider
>> supports this key: (null)
>> at javax.crypto.Cipher.chooseProvider(Cipher.java:893)
>> at javax.crypto.Cipher.init(Cipher.java:1396)
>> at javax.crypto.Cipher.init(Cipher.java:1327)
>> at
>> org.apache.airavata.common.utils.SecurityUtil.encrypt(SecurityUtil.java:106)
>> at
>> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:439)
>> ... 11 more
>> [ERROR] Error occurred while registering SSH Credential
>> CredentialStoreException(message:Error occurred while saving SSH
>> Credentials.)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2949)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2927)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:2869)
>> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:171)
>> at
>> org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:158)
>> at
>> org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:284)
>> at
>> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.CGLIB$generateAndRegisterSSHKeys$130(<generated>)
>> at
>> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee$$FastClassByGuice$$85c2369d.invoke(<generated>)
>> at
>> com.google.inject.internal.cglib.proxy.$MethodProxy.invokeSuper(MethodProxy.java:228)
>> at
>> com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
>> at
>> org.apache.airavata.api.server.security.interceptor.SecurityInterceptor.invoke(SecurityInterceptor.java:57)
>> at
>> com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
>> at
>> com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
>> at
>> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.generateAndRegisterSSHKeys(<generated>)
>> at
>> org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13273)
>> at
>> org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13257)
>> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>> at
>> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
>> at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> ##########################################################################################################################
>>
>>
>> *BTW, I am also not seeing the 'register computing resource' menu as
>> Nachi mentioned before.*
>>
>> Thank you,
>> Heejoon.
>>
>> On Mon, Jan 4, 2016 at 8:12 PM, Suresh Marru <sm...@apache.org> wrote:
>>
>>> Hi Heejoon,
>>>
>>> Good Catch. Did you do a composer update in the airavata-php-gateway
>>> folder once you did a clone? This will pull the required dependencies into
>>> the vendor folder.
>>>
>>> Suresh
>>>
>>> On Jan 4, 2016, at 3:32 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>>
>>> Hi, Supun,
>>>
>>> I got this error when I locally try to open
>>>
>>> 'http://localhost/test/airavata-php-gateway/public/index.php' on latest
>>> PGA cloned from 'https://github.com/apache/airavata-php-gateway'
>>>
>>> It seems there is no 'vendor' folder which I guess previous version had.
>>>
>>> Thank you,
>>> Heejoon.
>>>
>>> On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <
>>> supun.nakandala@gmail.com> wrote:
>>>
>>>> In the current version navigation link to the previous home page was
>>>> removed. Instead a new landing page is shown. But the link to previous home
>>>> page
>>>> <server-root>/public/home will take you the previous home page.
>>>>
>>>> On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> For some reasons, I cannot see the main page of recent version of PGA.
>>>>> Is current one being in the middle of update or do I need to set it up
>>>>> differently?
>>>>>
>>>>> After clone from https://github.com/apache/airavata-php-gateway,
>>>>> I only set the app/config/pga_config.php.template to pga_config.php as
>>>>> I set before.
>>>>>
>>>>> I also checked previous version of PGA that I deployed couple of
>>>>> months ago and it is working correctly.
>>>>>
>>>>> Thank you,
>>>>> Heejoon.
>>>>>
>>>>> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway
>>>>>> '.
>>>>>>
>>>>>> Please make the name as 'biovlab_snu'. Should this set to admin user
>>>>>> name?
>>>>>>
>>>>>> Customizing the theme is good addition :)
>>>>>>
>>>>>> Thank you,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> Yes please upgrade PGA as well. As well as the default name will not
>>>>>>> work, pick a name for your gateway. We can assist you in customizing the
>>>>>>> theme for your gateway. You can look at this as a example of a customized
>>>>>>> theme - https://seagrid.org/
>>>>>>>
>>>>>>> Suresh
>>>>>>>
>>>>>>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Suresh,
>>>>>>>
>>>>>>> Should I use latest PGA as well? I only updated Airavata server
>>>>>>> recently. I am currently using identity server hosted by SciGaP.
>>>>>>>
>>>>>>> Is the name of gateway written in this section?
>>>>>>> /**
>>>>>>> * PGA Gateway ID
>>>>>>> */
>>>>>>> 'gateway-id' => 'php_reference_gateway',
>>>>>>>
>>>>>>> or
>>>>>>>
>>>>>>> /**
>>>>>>> * Tenant Domain
>>>>>>> */
>>>>>>> 'tenant-domain' => 'master.airavata',
>>>>>>>
>>>>>>> /**
>>>>>>> * Tenant admin's username
>>>>>>> */
>>>>>>> 'admin-username' => 'master',
>>>>>>>
>>>>>>> /**
>>>>>>> * Tenant admin's password
>>>>>>> */
>>>>>>> 'admin-password' => 'master',
>>>>>>>
>>>>>>>
>>>>>>> By the way, I have admin permission with default ID 'master' if the
>>>>>>> admin you mentioned is same as this.
>>>>>>>
>>>>>>> Briefly, I am using locally hosted lastest Airavata server with 1 or
>>>>>>> 2 month old locally running PGA, and use identity server hosted by SciGaP.
>>>>>>> I registered own computing resource locally with SLURM job submission
>>>>>>> interface.
>>>>>>>
>>>>>>> Thank you!
>>>>>>> Heejoon.
>>>>>>>
>>>>>>>
>>>>>>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Heejoon,
>>>>>>>>
>>>>>>>> If you have latest Airavata (master), then you can use the user
>>>>>>>> interface in PGA to create credential store tokens. Only admins can
>>>>>>>> register tokens. Are you using your own identity server or the one hosted
>>>>>>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>>>>>>> set up a tenant for you and make you an admin for it.
>>>>>>>>
>>>>>>>> Suresh
>>>>>>>>
>>>>>>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have succeeded to build recent version. Now I have compiled
>>>>>>>> class located at
>>>>>>>>
>>>>>>>>
>>>>>>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>>>>>>
>>>>>>>> How can I run that to generate credential token?
>>>>>>>>
>>>>>>>> I tried
>>>>>>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>>>>>>> but it says
>>>>>>>>
>>>>>>>>
>>>>>>>> #############################################################################################
>>>>>>>> [heechae@biobrainpool test-classes]$ java
>>>>>>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>>>>>>> Error: A JNI error has occurred, please check your installation and
>>>>>>>> try again
>>>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>>>>>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>>>>>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>>>>>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>>>>>>> at java.lang.Class.getMethod0(Class.java:3018)
>>>>>>>> at java.lang.Class.getMethod(Class.java:1784)
>>>>>>>> at
>>>>>>>> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>>>>>>> at
>>>>>>>> sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>>>>>>> Caused by: java.lang.ClassNotFoundException:
>>>>>>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>>>> ... 7 more
>>>>>>>>
>>>>>>>> ############################################################################################
>>>>>>>>
>>>>>>>>
>>>>>>>> it seems it cannot find dependent classes.
>>>>>>>>
>>>>>>>> I manually copied all required classes to same location and tried
>>>>>>>> to run, but at the end I still got
>>>>>>>>
>>>>>>>>
>>>>>>>> ##############################################################################################
>>>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>>>> org/slf4j/LoggerFactory
>>>>>>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>>>>>>> at
>>>>>>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>>>>>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>>>> ... 2 more
>>>>>>>>
>>>>>>>> ##############################################################################################
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> The build should work fine now.
>>>>>>>>>
>>>>>>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Unfortunately, the compile fails at certain point,
>>>>>>>>>>
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [INFO] Total time: 7:41.368s
>>>>>>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>>>>>>> [INFO] Final Memory: 95M/3073M
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>>>>>>> Compilation failure:
>>>>>>>>>> [ERROR]
>>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>>> [ERROR]
>>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>>> [ERROR]
>>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> Sorry, I found my JAVA_HOME set to different location even I use
>>>>>>>>>>> java 1.8.
>>>>>>>>>>>
>>>>>>>>>>> Now it seems building goes correctly!
>>>>>>>>>>>
>>>>>>>>>>> Thank you!
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Yes. I am using java 1.8
>>>>>>>>>>>>
>>>>>>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I hope you are using java 1.8.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi, Supun,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>>>>>>> I got some errors like,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>>> logging.
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] After correcting the problems, you can resume the
>>>>>>>>>>>>>> build with the command
>>>>>>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can
>>>>>>>>>>>>>>> you check whether your build is working now
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I got following as well,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Instead of building only credential store module, could
>>>>>>>>>>>>>>>>> you build from airavata source root. Credential store module depends on
>>>>>>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I cloned the git and tried to compile credential-store
>>>>>>>>>>>>>>>>>> with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but
>>>>>>>>>>>>>>>>>> got following errors.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>>>>>>> artifact
>>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots)
>>>>>>>>>>>>>>>>>> -> [Help 1]
>>>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>>>> [ERROR] For more information about the errors and
>>>>>>>>>>>>>>>>>> possible solutions, please read the following articles:
>>>>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Now I have another error caused by 'credential token'
>>>>>>>>>>>>>>>>>>>> as below,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error
>>>>>>>>>>>>>>>>>>>> while staging output data
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some
>>>>>>>>>>>>>>>>>>>>> errors as bellow.
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the
>>>>>>>>>>>>>>>>>>>>> email account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
>>>>>>>>>>>>>>>>>>>>> identify Resource job manager type from address
>>>>>>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>> Supun Nakandala
>>>>>>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>>>>>>> University of Moratuwa
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thank you
>>>>>>>>> Supun Nakandala
>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>> University of Moratuwa
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Thank you
>>>> Supun Nakandala
>>>> Dept. Computer Science and Engineering
>>>> University of Moratuwa
>>>>
>>>
>>> <???? 린샷 2016-01-04 오후 5.27.14.png>
>>>
>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Chathuri Wimalasena <ka...@gmail.com>.
Hi Heejon,
When you configure credential store, you need to give a symmetric key in
the configuration file. Please generate a symmetric key as mentioned in
step 4 in this link.
https://cwiki.apache.org/confluence/display/AIRAVATA/Credential+Store+Configuration+Guide
.
Thanks..
Chathuri
On Mon, Jan 4, 2016 at 9:16 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
> Good!
>
> I am now able to log in PGA with locally deployed Airavata server.
>
> Now I can see the menu for creating credential token. I tried to create
> credential token, but got following errors.
>
> I am using default
> '/usr/local/apache2/htdocs/apache-airavata-server-0.16-SNAPSHOT/bin/airavata.jks'
> as store.
>
>
> ##########################################################################################################################
> [ERROR] Error occurred while saving SSH Credentials.
> org.apache.airavata.credential.store.store.CredentialStoreException: Error
> encrypting data
> at
> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:441)
> at
> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:99)
> at
> org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:66)
> at
> org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:97)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:802)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:786)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.security.InvalidKeyException: No installed provider
> supports this key: (null)
> at javax.crypto.Cipher.chooseProvider(Cipher.java:893)
> at javax.crypto.Cipher.init(Cipher.java:1396)
> at javax.crypto.Cipher.init(Cipher.java:1327)
> at
> org.apache.airavata.common.utils.SecurityUtil.encrypt(SecurityUtil.java:106)
> at
> org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:439)
> ... 11 more
> [ERROR] Error occurred while registering SSH Credential
> CredentialStoreException(message:Error occurred while saving SSH
> Credentials.)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2949)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2927)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:2869)
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:171)
> at
> org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:158)
> at
> org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:284)
> at
> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.CGLIB$generateAndRegisterSSHKeys$130(<generated>)
> at
> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee$$FastClassByGuice$$85c2369d.invoke(<generated>)
> at
> com.google.inject.internal.cglib.proxy.$MethodProxy.invokeSuper(MethodProxy.java:228)
> at
> com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
> at
> org.apache.airavata.api.server.security.interceptor.SecurityInterceptor.invoke(SecurityInterceptor.java:57)
> at
> com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
> at
> com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
> at
> org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.generateAndRegisterSSHKeys(<generated>)
> at
> org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13273)
> at
> org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13257)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
> ##########################################################################################################################
>
>
> *BTW, I am also not seeing the 'register computing resource' menu as Nachi
> mentioned before.*
>
> Thank you,
> Heejoon.
>
> On Mon, Jan 4, 2016 at 8:12 PM, Suresh Marru <sm...@apache.org> wrote:
>
>> Hi Heejoon,
>>
>> Good Catch. Did you do a composer update in the airavata-php-gateway
>> folder once you did a clone? This will pull the required dependencies into
>> the vendor folder.
>>
>> Suresh
>>
>> On Jan 4, 2016, at 3:32 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>
>> Hi, Supun,
>>
>> I got this error when I locally try to open
>>
>> 'http://localhost/test/airavata-php-gateway/public/index.php' on latest
>> PGA cloned from 'https://github.com/apache/airavata-php-gateway'
>>
>> It seems there is no 'vendor' folder which I guess previous version had.
>>
>> Thank you,
>> Heejoon.
>>
>> On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <
>> supun.nakandala@gmail.com> wrote:
>>
>>> In the current version navigation link to the previous home page was
>>> removed. Instead a new landing page is shown. But the link to previous home
>>> page
>>> <server-root>/public/home will take you the previous home page.
>>>
>>> On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> For some reasons, I cannot see the main page of recent version of PGA.
>>>> Is current one being in the middle of update or do I need to set it up
>>>> differently?
>>>>
>>>> After clone from https://github.com/apache/airavata-php-gateway,
>>>> I only set the app/config/pga_config.php.template to pga_config.php as
>>>> I set before.
>>>>
>>>> I also checked previous version of PGA that I deployed couple of months
>>>> ago and it is working correctly.
>>>>
>>>> Thank you,
>>>> Heejoon.
>>>>
>>>> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway
>>>>> '.
>>>>>
>>>>> Please make the name as 'biovlab_snu'. Should this set to admin user
>>>>> name?
>>>>>
>>>>> Customizing the theme is good addition :)
>>>>>
>>>>> Thank you,
>>>>> Heejoon.
>>>>>
>>>>> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org>
>>>>> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> Yes please upgrade PGA as well. As well as the default name will not
>>>>>> work, pick a name for your gateway. We can assist you in customizing the
>>>>>> theme for your gateway. You can look at this as a example of a customized
>>>>>> theme - https://seagrid.org/
>>>>>>
>>>>>> Suresh
>>>>>>
>>>>>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Hi Suresh,
>>>>>>
>>>>>> Should I use latest PGA as well? I only updated Airavata server
>>>>>> recently. I am currently using identity server hosted by SciGaP.
>>>>>>
>>>>>> Is the name of gateway written in this section?
>>>>>> /**
>>>>>> * PGA Gateway ID
>>>>>> */
>>>>>> 'gateway-id' => 'php_reference_gateway',
>>>>>>
>>>>>> or
>>>>>>
>>>>>> /**
>>>>>> * Tenant Domain
>>>>>> */
>>>>>> 'tenant-domain' => 'master.airavata',
>>>>>>
>>>>>> /**
>>>>>> * Tenant admin's username
>>>>>> */
>>>>>> 'admin-username' => 'master',
>>>>>>
>>>>>> /**
>>>>>> * Tenant admin's password
>>>>>> */
>>>>>> 'admin-password' => 'master',
>>>>>>
>>>>>>
>>>>>> By the way, I have admin permission with default ID 'master' if the
>>>>>> admin you mentioned is same as this.
>>>>>>
>>>>>> Briefly, I am using locally hosted lastest Airavata server with 1 or
>>>>>> 2 month old locally running PGA, and use identity server hosted by SciGaP.
>>>>>> I registered own computing resource locally with SLURM job submission
>>>>>> interface.
>>>>>>
>>>>>> Thank you!
>>>>>> Heejoon.
>>>>>>
>>>>>>
>>>>>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> If you have latest Airavata (master), then you can use the user
>>>>>>> interface in PGA to create credential store tokens. Only admins can
>>>>>>> register tokens. Are you using your own identity server or the one hosted
>>>>>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>>>>>> set up a tenant for you and make you an admin for it.
>>>>>>>
>>>>>>> Suresh
>>>>>>>
>>>>>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have succeeded to build recent version. Now I have compiled class
>>>>>>> located at
>>>>>>>
>>>>>>>
>>>>>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>>>>>
>>>>>>> How can I run that to generate credential token?
>>>>>>>
>>>>>>> I tried
>>>>>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>>>>>> but it says
>>>>>>>
>>>>>>>
>>>>>>> #############################################################################################
>>>>>>> [heechae@biobrainpool test-classes]$ java
>>>>>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>>>>>> Error: A JNI error has occurred, please check your installation and
>>>>>>> try again
>>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>>>>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>>>>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>>>>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>>>>>> at java.lang.Class.getMethod0(Class.java:3018)
>>>>>>> at java.lang.Class.getMethod(Class.java:1784)
>>>>>>> at
>>>>>>> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>>>>>> at
>>>>>>> sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>>>>>> Caused by: java.lang.ClassNotFoundException:
>>>>>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>>> ... 7 more
>>>>>>>
>>>>>>> ############################################################################################
>>>>>>>
>>>>>>>
>>>>>>> it seems it cannot find dependent classes.
>>>>>>>
>>>>>>> I manually copied all required classes to same location and tried to
>>>>>>> run, but at the end I still got
>>>>>>>
>>>>>>>
>>>>>>> ##############################################################################################
>>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>>> org/slf4j/LoggerFactory
>>>>>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>>>>>> at
>>>>>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>>>>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>>> ... 2 more
>>>>>>>
>>>>>>> ##############################################################################################
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>
>>>>>>>> The build should work fine now.
>>>>>>>>
>>>>>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Unfortunately, the compile fails at certain point,
>>>>>>>>>
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [INFO] Total time: 7:41.368s
>>>>>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>>>>>> [INFO] Final Memory: 95M/3073M
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>>>>>> Compilation failure:
>>>>>>>>> [ERROR]
>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>> [ERROR]
>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>> [ERROR]
>>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Sorry, I found my JAVA_HOME set to different location even I use
>>>>>>>>>> java 1.8.
>>>>>>>>>>
>>>>>>>>>> Now it seems building goes correctly!
>>>>>>>>>>
>>>>>>>>>> Thank you!
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> Yes. I am using java 1.8
>>>>>>>>>>>
>>>>>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>
>>>>>>>>>>>> I hope you are using java 1.8.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks..
>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi, Supun,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>>>>>> I got some errors like,
>>>>>>>>>>>>>
>>>>>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>> logging.
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] After correcting the problems, you can resume the
>>>>>>>>>>>>> build with the command
>>>>>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can
>>>>>>>>>>>>>> you check whether your build is working now
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I got following as well,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I cloned the git and tried to compile credential-store
>>>>>>>>>>>>>>>>> with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but
>>>>>>>>>>>>>>>>> got following errors.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>>>>>> artifact
>>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots)
>>>>>>>>>>>>>>>>> -> [Help 1]
>>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some
>>>>>>>>>>>>>>>>>>>> errors as bellow.
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the
>>>>>>>>>>>>>>>>>>>> email account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
>>>>>>>>>>>>>>>>>>>> identify Resource job manager type from address
>>>>>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>> Supun Nakandala
>>>>>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>>>>>> University of Moratuwa
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thank you
>>>>>>>> Supun Nakandala
>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>> University of Moratuwa
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>
>> <???? 린샷 2016-01-04 오후 5.27.14.png>
>>
>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Good!
