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Posted to users@airavata.apache.org by Supun Nakandala <su...@gmail.com> on 2017/06/02 16:10:53 UTC
Re: Running Gaussian on Comet
Hi Jeff,
Can you run this commands in your credential store database and restart the
server and try.
DROP TABLE CREDENTIALS;
CREATE TABLE CREDENTIALS (
GATEWAY_ID VARCHAR(100) NOT NULL,
TOKEN_ID VARCHAR(100) NOT NULL,
CREDENTIAL BLOB NOT NULL,
PORTAL_USER_ID VARCHAR(256) NOT NULL,
TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
DESCRIPTION VARCHAR(500),
CREDENTIAL_OWNER_TYPE VARCHAR(10) DEFAULT 'GATEWAY' NOT NULL,
PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
);
On Wed, May 31, 2017 at 5:02 PM, Sale, Jeff <es...@ucsd.edu> wrote:
> Sorry, I should have done that. The errors are below. There may be some
> duplication because I may have clicked the button more than once. In
> particular I noticed the reference to "Unknown column 'DESCRIPTION' in
> 'field list'". Not sure how to resolve it though.
>
> Thanks for your help!
>
> Jeff
>
>
> [ERROR] Error persisting credentials. gateway - php_reference_gateway
> token id - 191e342c-d7a1-4e54-980e-9ccd14adfbb1
>
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column
> 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [ERROR] Error occurred while saving SSH Credentials.
>
> org.apache.airavata.credential.store.store.CredentialStoreException:
> Error persisting credentials. gateway - php_reference_gateway token id -
> 191e342c-d7a1-4e54-980e-9ccd14adfbb1
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:121)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> ... 10 common frames omitted
>
> [ERROR] Error occurred while registering SSH Credential
>
> org.apache.airavata.credential.store.exception.CredentialStoreException:
> Error occurred while saving SSH Credentials.
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3719)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3697)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result.read(CredentialStoreService.java:3639)
>
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> recv_addSSHCredential(CredentialStoreService.java:210)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> addSSHCredential(CredentialStoreService.java:197)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler.
> generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608.CGLIB$generateAndRegisterSSHKeys$
> 168(<generated>)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608$$FastClassByGuice$$b0e29ae1.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:56)
>
> 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$$
> EnhancerByGuice$$5c8b1608.generateAndRegisterSSHKeys(<generated>)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16585)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16569)
>
> 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)
>
> [ERROR] Error persisting credentials. gateway - php_reference_gateway
> token id - 92e40c3f-9a6d-404e-928f-b1f06c8d60f6
>
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column
> 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addPasswordCredential(
> CredentialStoreServerHandler.java:151)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addPasswordCredential.getResult(CredentialStoreService.java:
> 1208)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addPasswordCredential.getResult(CredentialStoreService.java:
> 1192)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [ERROR] Error occurred while saving PWD Credentials.
>
> org.apache.airavata.credential.store.store.CredentialStoreException:
> Error persisting credentials. gateway - php_reference_gateway token id -
> 92e40c3f-9a6d-404e-928f-b1f06c8d60f6
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:121)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addPasswordCredential(
> CredentialStoreServerHandler.java:151)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addPasswordCredential.getResult(CredentialStoreService.java:
> 1208)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addPasswordCredential.getResult(CredentialStoreService.java:
> 1192)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> ... 10 common frames omitted
>
> [ERROR] Error occurred while registering PWD Credential
>
> org.apache.airavata.credential.store.exception.CredentialStoreException:
> Error occurred while saving PWD Credentials.
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addPasswordCredential_result$addPasswordCredential_
> resultStandardScheme.read(CredentialStoreService.java:5373)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addPasswordCredential_result$addPasswordCredential_
> resultStandardScheme.read(CredentialStoreService.java:5351)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addPasswordCredential_result.read(CredentialStoreService.java:5293)
>
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> recv_addPasswordCredential(CredentialStoreService.java:262)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> addPasswordCredential(CredentialStoreService.java:249)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler.