I am now able to log in PGA with locally deployed Airavata server.
Now I can see the menu for creating credential token. I tried to create
credential token, but got following errors.
I am using default
'/usr/local/apache2/htdocs/apache-airavata-server-0.16-SNAPSHOT/bin/airavata.jks'
as store.
##########################################################################################################################
[ERROR] Error occurred while saving SSH Credentials.
org.apache.airavata.credential.store.store.CredentialStoreException: Error
encrypting data
at
org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:441)
at
org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:99)
at
org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:66)
at
org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:97)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:802)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:786)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.security.InvalidKeyException: No installed provider
supports this key: (null)
at javax.crypto.Cipher.chooseProvider(Cipher.java:893)
at javax.crypto.Cipher.init(Cipher.java:1396)
at javax.crypto.Cipher.init(Cipher.java:1327)
at
org.apache.airavata.common.utils.SecurityUtil.encrypt(SecurityUtil.java:106)
at
org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.convertObjectToByteArray(CredentialsDAO.java:439)
... 11 more
[ERROR] Error occurred while registering SSH Credential
CredentialStoreException(message:Error occurred while saving SSH
Credentials.)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2949)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:2927)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:2869)
at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:171)
at
org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:158)
at
org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:284)
at
org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.CGLIB$generateAndRegisterSSHKeys$130(<generated>)
at
org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee$$FastClassByGuice$$85c2369d.invoke(<generated>)
at
com.google.inject.internal.cglib.proxy.$MethodProxy.invokeSuper(MethodProxy.java:228)
at
com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
at
org.apache.airavata.api.server.security.interceptor.SecurityInterceptor.invoke(SecurityInterceptor.java:57)
at
com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75)
at
com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
at
org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$523447ee.generateAndRegisterSSHKeys(<generated>)
at
org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13273)
at
org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:13257)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
##########################################################################################################################
*BTW, I am also not seeing the 'register computing resource' menu as Nachi
mentioned before.*
Thank you,
Heejoon.
On Mon, Jan 4, 2016 at 8:12 PM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> Good Catch. Did you do a composer update in the airavata-php-gateway
> folder once you did a clone? This will pull the required dependencies into
> the vendor folder.
>
> Suresh
>
> On Jan 4, 2016, at 3:32 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi, Supun,
>
> I got this error when I locally try to open
>
> 'http://localhost/test/airavata-php-gateway/public/index.php' on latest
> PGA cloned from 'https://github.com/apache/airavata-php-gateway'
>
> It seems there is no 'vendor' folder which I guess previous version had.
>
> Thank you,
> Heejoon.
>
> On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <
> supun.nakandala@gmail.com> wrote:
>
>> In the current version navigation link to the previous home page was
>> removed. Instead a new landing page is shown. But the link to previous home
>> page
>> <server-root>/public/home will take you the previous home page.
>>
>> On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> For some reasons, I cannot see the main page of recent version of PGA.
>>> Is current one being in the middle of update or do I need to set it up
>>> differently?
>>>
>>> After clone from https://github.com/apache/airavata-php-gateway,
>>> I only set the app/config/pga_config.php.template to pga_config.php as I
>>> set before.
>>>
>>> I also checked previous version of PGA that I deployed couple of months
>>> ago and it is working correctly.
>>>
>>> Thank you,
>>> Heejoon.
>>>
>>> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway'.
>>>>
>>>> Please make the name as 'biovlab_snu'. Should this set to admin user
>>>> name?
>>>>
>>>> Customizing the theme is good addition :)
>>>>
>>>> Thank you,
>>>> Heejoon.
>>>>
>>>> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> Yes please upgrade PGA as well. As well as the default name will not
>>>>> work, pick a name for your gateway. We can assist you in customizing the
>>>>> theme for your gateway. You can look at this as a example of a customized
>>>>> theme - https://seagrid.org/
>>>>>
>>>>> Suresh
>>>>>
>>>>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>> Hi Suresh,
>>>>>
>>>>> Should I use latest PGA as well? I only updated Airavata server
>>>>> recently. I am currently using identity server hosted by SciGaP.
>>>>>
>>>>> Is the name of gateway written in this section?
>>>>> /**
>>>>> * PGA Gateway ID
>>>>> */
>>>>> 'gateway-id' => 'php_reference_gateway',
>>>>>
>>>>> or
>>>>>
>>>>> /**
>>>>> * Tenant Domain
>>>>> */
>>>>> 'tenant-domain' => 'master.airavata',
>>>>>
>>>>> /**
>>>>> * Tenant admin's username
>>>>> */
>>>>> 'admin-username' => 'master',
>>>>>
>>>>> /**
>>>>> * Tenant admin's password
>>>>> */
>>>>> 'admin-password' => 'master',
>>>>>
>>>>>
>>>>> By the way, I have admin permission with default ID 'master' if the
>>>>> admin you mentioned is same as this.
>>>>>
>>>>> Briefly, I am using locally hosted lastest Airavata server with 1 or 2
>>>>> month old locally running PGA, and use identity server hosted by SciGaP. I
>>>>> registered own computing resource locally with SLURM job submission
>>>>> interface.
>>>>>
>>>>> Thank you!
>>>>> Heejoon.
>>>>>
>>>>>
>>>>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org>
>>>>> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> If you have latest Airavata (master), then you can use the user
>>>>>> interface in PGA to create credential store tokens. Only admins can
>>>>>> register tokens. Are you using your own identity server or the one hosted
>>>>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>>>>> set up a tenant for you and make you an admin for it.
>>>>>>
>>>>>> Suresh
>>>>>>
>>>>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have succeeded to build recent version. Now I have compiled class
>>>>>> located at
>>>>>>
>>>>>>
>>>>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>>>>
>>>>>> How can I run that to generate credential token?
>>>>>>
>>>>>> I tried
>>>>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>>>>> but it says
>>>>>>
>>>>>>
>>>>>> #############################################################################################
>>>>>> [heechae@biobrainpool test-classes]$ java
>>>>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>>>>> Error: A JNI error has occurred, please check your installation and
>>>>>> try again
>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>>>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>>>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>>>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>>>>> at java.lang.Class.getMethod0(Class.java:3018)
>>>>>> at java.lang.Class.getMethod(Class.java:1784)
>>>>>> at
>>>>>> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>>>>> at
>>>>>> sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>>>>> Caused by: java.lang.ClassNotFoundException:
>>>>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>> ... 7 more
>>>>>>
>>>>>> ############################################################################################
>>>>>>
>>>>>>
>>>>>> it seems it cannot find dependent classes.
>>>>>>
>>>>>> I manually copied all required classes to same location and tried to
>>>>>> run, but at the end I still got
>>>>>>
>>>>>>
>>>>>> ##############################################################################################
>>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>>> org/slf4j/LoggerFactory
>>>>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>>>>> at
>>>>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>>>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>>> ... 2 more
>>>>>>
>>>>>> ##############################################################################################
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>
>>>>>>> The build should work fine now.
>>>>>>>
>>>>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Unfortunately, the compile fails at certain point,
>>>>>>>>
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [INFO] Total time: 7:41.368s
>>>>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>>>>> [INFO] Final Memory: 95M/3073M
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>>>>> Compilation failure:
>>>>>>>> [ERROR]
>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>> [ERROR]
>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>> [ERROR]
>>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Sorry, I found my JAVA_HOME set to different location even I use
>>>>>>>>> java 1.8.
>>>>>>>>>
>>>>>>>>> Now it seems building goes correctly!
>>>>>>>>>
>>>>>>>>> Thank you!
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Yes. I am using java 1.8
>>>>>>>>>>
>>>>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>
>>>>>>>>>>> I hope you are using java 1.8.
>>>>>>>>>>>
>>>>>>>>>>> Thanks..
>>>>>>>>>>> Chathuri
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi, Supun,
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>>>>> I got some errors like,
>>>>>>>>>>>>
>>>>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>>>>> [INFO]
>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>>>>> [INFO]
>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>>> with the -e switch.
>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>> logging.
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] After correcting the problems, you can resume the build
>>>>>>>>>>>> with the command
>>>>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>
>>>>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can
>>>>>>>>>>>>> you check whether your build is working now
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I got following as well,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find
>>>>>>>>>>>>>> artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and
>>>>>>>>>>>>>> 'parent.relativePath' points at wrong local POM @ line 5, column 13 ->
>>>>>>>>>>>>>> [Help 2]
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>>> logging.
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I cloned the git and tried to compile credential-store with
>>>>>>>>>>>>>>>> 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>>>>>>> following errors.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>>>>> artifact
>>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots)
>>>>>>>>>>>>>>>> -> [Help 1]
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some
>>>>>>>>>>>>>>>>>>> errors as bellow.
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the
>>>>>>>>>>>>>>>>>>> email account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
>>>>>>>>>>>>>>>>>>> identify Resource job manager type from address
>>>>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>> Supun Nakandala
>>>>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>>>>> University of Moratuwa
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Thank you
>>>>>>> Supun Nakandala
>>>>>>> Dept. Computer Science and Engineering
>>>>>>> University of Moratuwa
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> --
>> Thank you
>> Supun Nakandala
>> Dept. Computer Science and Engineering
>> University of Moratuwa
>>
>
> <???? 린샷 2016-01-04 오후 5.27.14.png>
>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Hi Heejoon,
Good Catch. Did you do a composer update in the airavata-php-gateway folder once you did a clone? This will pull the required dependencies into the vendor folder.
Suresh
> On Jan 4, 2016, at 3:32 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi, Supun,
>
> I got this error when I locally try to open
>
> 'http://localhost/test/airavata-php-gateway/public/index.php <http://localhost/test/airavata-php-gateway/public/index.php>' on latest PGA cloned from 'https://github.com/apache/airavata-php-gateway <https://github.com/apache/airavata-php-gateway>'
>
> It seems there is no 'vendor' folder which I guess previous version had.
>
> Thank you,
> Heejoon.
>
> On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
> In the current version navigation link to the previous home page was removed. Instead a new landing page is shown. But the link to previous home page
> <server-root>/public/home will take you the previous home page.
>
> On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi,
>
> For some reasons, I cannot see the main page of recent version of PGA.
> Is current one being in the middle of update or do I need to set it up differently?
>
> After clone from https://github.com/apache/airavata-php-gateway <https://github.com/apache/airavata-php-gateway>,
> I only set the app/config/pga_config.php.template to pga_config.php as I set before.
>
> I also checked previous version of PGA that I deployed couple of months ago and it is working correctly.
>
> Thank you,
> Heejoon.
>
> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway <https://github.com/apache/airavata-php-gateway>'.
>
> Please make the name as 'biovlab_snu'. Should this set to admin user name?
>
> Customizing the theme is good addition :)
>
> Thank you,
> Heejoon.
>
> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> Hi Heejoon,
>
> Yes please upgrade PGA as well. As well as the default name will not work, pick a name for your gateway. We can assist you in customizing the theme for your gateway. You can look at this as a example of a customized theme - https://seagrid.org/ <https://seagrid.org/>
>
> Suresh
>
>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>
>> Hi Suresh,
>>
>> Should I use latest PGA as well? I only updated Airavata server recently. I am currently using identity server hosted by SciGaP.
>>
>> Is the name of gateway written in this section?
>> /**
>> * PGA Gateway ID
>> */
>> 'gateway-id' => 'php_reference_gateway',
>>
>> or
>>
>> /**
>> * Tenant Domain
>> */
>> 'tenant-domain' => 'master.airavata',
>>
>> /**
>> * Tenant admin's username
>> */
>> 'admin-username' => 'master',
>>
>> /**
>> * Tenant admin's password
>> */
>> 'admin-password' => 'master',
>>
>>
>> By the way, I have admin permission with default ID 'master' if the admin you mentioned is same as this.
>>
>> Briefly, I am using locally hosted lastest Airavata server with 1 or 2 month old locally running PGA, and use identity server hosted by SciGaP. I registered own computing resource locally with SLURM job submission interface.
>>
>> Thank you!
>> Heejoon.
>>
>>
>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
>> Hi Heejoon,
>>
>> If you have latest Airavata (master), then you can use the user interface in PGA to create credential store tokens. Only admins can register tokens. Are you using your own identity server or the one hosted by SciGaP? Can you briefly tell what is the name of your gateway so we can set up a tenant for you and make you an admin for it.
>>
>> Suresh
>>
>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>>
>>> Hi,
>>>
>>> I have succeeded to build recent version. Now I have compiled class located at
>>>
>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>
>>> How can I run that to generate credential token?
>>>
>>> I tried 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest', but it says
>>>
>>> #############################################################################################
>>> [heechae@biobrainpool test-classes]$ java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>> Error: A JNI error has occurred, please check your installation and try again
>>> Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/airavata/common/exception/ApplicationSettingsException
>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>> at java.lang.Class.getMethod0(Class.java:3018)
>>> at java.lang.Class.getMethod(Class.java:1784)
>>> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>> Caused by: java.lang.ClassNotFoundException: org.apache.airavata.common.exception.ApplicationSettingsException
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>> ... 7 more
>>> ############################################################################################
>>>
>>>
>>> it seems it cannot find dependent classes.
>>>
>>> I manually copied all required classes to same location and tried to run, but at the end I still got
>>>
>>> ##############################################################################################
>>> Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>> at org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>> ... 2 more
>>> ##############################################################################################
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
>>> The build should work fine now.
>>>
>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Unfortunately, the compile fails at certain point,
>>>
>>> [INFO] ------------------------------------------------------------------------
>>> [INFO] BUILD FAILURE
>>> [INFO] ------------------------------------------------------------------------
>>> [INFO] Total time: 7:41.368s
>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>> [INFO] Final Memory: 95M/3073M
>>> [INFO] ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-client-samples: Compilation failure: Compilation failure:
>>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>>>
>>> Now it seems building goes correctly!
>>>
>>> Thank you!
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Yes. I am using java 1.8
>>>
>>> [heechae@biobrainpool airavata]$ which java
>>> /packages/jdk1.8.0_65/bin/java
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>>> Hi Heejoon,
>>>
>>> I hope you are using java 1.8.
>>>
>>> Thanks..
>>> Chathuri
>>>
>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Hi, Supun,
>>>
>>> Thank you for fixing that. I updated and do mvn clean install.
>>> I got some errors like,
>>>
>>> INFO] BUILD FAILURE
>>> [INFO] ------------------------------------------------------------------------
>>> [INFO] Total time: 7.754s
>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>> [INFO] Final Memory: 36M/1931M
>>> [INFO] ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-data-models: Fatal error compiling: invalid target release: 1.8 -> [Help 1]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException <http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException>
>>> [ERROR]
>>> [ERROR] After correcting the problems, you can resume the build with the command
>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
>>> Hi Heejoon,
>>>
>>> There was an issue in the pom files and I fixed it now. Can you check whether your build is working now
>>>
>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> I got following as well,
>>>
>>> [INFO] Scanning for projects...
>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>> [ERROR]
>>> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) has 1 error
>>> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
>>> [ERROR]
>>> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) has 1 error
>>> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException <http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException>
>>> [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException <http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException>
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>>> Instead of building only credential store module, could you build from airavata source root. Credential store module depends on airavata-server-configuration and other jars. That should resolve your issue..
>>>
>>> Thanks.
>>> Chathuri
>>>
>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Hi, Chathuri,
>>>
>>> Thank you for the explanation.
>>>
>>> I cloned the git and tried to compile credential-store with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following errors.
>>>
>>>
>>> ###############################################################################################################
>>> Downloaded: http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar <http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar> (571 KB at 2.8 KB/sec)
>>> [INFO] ------------------------------------------------------------------------
>>> [INFO] BUILD FAILURE
>>> [INFO] ------------------------------------------------------------------------
>>> [INFO] Total time: 3:53.576s
>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>> [INFO] Final Memory: 11M/1931M
>>> [INFO] ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal on project airavata-credential-store: Could not resolve dependencies for project org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The following artifacts could not be resolved: org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots <http://repository.apache.org/snapshots>) -> [Help 1]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException <http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException>
>>> ###############################################################################################################
>>>
>>> Any suggestion?
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>>> Hi Heejoon,
>>>
>>> You need to set up a valid credential store token in the credential store (experiment-catalog database has tables related to credential store). Same credential store token needs to be set in gateway profiles. This token is used when airavata ssh to resource, input staging and all the remote connections with the resource. Credential store token is the identifier for SSH credential object which contains valid SSH keys. Refer this code https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java <https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java>. There are API methods to generate SSH keys as well. You can use any of the two methods.
>>>
>>> Thanks..
>>> Chathuri
>>>
>>>
>>>
>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> Hi, Suresh,
>>>
>>> Thank you for the help. It correctly parses the email.
>>>
>>> Now I have another error caused by 'credential token' as below,
>>>
>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output staging failed, reason: Provided credential store token is not valid. Please provide the correct credential store token
>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed FAILED -> FAILED
>>> [INFO] Publishing status to rabbitmq...
>>> [ERROR] GFac Worker throws an exception
>>> org.apache.airavata.gfac.core.GFacException: Error while staging output data
>>> at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>> at org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>> at org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> I actually set 'false' for storing credential in the 'airavata-server.properties' file as bellow
>>>
>>> start.credential.store=false
>>>
>>> but it seems still they are active.
>>>
>>> Thank you,
>>> Heejoon.
>>>
>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
>>> Hi Heejoon,
>>>
>>> You will need to configure your email within gfac-config.yaml (you will find it in the bin directory).
>>>
>>> If you can add your email to:
>>>
>>> - jobManagerType: SLURM
>>> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>> emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>> resourceEmailAddresses:
>>> - SDSC Admin <slurm@comet-fe3.sdsc.edu <ma...@comet-fe3.sdsc.edu>> # comet
>>> - slurm@batch1.stampede.tacc.utexas.edu <ma...@batch1.stampede.tacc.utexas.edu> # stampede
>>> - airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>>>
>>>
>>> Thanks,
>>> Suresh
>>>
>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> >
>>> > Hi, Suresh,
>>> >
>>> > I am using one month old version of PGA and Airavata server. Both were recent version at that time.
>>> >
>>> > apache-airavata-server-0.16-SNAPSHOT
>>> >
>>> > Thank you,
>>> > Heejoon.
>>> >
>>> >
>>> >
>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
>>> > Hi Heejoon,
>>> >
>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>> >
>>> > Suresh
>>> >
>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> I have succeeded run job with SLURM.
>>> >>
>>> >> Now, the job monitoring through email causes some errors as bellow.
>>> >>
>>> >> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
>>> >>
>>> >> #################################################################################
>>> >> [ERROR] [EJM]: Error parsing email message =====================================>
>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>> >> at java.lang.Thread.run(Thread.java:745)
>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>>> >> [ERROR] TO: snu.biovlab@gmail.com <ma...@gmail.com>
>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>> >> #################################################################################
>>> >>
>>> >> Thank you,
>>> >> Heejoon.
>>> >
>>> >
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>
>>
>
>
>
>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
> <???? 린샷 2016-01-04 오후 5.27.14.png>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi, Supun,
I got this error when I locally try to open
'http://localhost/test/airavata-php-gateway/public/index.php' on latest PGA
cloned from 'https://github.com/apache/airavata-php-gateway'
It seems there is no 'vendor' folder which I guess previous version had.
Thank you,
Heejoon.
On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <su...@gmail.com>
wrote:
> In the current version navigation link to the previous home page was
> removed. Instead a new landing page is shown. But the link to previous home
> page
> <server-root>/public/home will take you the previous home page.
>
> On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Hi,
>>
>> For some reasons, I cannot see the main page of recent version of PGA.
>> Is current one being in the middle of update or do I need to set it up
>> differently?
>>
>> After clone from https://github.com/apache/airavata-php-gateway,
>> I only set the app/config/pga_config.php.template to pga_config.php as I
>> set before.
>>
>> I also checked previous version of PGA that I deployed couple of months
>> ago and it is working correctly.
>>
>> Thank you,
>> Heejoon.
>>
>> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway'.
>>>
>>> Please make the name as 'biovlab_snu'. Should this set to admin user
>>> name?
>>>
>>> Customizing the theme is good addition :)
>>>
>>> Thank you,
>>> Heejoon.
>>>
>>> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> Yes please upgrade PGA as well. As well as the default name will not
>>>> work, pick a name for your gateway. We can assist you in customizing the
>>>> theme for your gateway. You can look at this as a example of a customized
>>>> theme - https://seagrid.org/
>>>>
>>>> Suresh
>>>>
>>>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>> Hi Suresh,
>>>>
>>>> Should I use latest PGA as well? I only updated Airavata server
>>>> recently. I am currently using identity server hosted by SciGaP.
>>>>
>>>> Is the name of gateway written in this section?
>>>> /**
>>>> * PGA Gateway ID
>>>> */
>>>> 'gateway-id' => 'php_reference_gateway',
>>>>
>>>> or
>>>>
>>>> /**
>>>> * Tenant Domain
>>>> */
>>>> 'tenant-domain' => 'master.airavata',
>>>>
>>>> /**
>>>> * Tenant admin's username
>>>> */
>>>> 'admin-username' => 'master',
>>>>
>>>> /**
>>>> * Tenant admin's password
>>>> */
>>>> 'admin-password' => 'master',
>>>>
>>>>
>>>> By the way, I have admin permission with default ID 'master' if the
>>>> admin you mentioned is same as this.
>>>>
>>>> Briefly, I am using locally hosted lastest Airavata server with 1 or 2
>>>> month old locally running PGA, and use identity server hosted by SciGaP. I
>>>> registered own computing resource locally with SLURM job submission
>>>> interface.
>>>>
>>>> Thank you!
>>>> Heejoon.
>>>>
>>>>
>>>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org>
>>>> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> If you have latest Airavata (master), then you can use the user
>>>>> interface in PGA to create credential store tokens. Only admins can
>>>>> register tokens. Are you using your own identity server or the one hosted
>>>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>>>> set up a tenant for you and make you an admin for it.
>>>>>
>>>>> Suresh
>>>>>
>>>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have succeeded to build recent version. Now I have compiled class
>>>>> located at
>>>>>
>>>>>
>>>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>>>
>>>>> How can I run that to generate credential token?
>>>>>
>>>>> I tried
>>>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>>>> but it says
>>>>>
>>>>>
>>>>> #############################################################################################
>>>>> [heechae@biobrainpool test-classes]$ java
>>>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>>>> Error: A JNI error has occurred, please check your installation and
>>>>> try again
>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>>>> at java.lang.Class.getMethod0(Class.java:3018)
>>>>> at java.lang.Class.getMethod(Class.java:1784)
>>>>> at
>>>>> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>>>> at
>>>>> sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>>>> Caused by: java.lang.ClassNotFoundException:
>>>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>> ... 7 more
>>>>>
>>>>> ############################################################################################
>>>>>
>>>>>
>>>>> it seems it cannot find dependent classes.
>>>>>
>>>>> I manually copied all required classes to same location and tried to
>>>>> run, but at the end I still got
>>>>>
>>>>>
>>>>> ##############################################################################################
>>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>>> org/slf4j/LoggerFactory
>>>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>>>> at
>>>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>>> ... 2 more
>>>>>
>>>>> ##############################################################################################
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>>>> supun.nakandala@gmail.com> wrote:
>>>>>
>>>>>> The build should work fine now.
>>>>>>
>>>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <heechae@cs.indiana.edu
>>>>>> > wrote:
>>>>>>
>>>>>>> Unfortunately, the compile fails at certain point,
>>>>>>>
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [INFO] BUILD FAILURE
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [INFO] Total time: 7:41.368s
>>>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>>>> [INFO] Final Memory: 95M/3073M
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [ERROR] Failed to execute goal
>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>>>> Compilation failure:
>>>>>>> [ERROR]
>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>> [ERROR]
>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>> [ERROR]
>>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Sorry, I found my JAVA_HOME set to different location even I use
>>>>>>>> java 1.8.
>>>>>>>>
>>>>>>>> Now it seems building goes correctly!
>>>>>>>>
>>>>>>>> Thank you!
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Yes. I am using java 1.8
>>>>>>>>>
>>>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>
>>>>>>>>>> I hope you are using java 1.8.
>>>>>>>>>>
>>>>>>>>>> Thanks..
>>>>>>>>>> Chathuri
>>>>>>>>>>
>>>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi, Supun,
>>>>>>>>>>>
>>>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>>>> I got some errors like,
>>>>>>>>>>>
>>>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>>>> [INFO]
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>>>> [INFO]
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>> with the -e switch.
>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>> logging.
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] After correcting the problems, you can resume the build
>>>>>>>>>>> with the command
>>>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>
>>>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>>>>>>> check whether your build is working now
>>>>>>>>>>>>
>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> I got following as well,
>>>>>>>>>>>>>
>>>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>>>> has 1 error
>>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>> logging.
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I cloned the git and tried to compile credential-store with
>>>>>>>>>>>>>>> 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>>>>>> following errors.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>>>> artifact
>>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots)
>>>>>>>>>>>>>>> -> [Help 1]
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full
>>>>>>>>>>>>>>> debug logging.
>>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some
>>>>>>>>>>>>>>>>>> errors as bellow.
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the
>>>>>>>>>>>>>>>>>> email account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
>>>>>>>>>>>>>>>>>> identify Resource job manager type from address
>>>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Thank you
>>>>>>>>>>>> Supun Nakandala
>>>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>>>> University of Moratuwa
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Thank you
>>>>>> Supun Nakandala
>>>>>> Dept. Computer Science and Engineering
>>>>>> University of Moratuwa
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Supun Nakandala <su...@gmail.com>.
In the current version navigation link to the previous home page was
removed. Instead a new landing page is shown. But the link to previous home
page
<server-root>/public/home will take you the previous home page.
On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
> Hi,
>
> For some reasons, I cannot see the main page of recent version of PGA.
> Is current one being in the middle of update or do I need to set it up
> differently?
>
> After clone from https://github.com/apache/airavata-php-gateway,
> I only set the app/config/pga_config.php.template to pga_config.php as I
> set before.
>
> I also checked previous version of PGA that I deployed couple of months
> ago and it is working correctly.
>
> Thank you,
> Heejoon.
>
> On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway'.
>>
>> Please make the name as 'biovlab_snu'. Should this set to admin user name?
>>
>> Customizing the theme is good addition :)
>>
>> Thank you,
>> Heejoon.
>>
>> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org> wrote:
>>
>>> Hi Heejoon,
>>>
>>> Yes please upgrade PGA as well. As well as the default name will not
>>> work, pick a name for your gateway. We can assist you in customizing the
>>> theme for your gateway. You can look at this as a example of a customized
>>> theme - https://seagrid.org/
>>>
>>> Suresh
>>>
>>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>>
>>> Hi Suresh,
>>>
>>> Should I use latest PGA as well? I only updated Airavata server
>>> recently. I am currently using identity server hosted by SciGaP.
>>>
>>> Is the name of gateway written in this section?
>>> /**
>>> * PGA Gateway ID
>>> */
>>> 'gateway-id' => 'php_reference_gateway',
>>>
>>> or
>>>
>>> /**
>>> * Tenant Domain
>>> */
>>> 'tenant-domain' => 'master.airavata',
>>>
>>> /**
>>> * Tenant admin's username
>>> */
>>> 'admin-username' => 'master',
>>>
>>> /**
>>> * Tenant admin's password
>>> */
>>> 'admin-password' => 'master',
>>>
>>>
>>> By the way, I have admin permission with default ID 'master' if the
>>> admin you mentioned is same as this.
>>>
>>> Briefly, I am using locally hosted lastest Airavata server with 1 or 2
>>> month old locally running PGA, and use identity server hosted by SciGaP. I
>>> registered own computing resource locally with SLURM job submission
>>> interface.
>>>
>>> Thank you!
>>> Heejoon.
>>>
>>>
>>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> If you have latest Airavata (master), then you can use the user
>>>> interface in PGA to create credential store tokens. Only admins can
>>>> register tokens. Are you using your own identity server or the one hosted
>>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>>> set up a tenant for you and make you an admin for it.
>>>>
>>>> Suresh
>>>>
>>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have succeeded to build recent version. Now I have compiled class
>>>> located at
>>>>
>>>>
>>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>>
>>>> How can I run that to generate credential token?
>>>>
>>>> I tried
>>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>>> but it says
>>>>
>>>>
>>>> #############################################################################################
>>>> [heechae@biobrainpool test-classes]$ java
>>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>>> Error: A JNI error has occurred, please check your installation and try
>>>> again
>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>>> at java.lang.Class.getMethod0(Class.java:3018)
>>>> at java.lang.Class.getMethod(Class.java:1784)
>>>> at
>>>> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>>> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>>> Caused by: java.lang.ClassNotFoundException:
>>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>> ... 7 more
>>>>
>>>> ############################################################################################
>>>>
>>>>
>>>> it seems it cannot find dependent classes.
>>>>
>>>> I manually copied all required classes to same location and tried to
>>>> run, but at the end I still got
>>>>
>>>>
>>>> ##############################################################################################
>>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>>> org/slf4j/LoggerFactory
>>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>>> at
>>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>> ... 2 more
>>>>
>>>> ##############################################################################################
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>>> supun.nakandala@gmail.com> wrote:
>>>>
>>>>> The build should work fine now.
>>>>>
>>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> Unfortunately, the compile fails at certain point,
>>>>>>
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [INFO] BUILD FAILURE
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [INFO] Total time: 7:41.368s
>>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>>> [INFO] Final Memory: 95M/3073M
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [ERROR] Failed to execute goal
>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>>> Compilation failure:
>>>>>> [ERROR]
>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>> [ERROR]
>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>> [ERROR]
>>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>>> incompatible types: java.lang.String cannot be converted to
>>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <
>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>
>>>>>>> Sorry, I found my JAVA_HOME set to different location even I use
>>>>>>> java 1.8.
>>>>>>>
>>>>>>> Now it seems building goes correctly!
>>>>>>>
>>>>>>> Thank you!
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Yes. I am using java 1.8
>>>>>>>>
>>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Heejoon,
>>>>>>>>>
>>>>>>>>> I hope you are using java 1.8.
>>>>>>>>>
>>>>>>>>> Thanks..
>>>>>>>>> Chathuri
>>>>>>>>>
>>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi, Supun,
>>>>>>>>>>
>>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>>> I got some errors like,
>>>>>>>>>>
>>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>> with the -e switch.
>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>> logging.
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] After correcting the problems, you can resume the build
>>>>>>>>>> with the command
>>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>
>>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>>>>>> check whether your build is working now
>>>>>>>>>>>
>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> I got following as well,
>>>>>>>>>>>>
>>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>>> has 1 error
>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>>> has 1 error
>>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>>> with the -e switch.
>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>> logging.
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks.
>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I cloned the git and tried to compile credential-store with
>>>>>>>>>>>>>> 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>>>>> following errors.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>>> artifact
>>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>>>>>>> [Help 1]
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>>> logging.
>>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some
>>>>>>>>>>>>>>>>> errors as bellow.
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Thank you
>>>>>>>>>>> Supun Nakandala
>>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>>> University of Moratuwa
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Thank you
>>>>> Supun Nakandala
>>>>> Dept. Computer Science and Engineering
>>>>> University of Moratuwa
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi,
For some reasons, I cannot see the main page of recent version of PGA.
Is current one being in the middle of update or do I need to set it up
differently?
After clone from https://github.com/apache/airavata-php-gateway,
I only set the app/config/pga_config.php.template to pga_config.php as I
set before.
I also checked previous version of PGA that I deployed couple of months ago
and it is working correctly.
Thank you,
Heejoon.
On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
> Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway'.
>
> Please make the name as 'biovlab_snu'. Should this set to admin user name?
>
> Customizing the theme is good addition :)
>
> Thank you,
> Heejoon.
>
> On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org> wrote:
>
>> Hi Heejoon,
>>
>> Yes please upgrade PGA as well. As well as the default name will not
>> work, pick a name for your gateway. We can assist you in customizing the
>> theme for your gateway. You can look at this as a example of a customized
>> theme - https://seagrid.org/
>>
>> Suresh
>>
>> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>
>> Hi Suresh,
>>
>> Should I use latest PGA as well? I only updated Airavata server recently.
>> I am currently using identity server hosted by SciGaP.
>>
>> Is the name of gateway written in this section?
>> /**
>> * PGA Gateway ID
>> */
>> 'gateway-id' => 'php_reference_gateway',
>>
>> or
>>
>> /**
>> * Tenant Domain
>> */
>> 'tenant-domain' => 'master.airavata',
>>
>> /**
>> * Tenant admin's username
>> */
>> 'admin-username' => 'master',
>>
>> /**
>> * Tenant admin's password
>> */
>> 'admin-password' => 'master',
>>
>>
>> By the way, I have admin permission with default ID 'master' if the admin
>> you mentioned is same as this.
>>
>> Briefly, I am using locally hosted lastest Airavata server with 1 or 2
>> month old locally running PGA, and use identity server hosted by SciGaP. I
>> registered own computing resource locally with SLURM job submission
>> interface.
>>
>> Thank you!
>> Heejoon.
>>
>>
>> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org> wrote:
>>
>>> Hi Heejoon,
>>>
>>> If you have latest Airavata (master), then you can use the user
>>> interface in PGA to create credential store tokens. Only admins can
>>> register tokens. Are you using your own identity server or the one hosted
>>> by SciGaP? Can you briefly tell what is the name of your gateway so we can
>>> set up a tenant for you and make you an admin for it.
>>>
>>> Suresh
>>>
>>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>>
>>> Hi,
>>>
>>> I have succeeded to build recent version. Now I have compiled class
>>> located at
>>>
>>>
>>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>>
>>> How can I run that to generate credential token?
>>>
>>> I tried
>>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>>> but it says
>>>
>>>
>>> #############################################################################################
>>> [heechae@biobrainpool test-classes]$ java
>>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>>> Error: A JNI error has occurred, please check your installation and try
>>> again
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> org/apache/airavata/common/exception/ApplicationSettingsException
>>> at java.lang.Class.getDeclaredMethods0(Native Method)
>>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>>> at java.lang.Class.getMethod0(Class.java:3018)
>>> at java.lang.Class.getMethod(Class.java:1784)
>>> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>>> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.apache.airavata.common.exception.ApplicationSettingsException
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>> ... 7 more
>>>
>>> ############################################################################################
>>>
>>>
>>> it seems it cannot find dependent classes.
>>>
>>> I manually copied all required classes to same location and tried to
>>> run, but at the end I still got
>>>
>>>
>>> ##############################################################################################
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> org/slf4j/LoggerFactory
>>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>>> at
>>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>> ... 2 more
>>>
>>> ##############################################################################################
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>>> supun.nakandala@gmail.com> wrote:
>>>
>>>> The build should work fine now.
>>>>
>>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Unfortunately, the compile fails at certain point,
>>>>>
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [INFO] BUILD FAILURE
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [INFO] Total time: 7:41.368s
>>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>>> [INFO] Final Memory: 95M/3073M
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [ERROR] Failed to execute goal
>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>>> Compilation failure:
>>>>> [ERROR]
>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>>> incompatible types: java.lang.String cannot be converted to
>>>>> org.apache.airavata.model.security.AuthzToken
>>>>> [ERROR]
>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>>> incompatible types: java.lang.String cannot be converted to
>>>>> org.apache.airavata.model.security.AuthzToken
>>>>> [ERROR]
>>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>>> incompatible types: java.lang.String cannot be converted to
>>>>> org.apache.airavata.model.security.AuthzToken
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <heechae@cs.indiana.edu
>>>>> > wrote:
>>>>>
>>>>>> Sorry, I found my JAVA_HOME set to different location even I use java
>>>>>> 1.8.
>>>>>>
>>>>>> Now it seems building goes correctly!
>>>>>>
>>>>>> Thank you!
>>>>>> Heejoon.
>>>>>>
>>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <heechae@cs.indiana.edu
>>>>>> > wrote:
>>>>>>
>>>>>>> Yes. I am using java 1.8
>>>>>>>
>>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Heejoon,
>>>>>>>>
>>>>>>>> I hope you are using java 1.8.
>>>>>>>>
>>>>>>>> Thanks..
>>>>>>>> Chathuri
>>>>>>>>
>>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi, Supun,
>>>>>>>>>
>>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>>> I got some errors like,
>>>>>>>>>
>>>>>>>>> INFO] BUILD FAILURE
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>> with the -e switch.
>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>> logging.
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>> solutions, please read the following articles:
>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] After correcting the problems, you can resume the build
>>>>>>>>> with the command
>>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>
>>>>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>>>>> check whether your build is working now
>>>>>>>>>>
>>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> I got following as well,
>>>>>>>>>>>
>>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>>> has 1 error
>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] The project
>>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>>> has 1 error
>>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>> with the -e switch.
>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>> logging.
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks.
>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>
>>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I cloned the git and tried to compile credential-store with
>>>>>>>>>>>>> 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>>>> following errors.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>>> [INFO]
>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>>> artifact
>>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>>>>>> [Help 1]
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run
>>>>>>>>>>>>> Maven with the -e switch.
>>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>>> logging.
>>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>>
>>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>>
>>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors
>>>>>>>>>>>>>>>> as bellow.
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207
>>>>>>>>>>>>>>>> Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Thank you
>>>>>>>>>> Supun Nakandala
>>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>>> University of Moratuwa
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Thank you
>>>> Supun Nakandala
>>>> Dept. Computer Science and Engineering
>>>> University of Moratuwa
>>>>
>>>
>>>
>>>
>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway'.
Please make the name as 'biovlab_snu'. Should this set to admin user name?
Customizing the theme is good addition :)
Thank you,
Heejoon.
On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> Yes please upgrade PGA as well. As well as the default name will not work,
> pick a name for your gateway. We can assist you in customizing the theme
> for your gateway. You can look at this as a example of a customized theme -
> https://seagrid.org/
>
> Suresh
>
> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi Suresh,
>
> Should I use latest PGA as well? I only updated Airavata server recently.
> I am currently using identity server hosted by SciGaP.
>
> Is the name of gateway written in this section?
> /**
> * PGA Gateway ID
> */
> 'gateway-id' => 'php_reference_gateway',
>
> or
>
> /**
> * Tenant Domain
> */
> 'tenant-domain' => 'master.airavata',
>
> /**
> * Tenant admin's username
> */
> 'admin-username' => 'master',
>
> /**
> * Tenant admin's password
> */
> 'admin-password' => 'master',
>
>
> By the way, I have admin permission with default ID 'master' if the admin
> you mentioned is same as this.