> registerPwdCredential(AiravataServerHandler.java:566)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608.CGLIB$registerPwdCredential$167(<generated>)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608$$FastClassByGuice$$b0e29ae1.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:56)
>
> 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$$
> EnhancerByGuice$$5c8b1608.registerPwdCredential(<generated>)
>
> at org.apache.airavata.api.Airavata$Processor$registerPwdCredential.
> getResult(Airavata.java:16613)
>
> at org.apache.airavata.api.Airavata$Processor$registerPwdCredential.
> getResult(Airavata.java:16597)
>
> 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)
>
> [ERROR] Error persisting credentials. gateway - php_reference_gateway
> token id - 464bc41b-8687-40d0-8a39-0781dc687c29
>
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column
> 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [ERROR] Error occurred while saving SSH Credentials.
>
> org.apache.airavata.credential.store.store.CredentialStoreException:
> Error persisting credentials. gateway - php_reference_gateway token id -
> 464bc41b-8687-40d0-8a39-0781dc687c29
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:121)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> ... 10 common frames omitted
>
> [ERROR] Error occurred while registering SSH Credential
>
> org.apache.airavata.credential.store.exception.CredentialStoreException:
> Error occurred while saving SSH Credentials.
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3719)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3697)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result.read(CredentialStoreService.java:3639)
>
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> recv_addSSHCredential(CredentialStoreService.java:210)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> addSSHCredential(CredentialStoreService.java:197)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler.
> generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608.CGLIB$generateAndRegisterSSHKeys$
> 168(<generated>)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608$$FastClassByGuice$$b0e29ae1.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:56)
>
> 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$$
> EnhancerByGuice$$5c8b1608.generateAndRegisterSSHKeys(<generated>)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16585)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16569)
>
> 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)
>
> [ERROR] Error persisting credentials. gateway - php_reference_gateway
> token id - 4e0f0346-cd61-4e4c-b412-1076853139e2
>
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column
> 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [ERROR] Error occurred while saving SSH Credentials.
>
> org.apache.airavata.credential.store.store.CredentialStoreException:
> Error persisting credentials. gateway - php_reference_gateway token id -
> 4e0f0346-cd61-4e4c-b412-1076853139e2
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:121)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> ... 10 common frames omitted
>
> [ERROR] Error occurred while registering SSH Credential
>
> org.apache.airavata.credential.store.exception.CredentialStoreException:
> Error occurred while saving SSH Credentials.
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3719)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3697)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result.read(CredentialStoreService.java:3639)
>
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> recv_addSSHCredential(CredentialStoreService.java:210)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> addSSHCredential(CredentialStoreService.java:197)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler.
> generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608.CGLIB$generateAndRegisterSSHKeys$
> 168(<generated>)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$5c8b1608$$FastClassByGuice$$b0e29ae1.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:56)
>
> 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$$
> EnhancerByGuice$$5c8b1608.generateAndRegisterSSHKeys(<generated>)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16585)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16569)
>
> 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)
>
>
> ------------------------------
> *From:* Supun Nakandala [supun.nakandala@gmail.com]
> *Sent:* Wednesday, May 31, 2017 12:12 PM
>
> *To:* users@airavata.apache.org
> *Subject:* Re: Running Gaussian on Comet
>
> Hi Jeff,
>
> Can you share the error log file or the detailed console out?
>
> On Wed, May 31, 2017 at 2:48 PM, Sale, Jeff <es...@ucsd.edu> wrote:
>
>> Thanks, Eroma. Don't I also need to create key pairs in the Credential
>> Store? When I click the option to "Generate a new token" I get the
>> following error:
>>
>> "Error occurred while registering SSH Credential. More info: Error
>> occurred while saving SSH Credentials."