>
> Briefly, I am using locally hosted lastest Airavata server with 1 or 2
> month old locally running PGA, and use identity server hosted by SciGaP. I
> registered own computing resource locally with SLURM job submission
> interface.
>
> Thank you!
> Heejoon.
>
>
> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org> wrote:
>
>> Hi Heejoon,
>>
>> If you have latest Airavata (master), then you can use the user interface
>> in PGA to create credential store tokens. Only admins can register tokens.
>> Are you using your own identity server or the one hosted by SciGaP? Can you
>> briefly tell what is the name of your gateway so we can set up a tenant for
>> you and make you an admin for it.
>>
>> Suresh
>>
>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>
>> Hi,
>>
>> I have succeeded to build recent version. Now I have compiled class
>> located at
>>
>>
>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>
>> How can I run that to generate credential token?
>>
>> I tried
>> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
>> but it says
>>
>>
>> #############################################################################################
>> [heechae@biobrainpool test-classes]$ java
>> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>> Error: A JNI error has occurred, please check your installation and try
>> again
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/apache/airavata/common/exception/ApplicationSettingsException
>> at java.lang.Class.getDeclaredMethods0(Native Method)
>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>> at java.lang.Class.getMethod0(Class.java:3018)
>> at java.lang.Class.getMethod(Class.java:1784)
>> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>> Caused by: java.lang.ClassNotFoundException:
>> org.apache.airavata.common.exception.ApplicationSettingsException
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>> ... 7 more
>>
>> ############################################################################################
>>
>>
>> it seems it cannot find dependent classes.
>>
>> I manually copied all required classes to same location and tried to run,
>> but at the end I still got
>>
>>
>> ##############################################################################################
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/slf4j/LoggerFactory
>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>> at
>> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>> ... 2 more
>>
>> ##############################################################################################
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
>> supun.nakandala@gmail.com> wrote:
>>
>>> The build should work fine now.
>>>
>>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Unfortunately, the compile fails at certain point,
>>>>
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [INFO] BUILD FAILURE
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [INFO] Total time: 7:41.368s
>>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>>> [INFO] Final Memory: 95M/3073M
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [ERROR] Failed to execute goal
>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>>> Compilation failure:
>>>> [ERROR]
>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>>> incompatible types: java.lang.String cannot be converted to
>>>> org.apache.airavata.model.security.AuthzToken
>>>> [ERROR]
>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>>> incompatible types: java.lang.String cannot be converted to
>>>> org.apache.airavata.model.security.AuthzToken
>>>> [ERROR]
>>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>>> incompatible types: java.lang.String cannot be converted to
>>>> org.apache.airavata.model.security.AuthzToken
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Sorry, I found my JAVA_HOME set to different location even I use java
>>>>> 1.8.
>>>>>
>>>>> Now it seems building goes correctly!
>>>>>
>>>>> Thank you!
>>>>> Heejoon.
>>>>>
>>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> Yes. I am using java 1.8
>>>>>>
>>>>>> [heechae@biobrainpool airavata]$ which java
>>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>>> kamalasini@gmail.com> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> I hope you are using java 1.8.
>>>>>>>
>>>>>>> Thanks..
>>>>>>> Chathuri
>>>>>>>
>>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Hi, Supun,
>>>>>>>>
>>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>>> I got some errors like,
>>>>>>>>
>>>>>>>> INFO] BUILD FAILURE
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [INFO] Total time: 7.754s
>>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [ERROR] Failed to execute goal
>>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>> with the -e switch.
>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>> logging.
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>> solutions, please read the following articles:
>>>>>>>> [ERROR] [Help 1]
>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] After correcting the problems, you can resume the build
>>>>>>>> with the command
>>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Heejoon,
>>>>>>>>>
>>>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>>>> check whether your build is working now
>>>>>>>>>
>>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> I got following as well,
>>>>>>>>>>
>>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] The project
>>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>>> has 1 error
>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] The project
>>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>>> has 1 error
>>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>> with the -e switch.
>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>> logging.
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Instead of building only credential store module, could you
>>>>>>>>>>> build from airavata source root. Credential store module depends on
>>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>>> resolve your issue..
>>>>>>>>>>>
>>>>>>>>>>> Thanks.
>>>>>>>>>>> Chathuri
>>>>>>>>>>>
>>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>>
>>>>>>>>>>>> I cloned the git and tried to compile credential-store with
>>>>>>>>>>>> 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>>> following errors.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>> Downloaded:
>>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>>> [INFO]
>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>>> [INFO]
>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>>> [INFO]
>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>>> artifact
>>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>>>>> [Help 1]
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>>> with the -e switch.
>>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>>> logging.
>>>>>>>>>>>> [ERROR]
>>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>>
>>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>>
>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>
>>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>>> Refer this code
>>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>>> two methods.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks..
>>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Now I have another error caused by 'credential token' as
>>>>>>>>>>>>>> below,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>>> at
>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> You will need to configure your email within
>>>>>>>>>>>>>>> gfac-config.yaml (you will find it in the bin directory).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors
>>>>>>>>>>>>>>> as bellow.
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended,
>>>>>>>>>>>>>>> Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thank you
>>>>>>>>> Supun Nakandala
>>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>>> University of Moratuwa
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>
>>
>>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Hi Heejoon,
Yes please upgrade PGA as well. As well as the default name will not work, pick a name for your gateway. We can assist you in customizing the theme for your gateway. You can look at this as a example of a customized theme - https://seagrid.org/ <https://seagrid.org/>
Suresh
> On Jan 2, 2016, at 5:19 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi Suresh,
>
> Should I use latest PGA as well? I only updated Airavata server recently. I am currently using identity server hosted by SciGaP.
>
> Is the name of gateway written in this section?
> /**
> * PGA Gateway ID
> */
> 'gateway-id' => 'php_reference_gateway',
>
> or
>
> /**
> * Tenant Domain
> */
> 'tenant-domain' => 'master.airavata',
>
> /**
> * Tenant admin's username
> */
> 'admin-username' => 'master',
>
> /**
> * Tenant admin's password
> */
> 'admin-password' => 'master',
>
>
> By the way, I have admin permission with default ID 'master' if the admin you mentioned is same as this.
>
> Briefly, I am using locally hosted lastest Airavata server with 1 or 2 month old locally running PGA, and use identity server hosted by SciGaP. I registered own computing resource locally with SLURM job submission interface.
>
> Thank you!
> Heejoon.
>
>
> On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> Hi Heejoon,
>
> If you have latest Airavata (master), then you can use the user interface in PGA to create credential store tokens. Only admins can register tokens. Are you using your own identity server or the one hosted by SciGaP? Can you briefly tell what is the name of your gateway so we can set up a tenant for you and make you an admin for it.
>
> Suresh
>
>> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>>
>> Hi,
>>
>> I have succeeded to build recent version. Now I have compiled class located at
>>
>> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>>
>> How can I run that to generate credential token?
>>
>> I tried 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest', but it says
>>
>> #############################################################################################
>> [heechae@biobrainpool test-classes]$ java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
>> Error: A JNI error has occurred, please check your installation and try again
>> Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/airavata/common/exception/ApplicationSettingsException
>> at java.lang.Class.getDeclaredMethods0(Native Method)
>> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
>> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
>> at java.lang.Class.getMethod0(Class.java:3018)
>> at java.lang.Class.getMethod(Class.java:1784)
>> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
>> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
>> Caused by: java.lang.ClassNotFoundException: org.apache.airavata.common.exception.ApplicationSettingsException
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>> ... 7 more
>> ############################################################################################
>>
>>
>> it seems it cannot find dependent classes.
>>
>> I manually copied all required classes to same location and tried to run, but at the end I still got
>>
>> ##############################################################################################
>> Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
>> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
>> at org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
>> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>> ... 2 more
>> ##############################################################################################
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
>> The build should work fine now.
>>
>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Unfortunately, the compile fails at certain point,
>>
>> [INFO] ------------------------------------------------------------------------
>> [INFO] BUILD FAILURE
>> [INFO] ------------------------------------------------------------------------
>> [INFO] Total time: 7:41.368s
>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>> [INFO] Final Memory: 95M/3073M
>> [INFO] ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-client-samples: Compilation failure: Compilation failure:
>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>>
>> Now it seems building goes correctly!
>>
>> Thank you!
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Yes. I am using java 1.8
>>
>> [heechae@biobrainpool airavata]$ which java
>> /packages/jdk1.8.0_65/bin/java
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>> Hi Heejoon,
>>
>> I hope you are using java 1.8.
>>
>> Thanks..
>> Chathuri
>>
>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Hi, Supun,
>>
>> Thank you for fixing that. I updated and do mvn clean install.
>> I got some errors like,
>>
>> INFO] BUILD FAILURE
>> [INFO] ------------------------------------------------------------------------
>> [INFO] Total time: 7.754s
>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>> [INFO] Final Memory: 36M/1931M
>> [INFO] ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-data-models: Fatal error compiling: invalid target release: 1.8 -> [Help 1]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException <http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException>
>> [ERROR]
>> [ERROR] After correcting the problems, you can resume the build with the command
>> [ERROR] mvn <goals> -rf :airavata-data-models
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
>> Hi Heejoon,
>>
>> There was an issue in the pom files and I fixed it now. Can you check whether your build is working now
>>
>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> I got following as well,
>>
>> [INFO] Scanning for projects...
>> [ERROR] The build could not read 2 projects -> [Help 1]
>> [ERROR]
>> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) has 1 error
>> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
>> [ERROR]
>> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) has 1 error
>> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException <http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException>
>> [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException <http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException>
>>
>> Thanks,
>> Heejoon.
>>
>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>> Instead of building only credential store module, could you build from airavata source root. Credential store module depends on airavata-server-configuration and other jars. That should resolve your issue..
>>
>> Thanks.
>> Chathuri
>>
>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Hi, Chathuri,
>>
>> Thank you for the explanation.
>>
>> I cloned the git and tried to compile credential-store with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following errors.
>>
>>
>> ###############################################################################################################
>> Downloaded: http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar <http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar> (571 KB at 2.8 KB/sec)
>> [INFO] ------------------------------------------------------------------------
>> [INFO] BUILD FAILURE
>> [INFO] ------------------------------------------------------------------------
>> [INFO] Total time: 3:53.576s
>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>> [INFO] Final Memory: 11M/1931M
>> [INFO] ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal on project airavata-credential-store: Could not resolve dependencies for project org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The following artifacts could not be resolved: org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots <http://repository.apache.org/snapshots>) -> [Help 1]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException <http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException>
>> ###############################################################################################################
>>
>> Any suggestion?
>>
>> Thanks,
>> Heejoon.
>>
>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
>> Hi Heejoon,
>>
>> You need to set up a valid credential store token in the credential store (experiment-catalog database has tables related to credential store). Same credential store token needs to be set in gateway profiles. This token is used when airavata ssh to resource, input staging and all the remote connections with the resource. Credential store token is the identifier for SSH credential object which contains valid SSH keys. Refer this code https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java <https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java>. There are API methods to generate SSH keys as well. You can use any of the two methods.
>>
>> Thanks..
>> Chathuri
>>
>>
>>
>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> Hi, Suresh,
>>
>> Thank you for the help. It correctly parses the email.
>>
>> Now I have another error caused by 'credential token' as below,
>>
>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output staging failed, reason: Provided credential store token is not valid. Please provide the correct credential store token
>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed FAILED -> FAILED
>> [INFO] Publishing status to rabbitmq...
>> [ERROR] GFac Worker throws an exception
>> org.apache.airavata.gfac.core.GFacException: Error while staging output data
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>> at org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> I actually set 'false' for storing credential in the 'airavata-server.properties' file as bellow
>>
>> start.credential.store=false
>>
>> but it seems still they are active.
>>
>> Thank you,
>> Heejoon.
>>
>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
>> Hi Heejoon,
>>
>> You will need to configure your email within gfac-config.yaml (you will find it in the bin directory).
>>
>> If you can add your email to:
>>
>> - jobManagerType: SLURM
>> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
>> emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>> resourceEmailAddresses:
>> - SDSC Admin <slurm@comet-fe3.sdsc.edu <ma...@comet-fe3.sdsc.edu>> # comet
>> - slurm@batch1.stampede.tacc.utexas.edu <ma...@batch1.stampede.tacc.utexas.edu> # stampede
>> - airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>>
>>
>> Thanks,
>> Suresh
>>
>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> >
>> > Hi, Suresh,
>> >
>> > I am using one month old version of PGA and Airavata server. Both were recent version at that time.
>> >
>> > apache-airavata-server-0.16-SNAPSHOT
>> >
>> > Thank you,
>> > Heejoon.
>> >
>> >
>> >
>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
>> > Hi Heejoon,
>> >
>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>> >
>> > Suresh
>> >
>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
>> >>
>> >> Hi,
>> >>
>> >> I have succeeded run job with SLURM.
>> >>
>> >> Now, the job monitoring through email causes some errors as bellow.
>> >>
>> >> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
>> >>
>> >> #################################################################################
>> >> [ERROR] [EJM]: Error parsing email message =====================================>
>> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>> >> at java.lang.Thread.run(Thread.java:745)
>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>> >> [ERROR] TO: snu.biovlab@gmail.com <ma...@gmail.com>
>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>> >> #################################################################################
>> >>
>> >> Thank you,
>> >> Heejoon.
>> >
>> >
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Thank you
>> Supun Nakandala
>> Dept. Computer Science and Engineering
>> University of Moratuwa
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Thank you
>> Supun Nakandala
>> Dept. Computer Science and Engineering
>> University of Moratuwa
>>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi Suresh,
Should I use latest PGA as well? I only updated Airavata server recently. I
am currently using identity server hosted by SciGaP.
Is the name of gateway written in this section?
/**
* PGA Gateway ID
*/
'gateway-id' => 'php_reference_gateway',
or
/**
* Tenant Domain
*/
'tenant-domain' => 'master.airavata',
/**
* Tenant admin's username
*/
'admin-username' => 'master',
/**
* Tenant admin's password
*/
'admin-password' => 'master',
By the way, I have admin permission with default ID 'master' if the admin
you mentioned is same as this.
Briefly, I am using locally hosted lastest Airavata server with 1 or 2
month old locally running PGA, and use identity server hosted by SciGaP. I
registered own computing resource locally with SLURM job submission
interface.
Thank you!
Heejoon.
On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> If you have latest Airavata (master), then you can use the user interface
> in PGA to create credential store tokens. Only admins can register tokens.
> Are you using your own identity server or the one hosted by SciGaP? Can you
> briefly tell what is the name of your gateway so we can set up a tenant for
> you and make you an admin for it.
>
> Suresh
>
> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi,
>
> I have succeeded to build recent version. Now I have compiled class
> located at
>
>
> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>
> How can I run that to generate credential token?
>
> I tried
> 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
> but it says
>
>
> #############################################################################################
> [heechae@biobrainpool test-classes]$ java
> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
> Error: A JNI error has occurred, please check your installation and try
> again
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/apache/airavata/common/exception/ApplicationSettingsException
> at java.lang.Class.getDeclaredMethods0(Native Method)
> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
> at java.lang.Class.getMethod0(Class.java:3018)
> at java.lang.Class.getMethod(Class.java:1784)
> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
> Caused by: java.lang.ClassNotFoundException:
> org.apache.airavata.common.exception.ApplicationSettingsException
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 7 more
>
> ############################################################################################
>
>
> it seems it cannot find dependent classes.
>
> I manually copied all required classes to same location and tried to run,
> but at the end I still got
>
>
> ##############################################################################################
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/slf4j/LoggerFactory
> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
> at
> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 2 more
>
> ##############################################################################################
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <
> supun.nakandala@gmail.com> wrote:
>
>> The build should work fine now.
>>
>> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Unfortunately, the compile fails at certain point,
>>>
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [INFO] BUILD FAILURE
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [INFO] Total time: 7:41.368s
>>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>>> [INFO] Final Memory: 95M/3073M
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal
>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>> (default-compile) on project airavata-client-samples: Compilation failure:
>>> Compilation failure:
>>> [ERROR]
>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>>> incompatible types: java.lang.String cannot be converted to
>>> org.apache.airavata.model.security.AuthzToken
>>> [ERROR]
>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>>> incompatible types: java.lang.String cannot be converted to
>>> org.apache.airavata.model.security.AuthzToken
>>> [ERROR]
>>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>>> incompatible types: java.lang.String cannot be converted to
>>> org.apache.airavata.model.security.AuthzToken
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Sorry, I found my JAVA_HOME set to different location even I use java
>>>> 1.8.
>>>>
>>>> Now it seems building goes correctly!
>>>>
>>>> Thank you!
>>>> Heejoon.
>>>>
>>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Yes. I am using java 1.8
>>>>>
>>>>> [heechae@biobrainpool airavata]$ which java
>>>>> /packages/jdk1.8.0_65/bin/java
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>>> kamalasini@gmail.com> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> I hope you are using java 1.8.
>>>>>>
>>>>>> Thanks..
>>>>>> Chathuri
>>>>>>
>>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <heechae@cs.indiana.edu
>>>>>> > wrote:
>>>>>>
>>>>>>> Hi, Supun,
>>>>>>>
>>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>>> I got some errors like,
>>>>>>>
>>>>>>> INFO] BUILD FAILURE
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [INFO] Total time: 7.754s
>>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [ERROR] Failed to execute goal
>>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>>> [ERROR]
>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>>> the -e switch.
>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>> logging.
>>>>>>> [ERROR]
>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>> solutions, please read the following articles:
>>>>>>> [ERROR] [Help 1]
>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>>> [ERROR]
>>>>>>> [ERROR] After correcting the problems, you can resume the build with
>>>>>>> the command
>>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Heejoon,
>>>>>>>>
>>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>>> check whether your build is working now
>>>>>>>>
>>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> I got following as well,
>>>>>>>>>
>>>>>>>>> [INFO] Scanning for projects...
>>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] The project
>>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>>> has 1 error
>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] The project
>>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>>> has 1 error
>>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>> with the -e switch.
>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>> logging.
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>> solutions, please read the following articles:
>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>>> [ERROR] [Help 2]
>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Instead of building only credential store module, could you build
>>>>>>>>>> from airavata source root. Credential store module depends on
>>>>>>>>>> airavata-server-configuration and other jars. That should
>>>>>>>>>> resolve your issue..
>>>>>>>>>>
>>>>>>>>>> Thanks.
>>>>>>>>>> Chathuri
>>>>>>>>>>
>>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>>
>>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>>
>>>>>>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>>> following errors.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>> Downloaded:
>>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>>> [INFO]
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>>> [INFO]
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>>> [INFO]
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>>> artifact
>>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>>>> [Help 1]
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>>> with the -e switch.
>>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>>> logging.
>>>>>>>>>>> [ERROR]
>>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>>
>>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>>
>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>
>>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>>> Refer this code
>>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>>> two methods.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks..
>>>>>>>>>>>> Chathuri
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>>>>>>
>>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>>> staging output data
>>>>>>>>>>>>> at
>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>
>>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>>
>>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>>
>>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> You will need to configure your email within gfac-config.yaml
>>>>>>>>>>>>>> (you will find it in the bin directory).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata
>>>>>>>>>>>>>> server. Both were recent version at that time.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors
>>>>>>>>>>>>>> as bellow.