>>
>> Jeff
>>
>> ------------------------------
>> *From:* Eroma Abeysinghe [eroma.abeysinghe@gmail.com]
>> *Sent:* Wednesday, May 31, 2017 11:17 AM
>> *To:* users@airavata.apache.org
>> *Subject:* Re: Running Gaussian on Comet
>>
>> Hi Jeff,
>>
>> Sorry you are facing an issue with the job submission,
>> Could you please check whether you have a gateway preference defined for
>> Comet in Admin Dashboard --> Gateway Management
>> If not you have to add the preferences. please follow
>> http://airavata.readthedocs.io/en/latest/Gateway-
>> Configurations/#Preference
>>
>> Hope this helps
>>
>> Thanks,
>> Eroma
>>
>> On Wed, May 31, 2017 at 1:43 PM, Sale, Jeff <es...@ucsd.edu> wrote:
>>
>>> I decided to skip the Local Echo example due to problems with the
>>> definition of the Local Compute Resource and move on to the Gaussian
>>> tutorial. I used the testdrive.airavata.org Comet compute resource
>>> configuration settings as a guide for my own. I was able to submit an
>>> Experiment but got the following error which appears to be similar to the
>>> error I was getting with the Local Echo example:
>>>
>>> DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://local
>>> host:3306/replica_catalog?autoReconnect=true,Username=airava
>>> ta,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
>>>
>>> 5 replicacatalog_data INFO [pool-1-thread-124] openjpa.Runtime -
>>> Starting OpenJPA 2.2.0
>>>
>>> 26 replicacatalog_data INFO [pool-1-thread-124] openjpa.jdbc.JDBC -
>>> Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary"
>>> (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java
>>> mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5
>>> )).
>>>
>>> [INFO] Message Received with message id 'LAUNCH.EXP-03044130-2e70-431f-a07d-90125d1eaa55'
>>> and with message type 'EXPERIMENT' for experimentId:
>>> Gaussian_Job_1_ee4b0727-2503-42b6-a8cf-7792a0f45afb
>>>
>>> [INFO] Launching experiment with experimentId:
>>> Gaussian_Job_1_ee4b0727-2503-42b6-a8cf-7792a0f45afb gateway Id:
>>> php_reference_gateway
>>>
>>> [ERROR] Experiment launch failed due to Thrift conversion error,
>>> experimentId: Gaussian_Job_1_ee4b0727-2503-42b6-a8cf-7792a0f45afb,
>>> gatewayId: php_reference_gateway
>>>
>>> org.apache.thrift.TException: Experiment 'Gaussian_Job_1_ee4b0727-2503-42b6-a8cf-7792a0f45afb'
>>> launch failed. Unable to figureout execution type for application
>>> Gaussian_9598a0ff-1417-4dd5-bf73-39b8ebdaf521
>>>
>>> at org.apache.airavata.orchestrator.server.OrchestratorServerHa
>>> ndler.launchExperiment(OrchestratorServerHandler.java:251)
>>>
>>> at org.apache.airavata.orchestrator.server.OrchestratorServerHa
>>> ndler.launchExperiment(OrchestratorServerHandler.java:666)
>>>
>>> at org.apache.airavata.orchestrator.server.OrchestratorServerHa
>>> ndler.access$500(OrchestratorServerHandler.java:76)
>>>
>>> at org.apache.airavata.orchestrator.server.OrchestratorServerHa
>>> ndler$ExperimentHandler.onMessage(OrchestratorServerHandler.java:622)
>>>
>>> at org.apache.airavata.messaging.core.impl.ExperimentConsumer.h
>>> andleDelivery(ExperimentConsumer.java:84)
>>>
>>> at com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDi
>>> spatcher.java:144)
>>>
>>> at com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnabl
>>> e.run(ConsumerWorkService.java:99)
>>>
>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>>> Executor.java:1142)
>>>
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>>> lExecutor.java:617)
>>>
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> Caused by: java.lang.NullPointerException: null
>>>
>>> at org.apache.airavata.orchestrator.server.OrchestratorServerHa
>>> ndler.launchExperiment(OrchestratorServerHandler.java:156)
>>>
>>> ... 9 common frames omitted
>>>
>>
>>
>>
>> --
>> Thank You,
>> Best Regards,
>> Eroma
>>
>
>
>
> --
> 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: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Supun,
Thanks. It turns out there was no CREDENTIALS table in the credential_store database to DROP (perhaps not a surprise), but I did manage to create one. Unfortunately we are still getting the "Unknown column 'DESCRIPTION' in 'field list' " error.
I see there is also a database named airavata_credentialstore which also includes a CREDENTIALS table but has no DESCRIPTION field, but that's probably irrelevant. Just thought I'd mention it.
I still get the "Error occurred while registering SSH Credential. More info : Error occurred while saving SSH Credentials." in the browser. Below is the error and below that are some SQL queries to confirm that the table was built and contains the DESCRIPTION field. I restarted everything including mysql just to be safe, but still no luck.
Jeff
[ERROR] Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998)
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112)
at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ERROR] Error occurred while saving SSH Credentials.
org.apache.airavata.credential.store.store.CredentialStoreException: Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:121)
at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998)
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112)
... 10 common frames omitted
[ERROR] Error occurred while registering SSH Credential
org.apache.airavata.credential.store.exception.CredentialStoreException: Error occurred while saving SSH Credentials.
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3719)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3697)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:3639)
at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:210)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:197)
at org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2.CGLIB$generateAndRegisterSSHKeys$167(<generated>)
at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2$$FastClassByGuice$$4a3820fa.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:56)
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$$EnhancerByGuice$$a0d31de2.generateAndRegisterSSHKeys(<generated>)
at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16585)
at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16569)
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)
mysql> show databases;
+--------------------------+
| Database |
+--------------------------+
| airavata_credentialstore |
| app_catalog |
| credential_store |
| experiment_catalog |
| information_schema |
| mysql |
| performance_schema |
| replica_catalog |
| sharing_catalog |
| test |
| workflow_catalog |
+--------------------------+
11 rows in set (0.04 sec)
mysql> use credential_store;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+----------------------------+
| Tables_in_credential_store |
+----------------------------+
| CREDENTIALS |
+----------------------------+
1 row in set (0.00 sec)
mysql> show fields from CREDENTIALS;
+-----------------------+--------------+------+-----+-------------------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------------------+--------------+------+-----+-------------------+-------+
| GATEWAY_ID | varchar(100) | NO | PRI | NULL | |
| TOKEN_ID | varchar(100) | NO | PRI | NULL | |
| CREDENTIAL | blob | NO | | NULL | |
| PORTAL_USER_ID | varchar(256) | NO | | NULL | |
| TIME_PERSISTED | timestamp | NO | | CURRENT_TIMESTAMP | |
| DESCRIPTION | varchar(500) | YES | | NULL | |
| CREDENTIAL_OWNER_TYPE | varchar(10) | NO | | GATEWAY | |
+-----------------------+--------------+------+-----+-------------------+-------+
7 rows in set (0.01 sec)
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Supun,
Should I still share my airavata-server.properties file with you? I see there is a section containing the following commented lines. Is this what I should be modifying?
################# ---------- For ssh key pair sshKeyAuthentication ------------------- ################
#ssh.public.key=/path to public key for ssh
#ssh.private.key=/path to private key file for ssh
#ssh.keypass=passphrase for the private key
#ssh.username=username for ssh connection
## If you set "yes" for ssh.strict.hostKey.checking, then you must provide known hosts file path
#ssh.strict.hostKey.checking=yes/no
#ssh.known.hosts.file=/path to known hosts file
### Incase of password sshKeyAuthentication.
#ssh.password=Password for ssh connection
Jeff
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Supun,
Dang, still getting errors. Here's what I get when I try to submit an Experiment. It appears related to an invalid gateway storage resource. I cloned the Experiment a couple of times and tried some additional things, but I'm still confused how the Experiment authenticates with my jsale user account on Comet. There's not point at which I specify my password unless I'm missing something, which I probably am.