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>>> >> at
>>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended,
>>>>>>>>>>>>>> Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thank you
>>>>>>>> Supun Nakandala
>>>>>>>> Dept. Computer Science and Engineering
>>>>>>>> University of Moratuwa
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>> --
>> Thank you
>> Supun Nakandala
>> Dept. Computer Science and Engineering
>> University of Moratuwa
>>
>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Hi Heejoon,
If you have latest Airavata (master), then you can use the user interface in PGA to create credential store tokens. Only admins can register tokens. Are you using your own identity server or the one hosted by SciGaP? Can you briefly tell what is the name of your gateway so we can set up a tenant for you and make you an admin for it.
Suresh
> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi,
>
> I have succeeded to build recent version. Now I have compiled class located at
>
> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
>
> How can I run that to generate credential token?
>
> I tried 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest', but it says
>
> #############################################################################################
> [heechae@biobrainpool test-classes]$ java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
> Error: A JNI error has occurred, please check your installation and try again
> Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/airavata/common/exception/ApplicationSettingsException
> at java.lang.Class.getDeclaredMethods0(Native Method)
> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
> at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
> at java.lang.Class.getMethod0(Class.java:3018)
> at java.lang.Class.getMethod(Class.java:1784)
> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
> Caused by: java.lang.ClassNotFoundException: org.apache.airavata.common.exception.ApplicationSettingsException
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 7 more
> ############################################################################################
>
>
> it seems it cannot find dependent classes.
>
> I manually copied all required classes to same location and tried to run, but at the end I still got
>
> ##############################################################################################
> Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
> at org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 2 more
> ##############################################################################################
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
> The build should work fine now.
>
> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Unfortunately, the compile fails at certain point,
>
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 7:41.368s
> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
> [INFO] Final Memory: 95M/3073M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-client-samples: Compilation failure: Compilation failure:
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
> [ERROR] /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] incompatible types: java.lang.String cannot be converted to org.apache.airavata.model.security.AuthzToken
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>
> Now it seems building goes correctly!
>
> Thank you!
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Yes. I am using java 1.8
>
> [heechae@biobrainpool airavata]$ which java
> /packages/jdk1.8.0_65/bin/java
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> I hope you are using java 1.8.
>
> Thanks..
> Chathuri
>
> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Supun,
>
> Thank you for fixing that. I updated and do mvn clean install.
> I got some errors like,
>
> INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 7.754s
> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
> [INFO] Final Memory: 36M/1931M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project airavata-data-models: Fatal error compiling: invalid target release: 1.8 -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException <http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException>
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the command
> [ERROR] mvn <goals> -rf :airavata-data-models
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <supun.nakandala@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> There was an issue in the pom files and I fixed it now. Can you check whether your build is working now
>
> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> I got following as well,
>
> [INFO] Scanning for projects...
> [ERROR] The build could not read 2 projects -> [Help 1]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException <http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException>
> [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException <http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException>
>
> Thanks,
> Heejoon.
>
> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Instead of building only credential store module, could you build from airavata source root. Credential store module depends on airavata-server-configuration and other jars. That should resolve your issue..
>
> Thanks.
> Chathuri
>
> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Chathuri,
>
> Thank you for the explanation.
>
> I cloned the git and tried to compile credential-store with 'mvn clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following errors.
>
>
> ###############################################################################################################
> Downloaded: http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar <http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar> (571 KB at 2.8 KB/sec)
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 3:53.576s
> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
> [INFO] Final Memory: 11M/1931M
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project airavata-credential-store: Could not resolve dependencies for project org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The following artifacts could not be resolved: org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots <http://repository.apache.org/snapshots>) -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException <http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException>
> ###############################################################################################################
>
> Any suggestion?
>
> Thanks,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <kamalasini@gmail.com <ma...@gmail.com>> wrote:
> Hi Heejoon,
>
> You need to set up a valid credential store token in the credential store (experiment-catalog database has tables related to credential store). Same credential store token needs to be set in gateway profiles. This token is used when airavata ssh to resource, input staging and all the remote connections with the resource. Credential store token is the identifier for SSH credential object which contains valid SSH keys. Refer this code https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java <https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java>. There are API methods to generate SSH keys as well. You can use any of the two methods.
>
> Thanks..
> Chathuri
>
>
>
> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> Hi, Suresh,
>
> Thank you for the help. It correctly parses the email.
>
> Now I have another error caused by 'credential token' as below,
>
> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output staging failed, reason: Provided credential store token is not valid. Please provide the correct credential store token
> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed FAILED -> FAILED
> [INFO] Publishing status to rabbitmq...
> [ERROR] GFac Worker throws an exception
> org.apache.airavata.gfac.core.GFacException: Error while staging output data
> at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
> at org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
> at org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
> I actually set 'false' for storing credential in the 'airavata-server.properties' file as bellow
>
> start.credential.store=false
>
> but it seems still they are active.
>
> Thank you,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> Hi Heejoon,
>
> You will need to configure your email within gfac-config.yaml (you will find it in the bin directory).
>
> If you can add your email to:
>
> - jobManagerType: SLURM
> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
> emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
> resourceEmailAddresses:
> - SDSC Admin <slurm@comet-fe3.sdsc.edu <ma...@comet-fe3.sdsc.edu>> # comet
> - slurm@batch1.stampede.tacc.utexas.edu <ma...@batch1.stampede.tacc.utexas.edu> # stampede
> - airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
>
>
> Thanks,
> Suresh
>
> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> >
> > Hi, Suresh,
> >
> > I am using one month old version of PGA and Airavata server. Both were recent version at that time.
> >
> > apache-airavata-server-0.16-SNAPSHOT
> >
> > Thank you,
> > Heejoon.
> >
> >
> >
> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <smarru@apache.org <ma...@apache.org>> wrote:
> > Hi Heejoon,
> >
> > Are you using Airavata 0.15 or 0.16 for this purpose?
> >
> > Suresh
> >
> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <heechae@cs.indiana.edu <ma...@cs.indiana.edu>> wrote:
> >>
> >> Hi,
> >>
> >> I have succeeded run job with SLURM.
> >>
> >> Now, the job monitoring through email causes some errors as bellow.
> >>
> >> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
> >>
> >> #################################################################################
> >> [ERROR] [EJM]: Error parsing email message =====================================>
> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
> >> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
> >> at java.lang.Thread.run(Thread.java:745)
> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> >> [ERROR] TO: snu.biovlab@gmail.com <ma...@gmail.com>
> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
> >> #################################################################################
> >>
> >> Thank you,
> >> Heejoon.
> >
> >
>
>
>
>
>
>
>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
>
>
>
>
>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi,
I have succeeded to build recent version. Now I have compiled class
located at
'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class'
How can I run that to generate credential token?
I tried
'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest',
but it says
#############################################################################################
[heechae@biobrainpool test-classes]$ java
org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest
Error: A JNI error has occurred, please check your installation and try
again
Exception in thread "main" java.lang.NoClassDefFoundError:
org/apache/airavata/common/exception/ApplicationSettingsException
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
at java.lang.Class.getMethod0(Class.java:3018)
at java.lang.Class.getMethod(Class.java:1784)
at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException:
org.apache.airavata.common.exception.ApplicationSettingsException
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 7 more
############################################################################################
it seems it cannot find dependent classes.
I manually copied all required classes to same location and tried to run,
but at the end I still got
##############################################################################################
Exception in thread "main" java.lang.NoClassDefFoundError:
org/slf4j/LoggerFactory
at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43)
at
org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 2 more
##############################################################################################
Thanks,
Heejoon.
On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <supun.nakandala@gmail.com
> wrote:
> The build should work fine now.
>
> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Unfortunately, the compile fails at certain point,
>>
>> [INFO]
>> ------------------------------------------------------------------------
>> [INFO] BUILD FAILURE
>> [INFO]
>> ------------------------------------------------------------------------
>> [INFO] Total time: 7:41.368s
>> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
>> [INFO] Final Memory: 95M/3073M
>> [INFO]
>> ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal
>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>> (default-compile) on project airavata-client-samples: Compilation failure:
>> Compilation failure:
>> [ERROR]
>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
>> incompatible types: java.lang.String cannot be converted to
>> org.apache.airavata.model.security.AuthzToken
>> [ERROR]
>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
>> incompatible types: java.lang.String cannot be converted to
>> org.apache.airavata.model.security.AuthzToken
>> [ERROR]
>> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
>> incompatible types: java.lang.String cannot be converted to
>> org.apache.airavata.model.security.AuthzToken
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Sorry, I found my JAVA_HOME set to different location even I use java
>>> 1.8.
>>>
>>> Now it seems building goes correctly!
>>>
>>> Thank you!
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Yes. I am using java 1.8
>>>>
>>>> [heechae@biobrainpool airavata]$ which java
>>>> /packages/jdk1.8.0_65/bin/java
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>>> kamalasini@gmail.com> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> I hope you are using java 1.8.
>>>>>
>>>>> Thanks..
>>>>> Chathuri
>>>>>
>>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi, Supun,
>>>>>>
>>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>>> I got some errors like,
>>>>>>
>>>>>> INFO] BUILD FAILURE
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [INFO] Total time: 7.754s
>>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>>> [INFO] Final Memory: 36M/1931M
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [ERROR] Failed to execute goal
>>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>>> invalid target release: 1.8 -> [Help 1]
>>>>>> [ERROR]
>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>> the -e switch.
>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>>> [ERROR]
>>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>>> please read the following articles:
>>>>>> [ERROR] [Help 1]
>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>>> [ERROR]
>>>>>> [ERROR] After correcting the problems, you can resume the build with
>>>>>> the command
>>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>>> supun.nakandala@gmail.com> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> There was an issue in the pom files and I fixed it now. Can you
>>>>>>> check whether your build is working now
>>>>>>>
>>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> I got following as well,
>>>>>>>>
>>>>>>>> [INFO] Scanning for projects...
>>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] The project
>>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>>> has 1 error
>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] The project
>>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>>> has 1 error
>>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>> with the -e switch.
>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>> logging.
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>> solutions, please read the following articles:
>>>>>>>> [ERROR] [Help 1]
>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>>> [ERROR] [Help 2]
>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Instead of building only credential store module, could you build
>>>>>>>>> from airavata source root. Credential store module depends on
>>>>>>>>> airavata-server-configuration and other jars. That should resolve
>>>>>>>>> your issue..
>>>>>>>>>
>>>>>>>>> Thanks.
>>>>>>>>> Chathuri
>>>>>>>>>
>>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi, Chathuri,
>>>>>>>>>>
>>>>>>>>>> Thank you for the explanation.
>>>>>>>>>>
>>>>>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>>> following errors.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ###############################################################################################################
>>>>>>>>>> Downloaded:
>>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>>> [INFO]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>>> artifact
>>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>>> [Help 1]
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>>> with the -e switch.
>>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>>> logging.
>>>>>>>>>> [ERROR]
>>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>>> solutions, please read the following articles:
>>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>>
>>>>>>>>>> ###############################################################################################################
>>>>>>>>>>
>>>>>>>>>> Any suggestion?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>
>>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>>> Refer this code
>>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>>> two methods.
>>>>>>>>>>>
>>>>>>>>>>> Thanks..
>>>>>>>>>>> Chathuri
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>>
>>>>>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>>>>>
>>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while
>>>>>>>>>>>> staging output data
>>>>>>>>>>>> at
>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>>> at
>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>>> at
>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>>> at
>>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>>> at
>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>>> at
>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>
>>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>>
>>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>>
>>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you,
>>>>>>>>>>>> Heejoon.
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>>
>>>>>>>>>>>>> You will need to configure your email within gfac-config.yaml
>>>>>>>>>>>>> (you will find it in the bin directory).
>>>>>>>>>>>>>
>>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>>
>>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>>> emailParser:
>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>
>>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > I am using one month old version of PGA and Airavata server.
>>>>>>>>>>>>> Both were recent version at that time.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>>> >
>>>>>>>>>>>>> > Suresh
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>>>>>>> bellow.
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>>> =====================================>
>>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>> >> at
>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>>> >> at
>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>>> >> at
>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>>> >> at
>>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended,
>>>>>>>>>>>>> Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>>> >
>>>>>>>>>>>>> >
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Thank you
>>>>>>> Supun Nakandala
>>>>>>> Dept. Computer Science and Engineering
>>>>>>> University of Moratuwa
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Supun Nakandala <su...@gmail.com>.
The build should work fine now.
On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Unfortunately, the compile fails at certain point,
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 7:41.368s
> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
> [INFO] Final Memory: 95M/3073M
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
> (default-compile) on project airavata-client-samples: Compilation failure:
> Compilation failure:
> [ERROR]
> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
> incompatible types: java.lang.String cannot be converted to
> org.apache.airavata.model.security.AuthzToken
> [ERROR]
> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
> incompatible types: java.lang.String cannot be converted to
> org.apache.airavata.model.security.AuthzToken
> [ERROR]
> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
> incompatible types: java.lang.String cannot be converted to
> org.apache.airavata.model.security.AuthzToken
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>>
>> Now it seems building goes correctly!
>>
>> Thank you!
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Yes. I am using java 1.8
>>>
>>> [heechae@biobrainpool airavata]$ which java
>>> /packages/jdk1.8.0_65/bin/java
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>>> kamalasini@gmail.com> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> I hope you are using java 1.8.
>>>>
>>>> Thanks..
>>>> Chathuri
>>>>
>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Hi, Supun,
>>>>>
>>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>>> I got some errors like,
>>>>>
>>>>> INFO] BUILD FAILURE
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [INFO] Total time: 7.754s
>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>>> [INFO] Final Memory: 36M/1931M
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [ERROR] Failed to execute goal
>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>>> invalid target release: 1.8 -> [Help 1]
>>>>> [ERROR]
>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>> the -e switch.
>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>> [ERROR]
>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>> please read the following articles:
>>>>> [ERROR] [Help 1]
>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>>> [ERROR]
>>>>> [ERROR] After correcting the problems, you can resume the build with
>>>>> the command
>>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>>> supun.nakandala@gmail.com> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> There was an issue in the pom files and I fixed it now. Can you check
>>>>>> whether your build is working now
>>>>>>
>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <heechae@cs.indiana.edu
>>>>>> > wrote:
>>>>>>
>>>>>>> I got following as well,
>>>>>>>
>>>>>>> [INFO] Scanning for projects...
>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>>> [ERROR]
>>>>>>> [ERROR] The project
>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>>> has 1 error
>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>> [ERROR]
>>>>>>> [ERROR] The project
>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>>> has 1 error
>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>>> [ERROR]
>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>>> the -e switch.
>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>> logging.
>>>>>>> [ERROR]
>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>> solutions, please read the following articles:
>>>>>>> [ERROR] [Help 1]
>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>>> [ERROR] [Help 2]
>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>
>>>>>>>> Instead of building only credential store module, could you build
>>>>>>>> from airavata source root. Credential store module depends on
>>>>>>>> airavata-server-configuration and other jars. That should resolve
>>>>>>>> your issue..
>>>>>>>>
>>>>>>>> Thanks.
>>>>>>>> Chathuri
>>>>>>>>
>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi, Chathuri,
>>>>>>>>>
>>>>>>>>> Thank you for the explanation.
>>>>>>>>>
>>>>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>>> following errors.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ###############################################################################################################
>>>>>>>>> Downloaded:
>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>>> [INFO]
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>>> following artifacts could not be resolved:
>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>>> artifact
>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) ->
>>>>>>>>> [Help 1]
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>>> with the -e switch.
>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>>> logging.
>>>>>>>>> [ERROR]
>>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>>> solutions, please read the following articles:
>>>>>>>>> [ERROR] [Help 1]
>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>>
>>>>>>>>> ###############################################################################################################
>>>>>>>>>
>>>>>>>>> Any suggestion?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>
>>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>>> Refer this code
>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>>> two methods.
>>>>>>>>>>
>>>>>>>>>> Thanks..
>>>>>>>>>> Chathuri
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>>
>>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>>
>>>>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>>>>
>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>>>>>>> output data
>>>>>>>>>>> at
>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>>> at
>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>>> at
>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>>> at
>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>>> at
>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>>> at
>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>
>>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>>
>>>>>>>>>>> start.credential.store=false
>>>>>>>>>>>
>>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>>
>>>>>>>>>>> Thank you,
>>>>>>>>>>> Heejoon.
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <
>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>>
>>>>>>>>>>>> You will need to configure your email within gfac-config.yaml
>>>>>>>>>>>> (you will find it in the bin directory).
>>>>>>>>>>>>
>>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>>
>>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>>> emailParser:
>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Suresh
>>>>>>>>>>>>
>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>> >
>>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>>> >
>>>>>>>>>>>> > I am using one month old version of PGA and Airavata server.
>>>>>>>>>>>> Both were recent version at that time.
>>>>>>>>>>>> >
>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>>> >
>>>>>>>>>>>> > Thank you,
>>>>>>>>>>>> > Heejoon.
>>>>>>>>>>>> >
>>>>>>>>>>>> >
>>>>>>>>>>>> >
>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>>> >
>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>>> >
>>>>>>>>>>>> > Suresh
>>>>>>>>>>>> >
>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>>> >>
>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>> >>
>>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>>> >>
>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>>>>>> bellow.
>>>>>>>>>>>> >>
>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>>> >>
>>>>>>>>>>>> >>
>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>>> =====================================>
>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>>> >> at
>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>>> >> at
>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>>> >> at
>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>>> >> at
>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended,
>>>>>>>>>>>> Run time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>>> >>
>>>>>>>>>>>> #################################################################################
>>>>>>>>>>>> >>
>>>>>>>>>>>> >> Thank you,
>>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>>> >
>>>>>>>>>>>> >
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Thank you
>>>>>> Supun Nakandala
>>>>>> Dept. Computer Science and Engineering
>>>>>> University of Moratuwa
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Unfortunately, the compile fails at certain point,
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 7:41.368s
[INFO] Finished at: Tue Dec 22 10:05:36 KST 2015
[INFO] Final Memory: 95M/3073M
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
(default-compile) on project airavata-client-samples: Compilation failure:
Compilation failure:
[ERROR]
/data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55]
incompatible types: java.lang.String cannot be converted to
org.apache.airavata.model.security.AuthzToken
[ERROR]
/data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65]
incompatible types: java.lang.String cannot be converted to
org.apache.airavata.model.security.AuthzToken
[ERROR]
/data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81]
incompatible types: java.lang.String cannot be converted to
org.apache.airavata.model.security.AuthzToken
Thanks,
Heejoon.
On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
>
> Now it seems building goes correctly!
>
> Thank you!
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Yes. I am using java 1.8
>>
>> [heechae@biobrainpool airavata]$ which java
>> /packages/jdk1.8.0_65/bin/java
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <
>> kamalasini@gmail.com> wrote:
>>
>>> Hi Heejoon,
>>>
>>> I hope you are using java 1.8.
>>>
>>> Thanks..
>>> Chathuri
>>>
>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Hi, Supun,
>>>>
>>>> Thank you for fixing that. I updated and do mvn clean install.