Jeff
[INFO] Message Received with message id 'LAUNCH.EXP-90009151-9465-4efc-9793-487727486c2f' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130 gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-f26cfead-34d4-4c6b-a133-8de5a247d85c and with message type:LAUNCHPROCESS, for processId:PROCESS_07ca4975-8620-4e92-8bdb-924176717723, expId:Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-f26cfead-34d4-4c6b-a133-8de5a247d85c
[INFO] expId: Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130, processId: PROCESS_07ca4975-8620-4e92-8bdb-924176717723 :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130 :- Experiment status updated to EXECUTING
[ERROR] Failed to submit process
org.apache.airavata.gfac.core.GFacException: Invalid Gateway StoragePreference
at org.apache.airavata.gfac.core.context.ProcessContext$ProcessContextBuilder.throwError(ProcessContext.java:805)
at org.apache.airavata.gfac.core.context.ProcessContext$ProcessContextBuilder.build(ProcessContext.java:769)
at org.apache.airavata.gfac.impl.GFacEngineImpl.populateProcessContext(GFacEngineImpl.java:128)
at org.apache.airavata.gfac.impl.GFacWorker.<init>(GFacWorker.java:74)
at org.apache.airavata.gfac.server.GfacServerHandler.submitProcess(GfacServerHandler.java:164)
at org.apache.airavata.gfac.server.GfacServerHandler$ProcessLaunchMessageHandler.onMessage(GfacServerHandler.java:258)
at org.apache.airavata.messaging.core.impl.ProcessConsumer.handleDelivery(ProcessConsumer.java:81)
at com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
at com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
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)
[INFO] expId: Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130, processId: PROCESS_07ca4975-8620-4e92-8bdb-924176717723 :- Process status changed event received for status FAILED
[INFO] expId : Clone_of_Gaussian_Job_2_2f3f60f8-ef71-4131-84a1-369541c2a130 :- Experiment status updated to FAILED
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
I noticed that the airavata-server.properties file had a reference to airavata_credentialstore. I changed that to credential_store and restarted the server and it appears I successfully created a new token. I'm going to proceed on the assumption that this was ok to do and see if I can run the Gaussian job.
Jeff
________________________________
From: Supun Nakandala [supun.nakandala@gmail.com]
Sent: Monday, June 05, 2017 7:57 AM
To: users@airavata.apache.org
Subject: Re: Running Gaussian on Comet
Can you share the airavata-server.properties file(Please mask any sensitive passwords that you have in the file)?
On Mon, Jun 5, 2017 at 10:51 AM, Sale, Jeff <es...@ucsd.edu>> wrote:
Supun,
Thanks. It turns out there was no CREDENTIALS table in the credential_store database to DROP (perhaps not a surprise), but I did manage to create one. Unfortunately we are still getting the "Unknown column 'DESCRIPTION' in 'field list' " error.
I see there is also a database named airavata_credentialstore which also includes a CREDENTIALS table but has no DESCRIPTION field, but that's probably irrelevant. Just thought I'd mention it.
I still get the "Error occurred while registering SSH Credential. More info : Error occurred while saving SSH Credentials." in the browser. Below is the error and below that are some SQL queries to confirm that the table was built and contains the DESCRIPTION field. I restarted everything including mysql just to be safe, but still no luck.
Jeff
[ERROR] Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998)
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112)
at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ERROR] Error occurred while saving SSH Credentials.
org.apache.airavata.credential.store.store.CredentialStoreException: Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:121)
at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998)
at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112)
... 10 common frames omitted
[ERROR] Error occurred while registering SSH Credential
org.apache.airavata.credential.store.exception.CredentialStoreException: Error occurred while saving SSH Credentials.
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3719)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3697)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:3639)
at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:210)
at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:197)
at org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2.CGLIB$generateAndRegisterSSHKeys$167(<generated>)
at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2$$FastClassByGuice$$4a3820fa.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:56)
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$$EnhancerByGuice$$a0d31de2.generateAndRegisterSSHKeys(<generated>)
at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16585)
at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16569)
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)
mysql> show databases;
+--------------------------+
| Database |
+--------------------------+
| airavata_credentialstore |
| app_catalog |
| credential_store |
| experiment_catalog |
| information_schema |
| mysql |
| performance_schema |
| replica_catalog |
| sharing_catalog |
| test |
| workflow_catalog |
+--------------------------+
11 rows in set (0.04 sec)
mysql> use credential_store;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+----------------------------+
| Tables_in_credential_store |
+----------------------------+
| CREDENTIALS |
+----------------------------+
1 row in set (0.00 sec)
mysql> show fields from CREDENTIALS;
+-----------------------+--------------+------+-----+-------------------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------------------+--------------+------+-----+-------------------+-------+
| GATEWAY_ID | varchar(100) | NO | PRI | NULL | |
| TOKEN_ID | varchar(100) | NO | PRI | NULL | |
| CREDENTIAL | blob | NO | | NULL | |
| PORTAL_USER_ID | varchar(256) | NO | | NULL | |
| TIME_PERSISTED | timestamp | NO | | CURRENT_TIMESTAMP | |
| DESCRIPTION | varchar(500) | YES | | NULL | |
| CREDENTIAL_OWNER_TYPE | varchar(10) | NO | | GATEWAY | |
+-----------------------+--------------+------+-----+-------------------+-------+
7 rows in set (0.01 sec)
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
OK, I made that change and tried again and it looks like I am making progress. Still some errors with data staging. Here are the errors:
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/replica_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - Starting OpenJPA 2.2.0
10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )).