>>>> I got some errors like,
>>>>
>>>> INFO] BUILD FAILURE
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [INFO] Total time: 7.754s
>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>>> [INFO] Final Memory: 36M/1931M
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [ERROR] Failed to execute goal
>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>>> invalid target release: 1.8 -> [Help 1]
>>>> [ERROR]
>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>> the -e switch.
>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>> [ERROR]
>>>> [ERROR] For more information about the errors and possible solutions,
>>>> please read the following articles:
>>>> [ERROR] [Help 1]
>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>>> [ERROR]
>>>> [ERROR] After correcting the problems, you can resume the build with
>>>> the command
>>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>>> supun.nakandala@gmail.com> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> There was an issue in the pom files and I fixed it now. Can you check
>>>>> whether your build is working now
>>>>>
>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> I got following as well,
>>>>>>
>>>>>> [INFO] Scanning for projects...
>>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>>> [ERROR]
>>>>>> [ERROR] The project
>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>>> has 1 error
>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>> [ERROR]
>>>>>> [ERROR] The project
>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>>> has 1 error
>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>>> [ERROR]
>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>> the -e switch.
>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>>> [ERROR]
>>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>>> please read the following articles:
>>>>>> [ERROR] [Help 1]
>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>>> [ERROR] [Help 2]
>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>>> kamalasini@gmail.com> wrote:
>>>>>>
>>>>>>> Instead of building only credential store module, could you build
>>>>>>> from airavata source root. Credential store module depends on
>>>>>>> airavata-server-configuration and other jars. That should resolve
>>>>>>> your issue..
>>>>>>>
>>>>>>> Thanks.
>>>>>>> Chathuri
>>>>>>>
>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Hi, Chathuri,
>>>>>>>>
>>>>>>>> Thank you for the explanation.
>>>>>>>>
>>>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>>> following errors.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ###############################################################################################################
>>>>>>>> Downloaded:
>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [INFO] BUILD FAILURE
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>>> [INFO]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [ERROR] Failed to execute goal on project
>>>>>>>> airavata-credential-store: Could not resolve dependencies for project
>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>>> following artifacts could not be resolved:
>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>>> artifact
>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help
>>>>>>>> 1]
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven
>>>>>>>> with the -e switch.
>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>>> logging.
>>>>>>>> [ERROR]
>>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>>> solutions, please read the following articles:
>>>>>>>> [ERROR] [Help 1]
>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>>
>>>>>>>> ###############################################################################################################
>>>>>>>>
>>>>>>>> Any suggestion?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Heejoon,
>>>>>>>>>
>>>>>>>>> You need to set up a valid credential store token in the
>>>>>>>>> credential store (experiment-catalog database has tables related to
>>>>>>>>> credential store). Same credential store token needs to be set in gateway
>>>>>>>>> profiles. This token is used when airavata ssh to resource, input staging
>>>>>>>>> and all the remote connections with the resource. Credential store token is
>>>>>>>>> the identifier for SSH credential object which contains valid SSH keys.
>>>>>>>>> Refer this code
>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>>> two methods.
>>>>>>>>>
>>>>>>>>> Thanks..
>>>>>>>>> Chathuri
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi, Suresh,
>>>>>>>>>>
>>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>>
>>>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>>>
>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>>> Please provide the correct credential store token
>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8,
>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status
>>>>>>>>>> changed FAILED -> FAILED
>>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>>>>>> output data
>>>>>>>>>> at
>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>>> at
>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>>> at
>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>>> at
>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>>> at
>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>>> at
>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>
>>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>>
>>>>>>>>>> start.credential.store=false
>>>>>>>>>>
>>>>>>>>>> but it seems still they are active.
>>>>>>>>>>
>>>>>>>>>> Thank you,
>>>>>>>>>> Heejoon.
>>>>>>>>>>
>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <smarru@apache.org
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>>
>>>>>>>>>>> You will need to configure your email within gfac-config.yaml
>>>>>>>>>>> (you will find it in the bin directory).
>>>>>>>>>>>
>>>>>>>>>>> If you can add your email to:
>>>>>>>>>>>
>>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>>> commandOutputParser:
>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>>> emailParser:
>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Suresh
>>>>>>>>>>>
>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>> >
>>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>>> >
>>>>>>>>>>> > I am using one month old version of PGA and Airavata server.
>>>>>>>>>>> Both were recent version at that time.
>>>>>>>>>>> >
>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>>> >
>>>>>>>>>>> > Thank you,
>>>>>>>>>>> > Heejoon.
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>>> >
>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>>> >
>>>>>>>>>>> > Suresh
>>>>>>>>>>> >
>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>>> >>
>>>>>>>>>>> >> Hi,
>>>>>>>>>>> >>
>>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>>> >>
>>>>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>>>>> bellow.
>>>>>>>>>>> >>
>>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>>> >>
>>>>>>>>>>> >>
>>>>>>>>>>> #################################################################################
>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>>> =====================================>
>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException:
>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address
>>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>>> >> at
>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>>> >> at
>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>>> >> at
>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>>> >> at
>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run
>>>>>>>>>>> time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>>> >>
>>>>>>>>>>> #################################################################################
>>>>>>>>>>> >>
>>>>>>>>>>> >> Thank you,
>>>>>>>>>>> >> Heejoon.
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Thank you
>>>>> Supun Nakandala
>>>>> Dept. Computer Science and Engineering
>>>>> University of Moratuwa
>>>>>
>>>>
>>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Sorry, I found my JAVA_HOME set to different location even I use java 1.8.
Now it seems building goes correctly!
Thank you!
Heejoon.
On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Yes. I am using java 1.8
>
> [heechae@biobrainpool airavata]$ which java
> /packages/jdk1.8.0_65/bin/java
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <kamalasini@gmail.com
> > wrote:
>
>> Hi Heejoon,
>>
>> I hope you are using java 1.8.
>>
>> Thanks..
>> Chathuri
>>
>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Hi, Supun,
>>>
>>> Thank you for fixing that. I updated and do mvn clean install.
>>> I got some errors like,
>>>
>>> INFO] BUILD FAILURE
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [INFO] Total time: 7.754s
>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>>> [INFO] Final Memory: 36M/1931M
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal
>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>>> (default-compile) on project airavata-data-models: Fatal error compiling:
>>> invalid target release: 1.8 -> [Help 1]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>>> -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions,
>>> please read the following articles:
>>> [ERROR] [Help 1]
>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>>> [ERROR]
>>> [ERROR] After correcting the problems, you can resume the build with the
>>> command
>>> [ERROR] mvn <goals> -rf :airavata-data-models
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>>> supun.nakandala@gmail.com> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> There was an issue in the pom files and I fixed it now. Can you check
>>>> whether your build is working now
>>>>
>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> I got following as well,
>>>>>
>>>>> [INFO] Scanning for projects...
>>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>>> [ERROR]
>>>>> [ERROR] The project
>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>>> has 1 error
>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>> [ERROR]
>>>>> [ERROR] The project
>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>>> has 1 error
>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>>> [ERROR]
>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>> the -e switch.
>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>> [ERROR]
>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>> please read the following articles:
>>>>> [ERROR] [Help 1]
>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>>> [ERROR] [Help 2]
>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>>> kamalasini@gmail.com> wrote:
>>>>>
>>>>>> Instead of building only credential store module, could you build
>>>>>> from airavata source root. Credential store module depends on
>>>>>> airavata-server-configuration and other jars. That should resolve
>>>>>> your issue..
>>>>>>
>>>>>> Thanks.
>>>>>> Chathuri
>>>>>>
>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <heechae@cs.indiana.edu
>>>>>> > wrote:
>>>>>>
>>>>>>> Hi, Chathuri,
>>>>>>>
>>>>>>> Thank you for the explanation.
>>>>>>>
>>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>>> following errors.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ###############################################################################################################
>>>>>>> Downloaded:
>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>>> (571 KB at 2.8 KB/sec)
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [INFO] BUILD FAILURE
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [INFO] Total time: 3:53.576s
>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>>> [INFO]
>>>>>>> ------------------------------------------------------------------------
>>>>>>> [ERROR] Failed to execute goal on project airavata-credential-store:
>>>>>>> Could not resolve dependencies for project
>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>>> following artifacts could not be resolved:
>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>>> artifact
>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help
>>>>>>> 1]
>>>>>>> [ERROR]
>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>>> the -e switch.
>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug
>>>>>>> logging.
>>>>>>> [ERROR]
>>>>>>> [ERROR] For more information about the errors and possible
>>>>>>> solutions, please read the following articles:
>>>>>>> [ERROR] [Help 1]
>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>>
>>>>>>> ###############################################################################################################
>>>>>>>
>>>>>>> Any suggestion?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>>> kamalasini@gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Heejoon,
>>>>>>>>
>>>>>>>> You need to set up a valid credential store token in the credential
>>>>>>>> store (experiment-catalog database has tables related to credential store).
>>>>>>>> Same credential store token needs to be set in gateway profiles. This token
>>>>>>>> is used when airavata ssh to resource, input staging and all the remote
>>>>>>>> connections with the resource. Credential store token is the identifier for
>>>>>>>> SSH credential object which contains valid SSH keys. Refer this code
>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>>> two methods.
>>>>>>>>
>>>>>>>> Thanks..
>>>>>>>> Chathuri
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi, Suresh,
>>>>>>>>>
>>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>>
>>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>>
>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>>> Please provide the correct credential store token
>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>>>>>>> FAILED -> FAILED
>>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>>>>> output data
>>>>>>>>> at
>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>>> at
>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>>> at
>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>>> at
>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>>> at
>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>>> at
>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>
>>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>>
>>>>>>>>> start.credential.store=false
>>>>>>>>>
>>>>>>>>> but it seems still they are active.
>>>>>>>>>
>>>>>>>>> Thank you,
>>>>>>>>> Heejoon.
>>>>>>>>>
>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Heejoon,
>>>>>>>>>>
>>>>>>>>>> You will need to configure your email within gfac-config.yaml
>>>>>>>>>> (you will find it in the bin directory).
>>>>>>>>>>
>>>>>>>>>> If you can add your email to:
>>>>>>>>>>
>>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>>> commandOutputParser:
>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>>> emailParser:
>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>>> resourceEmailAddresses:
>>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Suresh
>>>>>>>>>>
>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>> >
>>>>>>>>>> > Hi, Suresh,
>>>>>>>>>> >
>>>>>>>>>> > I am using one month old version of PGA and Airavata server.
>>>>>>>>>> Both were recent version at that time.
>>>>>>>>>> >
>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>>> >
>>>>>>>>>> > Thank you,
>>>>>>>>>> > Heejoon.
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <
>>>>>>>>>> smarru@apache.org> wrote:
>>>>>>>>>> > Hi Heejoon,
>>>>>>>>>> >
>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>>> >
>>>>>>>>>> > Suresh
>>>>>>>>>> >
>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>>> >>
>>>>>>>>>> >> Hi,
>>>>>>>>>> >>
>>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>>> >>
>>>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>>>> bellow.
>>>>>>>>>> >>
>>>>>>>>>> >> It seems the Airavata server correctly log in the email
>>>>>>>>>> account and bring email list, but it could not parse it correctly.
>>>>>>>>>> >>
>>>>>>>>>> >>
>>>>>>>>>> #################################################################################
>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>>> =====================================>
>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>>>>>>> Couldn't identify Resource job manager type from address
>>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>>> >> at
>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>>> >> at
>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>>> >> at
>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>>> >> at
>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run
>>>>>>>>>> time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>>> >>
>>>>>>>>>> #################################################################################
>>>>>>>>>> >>
>>>>>>>>>> >> Thank you,
>>>>>>>>>> >> Heejoon.
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Thank you
>>>> Supun Nakandala
>>>> Dept. Computer Science and Engineering
>>>> University of Moratuwa
>>>>
>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Yes. I am using java 1.8
[heechae@biobrainpool airavata]$ which java
/packages/jdk1.8.0_65/bin/java
Thanks,
Heejoon.
On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <ka...@gmail.com>
wrote:
> Hi Heejoon,
>
> I hope you are using java 1.8.
>
> Thanks..
> Chathuri
>
> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Hi, Supun,
>>
>> Thank you for fixing that. I updated and do mvn clean install.
>> I got some errors like,
>>
>> INFO] BUILD FAILURE
>> [INFO]
>> ------------------------------------------------------------------------
>> [INFO] Total time: 7.754s
>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
>> [INFO] Final Memory: 36M/1931M
>> [INFO]
>> ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal
>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
>> (default-compile) on project airavata-data-models: Fatal error compiling:
>> invalid target release: 1.8 -> [Help 1]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>> -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions,
>> please read the following articles:
>> [ERROR] [Help 1]
>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>> [ERROR]
>> [ERROR] After correcting the problems, you can resume the build with the
>> command
>> [ERROR] mvn <goals> -rf :airavata-data-models
>>
>> Thanks,
>> Heejoon.
>>
>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
>> supun.nakandala@gmail.com> wrote:
>>
>>> Hi Heejoon,
>>>
>>> There was an issue in the pom files and I fixed it now. Can you check
>>> whether your build is working now
>>>
>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> I got following as well,
>>>>
>>>> [INFO] Scanning for projects...
>>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>>> [ERROR]
>>>> [ERROR] The project
>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>>> has 1 error
>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>> [ERROR]
>>>> [ERROR] The project
>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>>> has 1 error
>>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>>> [ERROR]
>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>> the -e switch.
>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>> [ERROR]
>>>> [ERROR] For more information about the errors and possible solutions,
>>>> please read the following articles:
>>>> [ERROR] [Help 1]
>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>>> [ERROR] [Help 2]
>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>>> kamalasini@gmail.com> wrote:
>>>>
>>>>> Instead of building only credential store module, could you build from
>>>>> airavata source root. Credential store module depends on airavata-server-configuration
>>>>> and other jars. That should resolve your issue..
>>>>>
>>>>> Thanks.
>>>>> Chathuri
>>>>>
>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi, Chathuri,
>>>>>>
>>>>>> Thank you for the explanation.
>>>>>>
>>>>>> I cloned the git and tried to compile credential-store with 'mvn
>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got
>>>>>> following errors.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ###############################################################################################################
>>>>>> Downloaded:
>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>>> (571 KB at 2.8 KB/sec)
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [INFO] BUILD FAILURE
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [INFO] Total time: 3:53.576s
>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>>> [INFO] Final Memory: 11M/1931M
>>>>>> [INFO]
>>>>>> ------------------------------------------------------------------------
>>>>>> [ERROR] Failed to execute goal on project airavata-credential-store:
>>>>>> Could not resolve dependencies for project
>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>>> following artifacts could not be resolved:
>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>>> artifact
>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
>>>>>> [ERROR]
>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>>> the -e switch.
>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>>> [ERROR]
>>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>>> please read the following articles:
>>>>>> [ERROR] [Help 1]
>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>>
>>>>>> ###############################################################################################################
>>>>>>
>>>>>> Any suggestion?
>>>>>>
>>>>>> Thanks,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>>> kamalasini@gmail.com> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> You need to set up a valid credential store token in the credential
>>>>>>> store (experiment-catalog database has tables related to credential store).
>>>>>>> Same credential store token needs to be set in gateway profiles. This token
>>>>>>> is used when airavata ssh to resource, input staging and all the remote
>>>>>>> connections with the resource. Credential store token is the identifier for
>>>>>>> SSH credential object which contains valid SSH keys. Refer this code
>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>>> two methods.
>>>>>>>
>>>>>>> Thanks..
>>>>>>> Chathuri
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>
>>>>>>>> Hi, Suresh,
>>>>>>>>
>>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>>
>>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>>
>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>>> Please provide the correct credential store token
>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>>>>>> FAILED -> FAILED
>>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>>>> output data
>>>>>>>> at
>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>>> at
>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>>> at
>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>>> at
>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>>> at
>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>
>>>>>>>> I actually set 'false' for storing credential in the
>>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>>
>>>>>>>> start.credential.store=false
>>>>>>>>
>>>>>>>> but it seems still they are active.
>>>>>>>>
>>>>>>>> Thank you,
>>>>>>>> Heejoon.
>>>>>>>>
>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Heejoon,
>>>>>>>>>
>>>>>>>>> You will need to configure your email within gfac-config.yaml (you
>>>>>>>>> will find it in the bin directory).
>>>>>>>>>
>>>>>>>>> If you can add your email to:
>>>>>>>>>
>>>>>>>>> - jobManagerType: SLURM
>>>>>>>>> commandOutputParser:
>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>>> emailParser:
>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>>> resourceEmailAddresses:
>>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Suresh
>>>>>>>>>
>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>> >
>>>>>>>>> > Hi, Suresh,
>>>>>>>>> >
>>>>>>>>> > I am using one month old version of PGA and Airavata server.
>>>>>>>>> Both were recent version at that time.
>>>>>>>>> >
>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>>> >
>>>>>>>>> > Thank you,
>>>>>>>>> > Heejoon.
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>>>>>>> wrote:
>>>>>>>>> > Hi Heejoon,
>>>>>>>>> >
>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>>> >
>>>>>>>>> > Suresh
>>>>>>>>> >
>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>>> >>
>>>>>>>>> >> Hi,
>>>>>>>>> >>
>>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>>> >>
>>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>>> bellow.
>>>>>>>>> >>
>>>>>>>>> >> It seems the Airavata server correctly log in the email account
>>>>>>>>> and bring email list, but it could not parse it correctly.
>>>>>>>>> >>
>>>>>>>>> >>
>>>>>>>>> #################################################################################
>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>>> =====================================>
>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>>>>>> Couldn't identify Resource job manager type from address
>>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>>> >> at
>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>>> >> at
>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>>> >> at
>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>>> >> at
>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run
>>>>>>>>> time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>>> >>
>>>>>>>>> #################################################################################
>>>>>>>>> >>
>>>>>>>>> >> Thank you,
>>>>>>>>> >> Heejoon.
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Thank you
>>> Supun Nakandala
>>> Dept. Computer Science and Engineering
>>> University of Moratuwa
>>>
>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Chathuri Wimalasena <ka...@gmail.com>.
Hi Heejoon,
I hope you are using java 1.8.
Thanks..
Chathuri
On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Hi, Supun,
>
> Thank you for fixing that. I updated and do mvn clean install.
> I got some errors like,
>
> INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 7.754s
> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
> [INFO] Final Memory: 36M/1931M
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
> (default-compile) on project airavata-data-models: Fatal error compiling:
> invalid target release: 1.8 -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the
> command
> [ERROR] mvn <goals> -rf :airavata-data-models
>
> Thanks,
> Heejoon.
>
> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <
> supun.nakandala@gmail.com> wrote:
>
>> Hi Heejoon,
>>
>> There was an issue in the pom files and I fixed it now. Can you check
>> whether your build is working now
>>
>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> I got following as well,
>>>
>>> [INFO] Scanning for projects...
>>> [ERROR] The build could not read 2 projects -> [Help 1]
>>> [ERROR]
>>> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>>> has 1 error
>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>> [ERROR]
>>> [ERROR] The project
>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>>> has 1 error
>>> [ERROR] Non-resolvable parent POM: Could not find artifact
>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>>> -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions,
>>> please read the following articles:
>>> [ERROR] [Help 1]
>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>>> [ERROR] [Help 2]
>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>>> kamalasini@gmail.com> wrote:
>>>
>>>> Instead of building only credential store module, could you build from
>>>> airavata source root. Credential store module depends on airavata-server-configuration
>>>> and other jars. That should resolve your issue..