[INFO] Message Received with message id 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529 and with message type:LAUNCHPROCESS, for processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, get process cancel data from zookeeper node /experiments/Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed STARTED -> CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed CREATED -> EXECUTING
[INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
[INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed EXECUTING -> COMPLETED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed CREATED -> EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status INPUT_DATA_STAGING
[INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Transferring from:/var/www/experimentData/jsale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/
[INFO] Session validation failed, key :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[ERROR] JSch initialization error
com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[ERROR] Data staging failed
org.apache.airavata.gfac.core.GFacException: JSch initialization error
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
... 15 common frames omitted
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed EXECUTING -> FAILED
[ERROR] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:- DATA_STAGING failed, reason: Data staging failed
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error while executing DATA_STAGING task, actual msg :expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :- DATA_STAGING failed. Reason: Data staging failed
at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed INPUT_DATA_STAGING -> FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Sent ack for deliveryTag 1
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to FAILED
Re: Running Gaussian on Comet
Posted by Eroma Abeysinghe <er...@gmail.com>.
Hi Jeff,
Storage resource is not compute resource(e.g.: comet) specific.
It is a generic storage location on gateway (PGA) side, common for all the
gateway jobs. In storage per user/project/experiment, a storage directory
will be created for each experiment.
The storage resource registration is simply identifying the actual storage
by registering and giving a storage resource ID, and this needs to to be a
location in the same machine/ server as PGA.
Since we use SCP for file transfer and use SSH keys, we need to assign an
ssh key in the admin dashboard --> gateway management --> storage
preferences
and then actually add the public key in the authorized_keys file.
Hope this helps.
Thanks,
Eroma
On Mon, Jun 12, 2017 at 1:44 PM, Sale, Jeff <es...@ucsd.edu> wrote:
> Supun,
>
> I believe I configured my storage resource settings for Comet correctly
> but I am still getting errors. However, the job is at least able to open a
> directory on Comet in the path that I specified as my scratch.
> Unfortunately the directory is empty. The directory name is:
>
> PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
>
>
> The same thing happened back on June 5 the last time I tried, but it was
> also empty.
>
> The errors I am getting appear to be related to ssh authentication. My
> Data Movement Protocol is set to SCP using SSH Keys. I assume this is
> correct, even though the instructions are not specific about these details.
> I used the testdrive.airavata.org for some guidance. I believe I have
> added my Comet Storage resource to the pga_config.php file correctly, i.e.
> as follows:
>
>
> /**
>
> * Gateway data store resource id
>
> */
>
> 'gateway-data-store-resource-id' => 'CometStorage_efa7abdf-ade7-
> 4adc-b97c-49f81d4dbcf0',
>
>
>
> Here are the errors I am still getting.
>
>
> [INFO] Started Gfac Server on Port 8950 ...
>
> DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://
> localhost:3306/replica_catalog?autoReconnect=true,
> Username=airavata,Password=airavata,validationQuery=SELECT 1 from
> CONFIGURATION
>
> 0 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime -
> Starting OpenJPA 2.2.0
>
> 16 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC -
> Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary"
> (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java
> mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5
> )).