>>>>
>>>> Thanks.
>>>> Chathuri
>>>>
>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Hi, Chathuri,
>>>>>
>>>>> Thank you for the explanation.
>>>>>
>>>>> I cloned the git and tried to compile credential-store with 'mvn clean
>>>>> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
>>>>> errors.
>>>>>
>>>>>
>>>>>
>>>>> ###############################################################################################################
>>>>> Downloaded:
>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>>> (571 KB at 2.8 KB/sec)
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [INFO] BUILD FAILURE
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [INFO] Total time: 3:53.576s
>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>>> [INFO] Final Memory: 11M/1931M
>>>>> [INFO]
>>>>> ------------------------------------------------------------------------
>>>>> [ERROR] Failed to execute goal on project airavata-credential-store:
>>>>> Could not resolve dependencies for project
>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>>> following artifacts could not be resolved:
>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>>> artifact
>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
>>>>> [ERROR]
>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>>> the -e switch.
>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>>> [ERROR]
>>>>> [ERROR] For more information about the errors and possible solutions,
>>>>> please read the following articles:
>>>>> [ERROR] [Help 1]
>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>>
>>>>> ###############################################################################################################
>>>>>
>>>>> Any suggestion?
>>>>>
>>>>> Thanks,
>>>>> Heejoon.
>>>>>
>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>>> kamalasini@gmail.com> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> You need to set up a valid credential store token in the credential
>>>>>> store (experiment-catalog database has tables related to credential store).
>>>>>> Same credential store token needs to be set in gateway profiles. This token
>>>>>> is used when airavata ssh to resource, input staging and all the remote
>>>>>> connections with the resource. Credential store token is the identifier for
>>>>>> SSH credential object which contains valid SSH keys. Refer this code
>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>>> two methods.
>>>>>>
>>>>>> Thanks..
>>>>>> Chathuri
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <
>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>
>>>>>>> Hi, Suresh,
>>>>>>>
>>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>>
>>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>>
>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>>> Please provide the correct credential store token
>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>>>>> FAILED -> FAILED
>>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>>> [ERROR] GFac Worker throws an exception
>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>>> output data
>>>>>>> at
>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>>> at
>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>>> at
>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>>> at
>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>>> at
>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>
>>>>>>> I actually set 'false' for storing credential in the
>>>>>>> 'airavata-server.properties' file as bellow
>>>>>>>
>>>>>>> start.credential.store=false
>>>>>>>
>>>>>>> but it seems still they are active.
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Heejoon.
>>>>>>>
>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Heejoon,
>>>>>>>>
>>>>>>>> You will need to configure your email within gfac-config.yaml (you
>>>>>>>> will find it in the bin directory).
>>>>>>>>
>>>>>>>> If you can add your email to:
>>>>>>>>
>>>>>>>> - jobManagerType: SLURM
>>>>>>>> commandOutputParser:
>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>>> emailParser:
>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>>> resourceEmailAddresses:
>>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Suresh
>>>>>>>>
>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>>> wrote:
>>>>>>>> >
>>>>>>>> > Hi, Suresh,
>>>>>>>> >
>>>>>>>> > I am using one month old version of PGA and Airavata server. Both
>>>>>>>> were recent version at that time.
>>>>>>>> >
>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>>> >
>>>>>>>> > Thank you,
>>>>>>>> > Heejoon.
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>>>>>> wrote:
>>>>>>>> > Hi Heejoon,
>>>>>>>> >
>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>>> >
>>>>>>>> > Suresh
>>>>>>>> >
>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <
>>>>>>>> heechae@cs.indiana.edu> wrote:
>>>>>>>> >>
>>>>>>>> >> Hi,
>>>>>>>> >>
>>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>>> >>
>>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>>> bellow.
>>>>>>>> >>
>>>>>>>> >> It seems the Airavata server correctly log in the email account
>>>>>>>> and bring email list, but it could not parse it correctly.
>>>>>>>> >>
>>>>>>>> >>
>>>>>>>> #################################################################################
>>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>>> =====================================>
>>>>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>>>>> Couldn't identify Resource job manager type from address
>>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>>> >> at
>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>>> >> at
>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>>> >> at
>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>>> >> at
>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run
>>>>>>>> time 00:00:01, COMPLETED, ExitCode 0
>>>>>>>> >>
>>>>>>>> #################################################################################
>>>>>>>> >>
>>>>>>>> >> Thank you,
>>>>>>>> >> Heejoon.
>>>>>>>> >
>>>>>>>> >
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>> --
>> Thank you
>> Supun Nakandala
>> Dept. Computer Science and Engineering
>> University of Moratuwa
>>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi, Supun,
Thank you for fixing that. I updated and do mvn clean install.
I got some errors like,
INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 7.754s
[INFO] Finished at: Tue Dec 22 09:05:21 KST 2015
[INFO] Final Memory: 36M/1931M
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:3.1:compile
(default-compile) on project airavata-data-models: Fatal error compiling:
invalid target release: 1.8 -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the
command
[ERROR] mvn <goals> -rf :airavata-data-models
Thanks,
Heejoon.
On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <supun.nakandala@gmail.com
> wrote:
> Hi Heejoon,
>
> There was an issue in the pom files and I fixed it now. Can you check
> whether your build is working now
>
> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> I got following as well,
>>
>> [INFO] Scanning for projects...
>> [ERROR] The build could not read 2 projects -> [Help 1]
>> [ERROR]
>> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
>> has 1 error
>> [ERROR] Non-resolvable parent POM: Could not find artifact
>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>> [ERROR]
>> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT
>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
>> has 1 error
>> [ERROR] Non-resolvable parent POM: Could not find artifact
>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
>> points at wrong local POM @ line 5, column 13 -> [Help 2]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>> -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions,
>> please read the following articles:
>> [ERROR] [Help 1]
>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
>> [ERROR] [Help 2]
>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>>
>> Thanks,
>> Heejoon.
>>
>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <
>> kamalasini@gmail.com> wrote:
>>
>>> Instead of building only credential store module, could you build from
>>> airavata source root. Credential store module depends on airavata-server-configuration
>>> and other jars. That should resolve your issue..
>>>
>>> Thanks.
>>> Chathuri
>>>
>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Hi, Chathuri,
>>>>
>>>> Thank you for the explanation.
>>>>
>>>> I cloned the git and tried to compile credential-store with 'mvn clean
>>>> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
>>>> errors.
>>>>
>>>>
>>>>
>>>> ###############################################################################################################
>>>> Downloaded:
>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>>> (571 KB at 2.8 KB/sec)
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [INFO] BUILD FAILURE
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [INFO] Total time: 3:53.576s
>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>>> [INFO] Final Memory: 11M/1931M
>>>> [INFO]
>>>> ------------------------------------------------------------------------
>>>> [ERROR] Failed to execute goal on project airavata-credential-store:
>>>> Could not resolve dependencies for project
>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>>> following artifacts could not be resolved:
>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>>> artifact
>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
>>>> [ERROR]
>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with
>>>> the -e switch.
>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>>> [ERROR]
>>>> [ERROR] For more information about the errors and possible solutions,
>>>> please read the following articles:
>>>> [ERROR] [Help 1]
>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>>
>>>> ###############################################################################################################
>>>>
>>>> Any suggestion?
>>>>
>>>> Thanks,
>>>> Heejoon.
>>>>
>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>>> kamalasini@gmail.com> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> You need to set up a valid credential store token in the credential
>>>>> store (experiment-catalog database has tables related to credential store).
>>>>> Same credential store token needs to be set in gateway profiles. This token
>>>>> is used when airavata ssh to resource, input staging and all the remote
>>>>> connections with the resource. Credential store token is the identifier for
>>>>> SSH credential object which contains valid SSH keys. Refer this code
>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>>> two methods.
>>>>>
>>>>> Thanks..
>>>>> Chathuri
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <heechae@cs.indiana.edu
>>>>> > wrote:
>>>>>
>>>>>> Hi, Suresh,
>>>>>>
>>>>>> Thank you for the help. It correctly parses the email.
>>>>>>
>>>>>> Now I have another error caused by 'credential token' as below,
>>>>>>
>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>>> Please provide the correct credential store token
>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>>>> FAILED -> FAILED
>>>>>> [INFO] Publishing status to rabbitmq...
>>>>>> [ERROR] GFac Worker throws an exception
>>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>>> output data
>>>>>> at
>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>>> at
>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>>> at
>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>>> at
>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>>> at
>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>
>>>>>> I actually set 'false' for storing credential in the
>>>>>> 'airavata-server.properties' file as bellow
>>>>>>
>>>>>> start.credential.store=false
>>>>>>
>>>>>> but it seems still they are active.
>>>>>>
>>>>>> Thank you,
>>>>>> Heejoon.
>>>>>>
>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Heejoon,
>>>>>>>
>>>>>>> You will need to configure your email within gfac-config.yaml (you
>>>>>>> will find it in the bin directory).
>>>>>>>
>>>>>>> If you can add your email to:
>>>>>>>
>>>>>>> - jobManagerType: SLURM
>>>>>>> commandOutputParser:
>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>>> emailParser:
>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>>> resourceEmailAddresses:
>>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Suresh
>>>>>>>
>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>> wrote:
>>>>>>> >
>>>>>>> > Hi, Suresh,
>>>>>>> >
>>>>>>> > I am using one month old version of PGA and Airavata server. Both
>>>>>>> were recent version at that time.
>>>>>>> >
>>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>>> >
>>>>>>> > Thank you,
>>>>>>> > Heejoon.
>>>>>>> >
>>>>>>> >
>>>>>>> >
>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>>>>> wrote:
>>>>>>> > Hi Heejoon,
>>>>>>> >
>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>>> >
>>>>>>> > Suresh
>>>>>>> >
>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>>> wrote:
>>>>>>> >>
>>>>>>> >> Hi,
>>>>>>> >>
>>>>>>> >> I have succeeded run job with SLURM.
>>>>>>> >>
>>>>>>> >> Now, the job monitoring through email causes some errors as
>>>>>>> bellow.
>>>>>>> >>
>>>>>>> >> It seems the Airavata server correctly log in the email account
>>>>>>> and bring email list, but it could not parse it correctly.
>>>>>>> >>
>>>>>>> >>
>>>>>>> #################################################################################
>>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>>> =====================================>
>>>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>>>> Couldn't identify Resource job manager type from address
>>>>>>> airavata@bhi2.snu.ac.kr
>>>>>>> >> at
>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>>> >> at
>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>>> >> at
>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>>> >> at
>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run
>>>>>>> time 00:00:01, COMPLETED, ExitCode 0
>>>>>>> >>
>>>>>>> #################################################################################
>>>>>>> >>
>>>>>>> >> Thank you,
>>>>>>> >> Heejoon.
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Supun Nakandala <su...@gmail.com>.
Hi Heejoon,
There was an issue in the pom files and I fixed it now. Can you check
whether your build is working now
On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> I got following as well,
>
> [INFO] Scanning for projects...
> [ERROR] The build could not read 2 projects -> [Help 1]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
> has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact
> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
> points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT
> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
> has 1 error
> [ERROR] Non-resolvable parent POM: Could not find artifact
> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
> points at wrong local POM @ line 5, column 13 -> [Help 2]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
> [ERROR] [Help 2]
> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
>
> Thanks,
> Heejoon.
>
> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <kamalasini@gmail.com
> > wrote:
>
>> Instead of building only credential store module, could you build from
>> airavata source root. Credential store module depends on airavata-server-configuration
>> and other jars. That should resolve your issue..
>>
>> Thanks.
>> Chathuri
>>
>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Hi, Chathuri,
>>>
>>> Thank you for the explanation.
>>>
>>> I cloned the git and tried to compile credential-store with 'mvn clean
>>> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
>>> errors.
>>>
>>>
>>>
>>> ###############################################################################################################
>>> Downloaded:
>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>>> (571 KB at 2.8 KB/sec)
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [INFO] BUILD FAILURE
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [INFO] Total time: 3:53.576s
>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>>> [INFO] Final Memory: 11M/1931M
>>> [INFO]
>>> ------------------------------------------------------------------------
>>> [ERROR] Failed to execute goal on project airavata-credential-store:
>>> Could not resolve dependencies for project
>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>>> following artifacts could not be resolved:
>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>>> artifact
>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
>>> [ERROR]
>>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>>> -e switch.
>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>>> [ERROR]
>>> [ERROR] For more information about the errors and possible solutions,
>>> please read the following articles:
>>> [ERROR] [Help 1]
>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>>
>>> ###############################################################################################################
>>>
>>> Any suggestion?
>>>
>>> Thanks,
>>> Heejoon.
>>>
>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>>> kamalasini@gmail.com> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> You need to set up a valid credential store token in the credential
>>>> store (experiment-catalog database has tables related to credential store).
>>>> Same credential store token needs to be set in gateway profiles. This token
>>>> is used when airavata ssh to resource, input staging and all the remote
>>>> connections with the resource. Credential store token is the identifier for
>>>> SSH credential object which contains valid SSH keys. Refer this code
>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>>> There are API methods to generate SSH keys as well. You can use any of the
>>>> two methods.
>>>>
>>>> Thanks..
>>>> Chathuri
>>>>
>>>>
>>>>
>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>>
>>>>> Hi, Suresh,
>>>>>
>>>>> Thank you for the help. It correctly parses the email.
>>>>>
>>>>> Now I have another error caused by 'credential token' as below,
>>>>>
>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>>> staging failed, reason: Provided credential store token is not valid.
>>>>> Please provide the correct credential store token
>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>>> FAILED -> FAILED
>>>>> [INFO] Publishing status to rabbitmq...
>>>>> [ERROR] GFac Worker throws an exception
>>>>> org.apache.airavata.gfac.core.GFacException: Error while staging
>>>>> output data
>>>>> at
>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>>> at
>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>>> at
>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>>> at
>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>> at
>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>
>>>>> I actually set 'false' for storing credential in the
>>>>> 'airavata-server.properties' file as bellow
>>>>>
>>>>> start.credential.store=false
>>>>>
>>>>> but it seems still they are active.
>>>>>
>>>>> Thank you,
>>>>> Heejoon.
>>>>>
>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>>> wrote:
>>>>>
>>>>>> Hi Heejoon,
>>>>>>
>>>>>> You will need to configure your email within gfac-config.yaml (you
>>>>>> will find it in the bin directory).
>>>>>>
>>>>>> If you can add your email to:
>>>>>>
>>>>>> - jobManagerType: SLURM
>>>>>> commandOutputParser:
>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>>> emailParser:
>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>>> resourceEmailAddresses:
>>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>>> - airavata@bhi2.snu.ac.kr
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Suresh
>>>>>>
>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>> wrote:
>>>>>> >
>>>>>> > Hi, Suresh,
>>>>>> >
>>>>>> > I am using one month old version of PGA and Airavata server. Both
>>>>>> were recent version at that time.
>>>>>> >
>>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>>> >
>>>>>> > Thank you,
>>>>>> > Heejoon.
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>>>> wrote:
>>>>>> > Hi Heejoon,
>>>>>> >
>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>>> >
>>>>>> > Suresh
>>>>>> >
>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>>> wrote:
>>>>>> >>
>>>>>> >> Hi,
>>>>>> >>
>>>>>> >> I have succeeded run job with SLURM.
>>>>>> >>
>>>>>> >> Now, the job monitoring through email causes some errors as bellow.
>>>>>> >>
>>>>>> >> It seems the Airavata server correctly log in the email account
>>>>>> and bring email list, but it could not parse it correctly.
>>>>>> >>
>>>>>> >>
>>>>>> #################################################################################
>>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>>> =====================================>
>>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>>> Couldn't identify Resource job manager type from address
>>>>>> airavata@bhi2.snu.ac.kr
>>>>>> >> at
>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>>> >> at
>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>>> >> at
>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>>> >> at
>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
>>>>>> 00:00:01, COMPLETED, ExitCode 0
>>>>>> >>
>>>>>> #################################################################################
>>>>>> >>
>>>>>> >> Thank you,
>>>>>> >> Heejoon.
>>>>>> >
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
I got following as well,
[INFO] Scanning for projects...
[ERROR] The build could not read 2 projects -> [Help 1]
[ERROR]
[ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT
(/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml)
has 1 error
[ERROR] Non-resolvable parent POM: Could not find artifact
org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
points at wrong local POM @ line 5, column 13 -> [Help 2]
[ERROR]
[ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT
(/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml)
has 1 error
[ERROR] Non-resolvable parent POM: Could not find artifact
org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath'
points at wrong local POM @ line 5, column 13 -> [Help 2]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
[ERROR] [Help 2]
http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
Thanks,
Heejoon.
On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <ka...@gmail.com>
wrote:
> Instead of building only credential store module, could you build from
> airavata source root. Credential store module depends on airavata-server-configuration
> and other jars. That should resolve your issue..
>
> Thanks.
> Chathuri
>
> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Hi, Chathuri,
>>
>> Thank you for the explanation.
>>
>> I cloned the git and tried to compile credential-store with 'mvn clean
>> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
>> errors.
>>
>>
>>
>> ###############################################################################################################
>> Downloaded:
>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
>> (571 KB at 2.8 KB/sec)
>> [INFO]
>> ------------------------------------------------------------------------
>> [INFO] BUILD FAILURE
>> [INFO]
>> ------------------------------------------------------------------------
>> [INFO] Total time: 3:53.576s
>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
>> [INFO] Final Memory: 11M/1931M
>> [INFO]
>> ------------------------------------------------------------------------
>> [ERROR] Failed to execute goal on project airavata-credential-store:
>> Could not resolve dependencies for project
>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
>> following artifacts could not be resolved:
>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
>> artifact
>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
>> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
>> [ERROR]
>> [ERROR] To see the full stack trace of the errors, re-run Maven with the
>> -e switch.
>> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>> [ERROR]
>> [ERROR] For more information about the errors and possible solutions,
>> please read the following articles:
>> [ERROR] [Help 1]
>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>
>> ###############################################################################################################
>>
>> Any suggestion?
>>
>> Thanks,
>> Heejoon.
>>
>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <
>> kamalasini@gmail.com> wrote:
>>
>>> Hi Heejoon,
>>>
>>> You need to set up a valid credential store token in the credential
>>> store (experiment-catalog database has tables related to credential store).
>>> Same credential store token needs to be set in gateway profiles. This token
>>> is used when airavata ssh to resource, input staging and all the remote
>>> connections with the resource. Credential store token is the identifier for
>>> SSH credential object which contains valid SSH keys. Refer this code
>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>>> There are API methods to generate SSH keys as well. You can use any of the
>>> two methods.
>>>
>>> Thanks..
>>> Chathuri
>>>
>>>
>>>
>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>>
>>>> Hi, Suresh,
>>>>
>>>> Thank you for the help. It correctly parses the email.
>>>>
>>>> Now I have another error caused by 'credential token' as below,
>>>>
>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>>> staging failed, reason: Provided credential store token is not valid.
>>>> Please provide the correct credential store token
>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>>> FAILED -> FAILED
>>>> [INFO] Publishing status to rabbitmq...
>>>> [ERROR] GFac Worker throws an exception
>>>> org.apache.airavata.gfac.core.GFacException: Error while staging output
>>>> data
>>>> at
>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>>> at
>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>>> at
>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>>> at
>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>> at
>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>> at java.lang.Thread.run(Thread.java:745)
>>>>
>>>> I actually set 'false' for storing credential in the
>>>> 'airavata-server.properties' file as bellow
>>>>
>>>> start.credential.store=false
>>>>
>>>> but it seems still they are active.
>>>>
>>>> Thank you,
>>>> Heejoon.
>>>>
>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>>> wrote:
>>>>
>>>>> Hi Heejoon,
>>>>>
>>>>> You will need to configure your email within gfac-config.yaml (you
>>>>> will find it in the bin directory).
>>>>>
>>>>> If you can add your email to:
>>>>>
>>>>> - jobManagerType: SLURM
>>>>> commandOutputParser:
>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>>> emailParser:
>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>>> resourceEmailAddresses:
>>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>>> - airavata@bhi2.snu.ac.kr
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Suresh
>>>>>
>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>> >
>>>>> > Hi, Suresh,
>>>>> >
>>>>> > I am using one month old version of PGA and Airavata server. Both
>>>>> were recent version at that time.
>>>>> >
>>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>>> >
>>>>> > Thank you,
>>>>> > Heejoon.
>>>>> >
>>>>> >
>>>>> >
>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>>> wrote:
>>>>> > Hi Heejoon,
>>>>> >
>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>>> >
>>>>> > Suresh
>>>>> >
>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>>> wrote:
>>>>> >>
>>>>> >> Hi,
>>>>> >>
>>>>> >> I have succeeded run job with SLURM.
>>>>> >>
>>>>> >> Now, the job monitoring through email causes some errors as bellow.
>>>>> >>
>>>>> >> It seems the Airavata server correctly log in the email account and
>>>>> bring email list, but it could not parse it correctly.
>>>>> >>
>>>>> >>
>>>>> #################################################################################
>>>>> >> [ERROR] [EJM]: Error parsing email message
>>>>> =====================================>
>>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>>> Couldn't identify Resource job manager type from address
>>>>> airavata@bhi2.snu.ac.kr
>>>>> >> at
>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>>> >> at
>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>>> >> at
>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>>> >> at
>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
>>>>> 00:00:01, COMPLETED, ExitCode 0
>>>>> >>
>>>>> #################################################################################
>>>>> >>
>>>>> >> Thank you,
>>>>> >> Heejoon.
>>>>> >
>>>>> >
>>>>>
>>>>>
>>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Chathuri Wimalasena <ka...@gmail.com>.
Instead of building only credential store module, could you build from
airavata source root. Credential store module depends on
airavata-server-configuration
and other jars. That should resolve your issue..
Thanks.
Chathuri
On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Hi, Chathuri,
>
> Thank you for the explanation.
>
> I cloned the git and tried to compile credential-store with 'mvn clean
> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
> errors.
>
>
>
> ###############################################################################################################
> Downloaded:
> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
> (571 KB at 2.8 KB/sec)
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 3:53.576s
> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
> [INFO] Final Memory: 11M/1931M
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project airavata-credential-store: Could
> not resolve dependencies for project
> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
> following artifacts could not be resolved:
> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
> artifact
> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
> apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>
> ###############################################################################################################
>
> Any suggestion?
>
> Thanks,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <kamalasini@gmail.com
> > wrote:
>
>> Hi Heejoon,
>>
>> You need to set up a valid credential store token in the credential store
>> (experiment-catalog database has tables related to credential store). Same
>> credential store token needs to be set in gateway profiles. This token is
>> used when airavata ssh to resource, input staging and all the remote
>> connections with the resource. Credential store token is the identifier for
>> SSH credential object which contains valid SSH keys. Refer this code
>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
>> There are API methods to generate SSH keys as well. You can use any of the
>> two methods.
>>
>> Thanks..
>> Chathuri
>>
>>
>>
>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>>
>>> Hi, Suresh,
>>>
>>> Thank you for the help. It correctly parses the email.
>>>
>>> Now I have another error caused by 'credential token' as below,
>>>
>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>>> staging failed, reason: Provided credential store token is not valid.
>>> Please provide the correct credential store token
>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>>> FAILED -> FAILED
>>> [INFO] Publishing status to rabbitmq...
>>> [ERROR] GFac Worker throws an exception
>>> org.apache.airavata.gfac.core.GFacException: Error while staging output
>>> data
>>> at
>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>>> at
>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>>> at
>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> I actually set 'false' for storing credential in the
>>> 'airavata-server.properties' file as bellow
>>>
>>> start.credential.store=false
>>>
>>> but it seems still they are active.
>>>
>>> Thank you,
>>> Heejoon.
>>>
>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org>
>>> wrote:
>>>
>>>> Hi Heejoon,
>>>>
>>>> You will need to configure your email within gfac-config.yaml (you will
>>>> find it in the bin directory).
>>>>
>>>> If you can add your email to:
>>>>
>>>> - jobManagerType: SLURM
>>>> commandOutputParser:
>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>>> emailParser:
>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>>> resourceEmailAddresses:
>>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>>> - airavata@bhi2.snu.ac.kr
>>>>
>>>>
>>>> Thanks,
>>>> Suresh
>>>>
>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>> >
>>>> > Hi, Suresh,
>>>> >
>>>> > I am using one month old version of PGA and Airavata server. Both
>>>> were recent version at that time.
>>>> >
>>>> > apache-airavata-server-0.16-SNAPSHOT
>>>> >
>>>> > Thank you,
>>>> > Heejoon.
>>>> >
>>>> >
>>>> >
>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>>> wrote:
>>>> > Hi Heejoon,
>>>> >
>>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>>> >
>>>> > Suresh
>>>> >
>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>>>> wrote:
>>>> >>
>>>> >> Hi,
>>>> >>
>>>> >> I have succeeded run job with SLURM.
>>>> >>
>>>> >> Now, the job monitoring through email causes some errors as bellow.
>>>> >>
>>>> >> It seems the Airavata server correctly log in the email account and
>>>> bring email list, but it could not parse it correctly.
>>>> >>
>>>> >>
>>>> #################################################################################
>>>> >> [ERROR] [EJM]: Error parsing email message
>>>> =====================================>
>>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>>> Couldn't identify Resource job manager type from address
>>>> airavata@bhi2.snu.ac.kr
>>>> >> at
>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>>> >> at
>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>>> >> at
>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>>> >> at
>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>>> >> at java.lang.Thread.run(Thread.java:745)
>>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
>>>> 00:00:01, COMPLETED, ExitCode 0
>>>> >>
>>>> #################################################################################
>>>> >>
>>>> >> Thank you,
>>>> >> Heejoon.
>>>> >
>>>> >
>>>>
>>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi, Chathuri,
Thank you for the explanation.
I cloned the git and tried to compile credential-store with 'mvn clean
install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following
errors.
###############################################################################################################
Downloaded:
http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar
(571 KB at 2.8 KB/sec)
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 3:53.576s
[INFO] Finished at: Mon Dec 21 09:38:34 KST 2015
[INFO] Final Memory: 11M/1931M
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal on project airavata-credential-store: Could
not resolve dependencies for project
org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The
following artifacts could not be resolved:
org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT,
org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT,
org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find
artifact
org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in
apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
###############################################################################################################
Any suggestion?
Thanks,
Heejoon.
On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <ka...@gmail.com>
wrote:
> Hi Heejoon,
>
> You need to set up a valid credential store token in the credential store
> (experiment-catalog database has tables related to credential store). Same
> credential store token needs to be set in gateway profiles. This token is
> used when airavata ssh to resource, input staging and all the remote
> connections with the resource. Credential store token is the identifier for
> SSH credential object which contains valid SSH keys. Refer this code
> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
> There are API methods to generate SSH keys as well. You can use any of the
> two methods.
>
> Thanks..
> Chathuri
>
>
>
> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
>
>> Hi, Suresh,
>>
>> Thank you for the help. It correctly parses the email.
>>
>> Now I have another error caused by 'credential token' as below,
>>
>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
>> staging failed, reason: Provided credential store token is not valid.
>> Please provide the correct credential store token
>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
>> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
>> FAILED -> FAILED
>> [INFO] Publishing status to rabbitmq...
>> [ERROR] GFac Worker throws an exception
>> org.apache.airavata.gfac.core.GFacException: Error while staging output
>> data
>> at
>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
>> at
>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
>> at
>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
>> at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> I actually set 'false' for storing credential in the
>> 'airavata-server.properties' file as bellow
>>
>> start.credential.store=false
>>
>> but it seems still they are active.
>>
>> Thank you,
>> Heejoon.
>>
>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org> wrote:
>>
>>> Hi Heejoon,
>>>
>>> You will need to configure your email within gfac-config.yaml (you will
>>> find it in the bin directory).
>>>
>>> If you can add your email to:
>>>
>>> - jobManagerType: SLURM
>>> commandOutputParser:
>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser
>>> emailParser:
>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>>> resourceEmailAddresses:
>>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>>> - airavata@bhi2.snu.ac.kr
>>>
>>>
>>> Thanks,
>>> Suresh
>>>
>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>> >
>>> > Hi, Suresh,
>>> >
>>> > I am using one month old version of PGA and Airavata server. Both were
>>> recent version at that time.
>>> >
>>> > apache-airavata-server-0.16-SNAPSHOT
>>> >
>>> > Thank you,
>>> > Heejoon.
>>> >
>>> >
>>> >
>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>>> wrote:
>>> > Hi Heejoon,
>>> >
>>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>>> >
>>> > Suresh
>>> >
>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>>> wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> I have succeeded run job with SLURM.
>>> >>
>>> >> Now, the job monitoring through email causes some errors as bellow.
>>> >>
>>> >> It seems the Airavata server correctly log in the email account and
>>> bring email list, but it could not parse it correctly.
>>> >>
>>> >>
>>> #################################################################################
>>> >> [ERROR] [EJM]: Error parsing email message
>>> =====================================>
>>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>>> Couldn't identify Resource job manager type from address
>>> airavata@bhi2.snu.ac.kr
>>> >> at
>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>>> >> at
>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>>> >> at
>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>>> >> at
>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>>> >> at java.lang.Thread.run(Thread.java:745)
>>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>>> >> [ERROR] TO: snu.biovlab@gmail.com
>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
>>> 00:00:01, COMPLETED, ExitCode 0
>>> >>
>>> #################################################################################
>>> >>
>>> >> Thank you,
>>> >> Heejoon.
>>> >
>>> >
>>>
>>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Chathuri Wimalasena <ka...@gmail.com>.
Hi Heejoon,
You need to set up a valid credential store token in the credential store
(experiment-catalog database has tables related to credential store). Same
credential store token needs to be set in gateway profiles. This token is
used when airavata ssh to resource, input staging and all the remote
connections with the resource. Credential store token is the identifier for
SSH credential object which contains valid SSH keys. Refer this code
https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java.
There are API methods to generate SSH keys as well. You can use any of the
two methods.
Thanks..
Chathuri
On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <he...@cs.indiana.edu>
wrote:
> Hi, Suresh,
>
> Thank you for the help. It correctly parses the email.
>
> Now I have another error caused by 'credential token' as below,
>
> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
> staging failed, reason: Provided credential store token is not valid.
> Please provide the correct credential store token
> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
> FAILED -> FAILED
> [INFO] Publishing status to rabbitmq...
> [ERROR] GFac Worker throws an exception
> org.apache.airavata.gfac.core.GFacException: Error while staging output
> data
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
> at
> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
> I actually set 'false' for storing credential in the
> 'airavata-server.properties' file as bellow
>
> start.credential.store=false
>
> but it seems still they are active.
>
> Thank you,
> Heejoon.
>
> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org> wrote:
>
>> Hi Heejoon,
>>
>> You will need to configure your email within gfac-config.yaml (you will
>> find it in the bin directory).
>>
>> If you can add your email to:
>>
>> - jobManagerType: SLURM
>> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
>> emailParser:
>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
>> resourceEmailAddresses:
>> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
>> - slurm@batch1.stampede.tacc.utexas.edu # stampede
>> - airavata@bhi2.snu.ac.kr
>>
>>
>> Thanks,
>> Suresh
>>
>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>> >
>> > Hi, Suresh,
>> >
>> > I am using one month old version of PGA and Airavata server. Both were
>> recent version at that time.
>> >
>> > apache-airavata-server-0.16-SNAPSHOT
>> >
>> > Thank you,
>> > Heejoon.
>> >
>> >
>> >
>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org>
>> wrote:
>> > Hi Heejoon,
>> >
>> > Are you using Airavata 0.15 or 0.16 for this purpose?
>> >
>> > Suresh
>> >
>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
>> wrote:
>> >>
>> >> Hi,
>> >>
>> >> I have succeeded run job with SLURM.
>> >>
>> >> Now, the job monitoring through email causes some errors as bellow.
>> >>
>> >> It seems the Airavata server correctly log in the email account and
>> bring email list, but it could not parse it correctly.
>> >>
>> >>
>> #################################################################################
>> >> [ERROR] [EJM]: Error parsing email message
>> =====================================>
>> >> org.apache.airavata.common.exception.AiravataException: [EJM]:
>> Couldn't identify Resource job manager type from address
>> airavata@bhi2.snu.ac.kr
>> >> at
>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>> >> at
>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>> >> at
>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>> >> at
>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>> >> at java.lang.Thread.run(Thread.java:745)
>> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>> >> [ERROR] TO: snu.biovlab@gmail.com
>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
>> 00:00:01, COMPLETED, ExitCode 0
>> >>
>> #################################################################################
>> >>
>> >> Thank you,
>> >> Heejoon.
>> >
>> >
>>
>>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi, Suresh,
Thank you for the help. It correctly parses the email.
Now I have another error caused by 'credential token' as below,
ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId:
TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output
staging failed, reason: Provided credential store token is not valid.
Please provide the correct credential store token
[INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId:
PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed
FAILED -> FAILED
[INFO] Publishing status to rabbitmq...
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error while staging output data
at
org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478)
at
org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393)
at
org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
I actually set 'false' for storing credential in the
'airavata-server.properties' file as bellow
start.credential.store=false
but it seems still they are active.
Thank you,
Heejoon.
On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> You will need to configure your email within gfac-config.yaml (you will
> find it in the bin directory).
>
> If you can add your email to:
>
> - jobManagerType: SLURM
> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
> emailParser:
> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
> resourceEmailAddresses:
> - SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
> - slurm@batch1.stampede.tacc.utexas.edu # stampede
> - airavata@bhi2.snu.ac.kr
>
>
> Thanks,
> Suresh
>
> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
> >
> > Hi, Suresh,
> >
> > I am using one month old version of PGA and Airavata server. Both were
> recent version at that time.
> >
> > apache-airavata-server-0.16-SNAPSHOT
> >
> > Thank you,
> > Heejoon.
> >
> >
> >
> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org> wrote:
> > Hi Heejoon,
> >
> > Are you using Airavata 0.15 or 0.16 for this purpose?
> >
> > Suresh
> >
> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu>
> wrote:
> >>
> >> Hi,
> >>
> >> I have succeeded run job with SLURM.
> >>
> >> Now, the job monitoring through email causes some errors as bellow.
> >>
> >> It seems the Airavata server correctly log in the email account and
> bring email list, but it could not parse it correctly.
> >>
> >>
> #################################################################################
> >> [ERROR] [EJM]: Error parsing email message
> =====================================>
> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
> identify Resource job manager type from address airavata@bhi2.snu.ac.kr
> >> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
> >> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
> >> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
> >> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
> >> at java.lang.Thread.run(Thread.java:745)
> >> [ERROR] FROM: airavata@bhi2.snu.ac.kr
> >> [ERROR] TO: snu.biovlab@gmail.com
> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
> 00:00:01, COMPLETED, ExitCode 0
> >>
> #################################################################################
> >>
> >> Thank you,
> >> Heejoon.
> >
> >
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Hi Heejoon,
You will need to configure your email within gfac-config.yaml (you will find it in the bin directory).
If you can add your email to:
- jobManagerType: SLURM
commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser
emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser
resourceEmailAddresses:
- SDSC Admin <sl...@comet-fe3.sdsc.edu> # comet
- slurm@batch1.stampede.tacc.utexas.edu # stampede
- airavata@bhi2.snu.ac.kr
Thanks,
Suresh
> On Dec 16, 2015, at 6:33 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi, Suresh,
>
> I am using one month old version of PGA and Airavata server. Both were recent version at that time.
>
> apache-airavata-server-0.16-SNAPSHOT
>
> Thank you,
> Heejoon.
>
>
>
> On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> Are you using Airavata 0.15 or 0.16 for this purpose?
>
> Suresh
>
>> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>>
>> Hi,
>>
>> I have succeeded run job with SLURM.
>>
>> Now, the job monitoring through email causes some errors as bellow.
>>
>> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
>>
>> #################################################################################
>> [ERROR] [EJM]: Error parsing email message =====================================>
>> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr
>> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
>> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
>> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
>> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
>> at java.lang.Thread.run(Thread.java:745)
>> [ERROR] FROM: airavata@bhi2.snu.ac.kr
>> [ERROR] TO: snu.biovlab@gmail.com
>> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
>> #################################################################################
>>
>> Thank you,
>> Heejoon.
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Heejoon Chae <he...@cs.indiana.edu>.
Hi, Suresh,
I am using one month old version of PGA and Airavata server. Both were
recent version at that time.
apache-airavata-server-0.16-SNAPSHOT
Thank you,
Heejoon.
On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <sm...@apache.org> wrote:
> Hi Heejoon,
>
> Are you using Airavata 0.15 or 0.16 for this purpose?
>
> Suresh
>
> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi,
>
> I have succeeded run job with SLURM.
>
> Now, the job monitoring through email causes some errors as bellow.
>
> It seems the Airavata server correctly log in the email account and bring
> email list, but it could not parse it correctly.
>
>
> #################################################################################
> [ERROR] [EJM]: Error parsing email message
> =====================================>
> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't
> identify Resource job manager type from address airavata@bhi2.snu.ac.kr
> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
> at
> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
> at java.lang.Thread.run(Thread.java:745)
> [ERROR] FROM: airavata@bhi2.snu.ac.kr
> [ERROR] TO: snu.biovlab@gmail.com
> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time
> 00:00:01, COMPLETED, ExitCode 0
>
> #################################################################################
>
> Thank you,
> Heejoon.
>
>
>
Re: Airavata, monitoring thourgh email : parsing error
Posted by Suresh Marru <sm...@apache.org>.
Hi Heejoon,
Are you using Airavata 0.15 or 0.16 for this purpose?
Suresh
> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <he...@cs.indiana.edu> wrote:
>
> Hi,
>
> I have succeeded run job with SLURM.
>
> Now, the job monitoring through email causes some errors as bellow.
>
> It seems the Airavata server correctly log in the email account and bring email list, but it could not parse it correctly.
>
> #################################################################################
> [ERROR] [EJM]: Error parsing email message =====================================>
> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't identify Resource job manager type from address airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160)
> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144)
> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239)
> at org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208)
> at java.lang.Thread.run(Thread.java:745)
> [ERROR] FROM: airavata@bhi2.snu.ac.kr <ma...@bhi2.snu.ac.kr>
> [ERROR] TO: snu.biovlab@gmail.com <ma...@gmail.com>
> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time 00:00:01, COMPLETED, ExitCode 0
> #################################################################################
>
> Thank you,
> Heejoon.