>
> [INFO] Message Received with message id 'LAUNCH.EXP-6956f6ca-3237-4f27-b0fd-5f085f24f4e5'
> and with message type 'EXPERIMENT' for experimentId:
> Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
>
> [INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_
> 849cde15-5a1b-4b14-adec-f3b5af2c48cb gateway Id: php_reference_gateway
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator
> is SUCCESSFUL
>
> [INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator
> is SUCCESSFUL
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> Launched experiment
>
> [INFO] Message Received with message id 'LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8
> and with message type:LAUNCHPROCESS, for processId:PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7,
> expId:Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
>
> [INFO] Message Received with message id LAUNCHPROCESS and with message
> type: {}LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed event received for status STARTED
>
> [INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
> :- Experiment status updated to EXECUTING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, get process
> cancel data from zookeeper node /experiments/Clone_of_
> Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb/
> PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7/cancelListener
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed STARTED -> CONFIGURING_WORKSPACE
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed event received for status CONFIGURING_WORKSPACE
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status
> changed CREATED -> EXECUTING
>
> [INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/
> comet/jsale/temp_project/pga/PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
>
> [INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status
> changed EXECUTING -> COMPLETED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task
> status changed CREATED -> EXECUTING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed event received for status INPUT_DATA_STAGING
>
> [INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Transferring from:/var/www/experimentData/
> jsale37/GaussianonComet/Clone_of_Gaussian_Job_51497288328/water_opt_8c.dat
> To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_
> 7a041582-fd6a-4d68-9237-3ff1f5d059e7/
>
> [INFO] Session validation failed, key :jsale_Comet
> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Initialize a new SSH session for :jsale_Comet
> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [ERROR] JSch initialization error
>
> com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
>
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>
> at com.jcraft.jsch.Session.connect(Session.java:215)
>
> at com.jcraft.jsch.Session.connect(Session.java:183)
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(
> HPCRemoteCluster.java:137)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(
> HPCRemoteCluster.java:274)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(
> HPCRemoteCluster.java:173)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(
> SCPDataStageTask.java:247)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
> SCPDataStageTask.java:158)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(
> GFacEngineImpl.java:814)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:604)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: java.net.UnknownHostException: Comet Storage
>
> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:
> 184)
>
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>
> at java.net.Socket.connect(Socket.java:589)
>
> at java.net.Socket.connect(Socket.java:538)
>
> at java.net.Socket.<init>(Socket.java:434)
>
> at java.net.Socket.<init>(Socket.java:211)
>
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>
> ... 18 common frames omitted
>
> [ERROR] Data staging failed
>
> org.apache.airavata.gfac.core.GFacException: JSch initialization error
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(
> HPCRemoteCluster.java:137)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(
> HPCRemoteCluster.java:274)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(
> HPCRemoteCluster.java:173)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(
> SCPDataStageTask.java:247)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
> SCPDataStageTask.java:158)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(
> GFacEngineImpl.java:814)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:604)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException:
> Comet Storage
>
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>
> at com.jcraft.jsch.Session.connect(Session.java:215)
>
> at com.jcraft.jsch.Session.connect(Session.java:183)
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>
> ... 15 common frames omitted
>
> Caused by: java.net.UnknownHostException: Comet Storage
>
> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:
> 184)
>
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>
> at java.net.Socket.connect(Socket.java:589)
>
> at java.net.Socket.connect(Socket.java:538)
>
> at java.net.Socket.<init>(Socket.java:434)
>
> at java.net.Socket.<init>(Socket.java:211)
>
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>
> ... 18 common frames omitted
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task
> status changed EXECUTING -> FAILED
>
> [ERROR] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_f3129550-e851-4699-8b09-e8909d17168b type: DATA_STAGING,:-
> DATA_STAGING failed, reason: Data staging failed
>
> [ERROR] GFac Worker throws an exception
>
> org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg
> :Error while executing DATA_STAGING task, actual msg :expId:
> Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId:
> PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId:
> TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING :-
> DATA_STAGING failed. Reason: Data staging failed
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(
> GFacEngineImpl.java:628)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:609)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed INPUT_DATA_STAGING -> FAILED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status
> changed event received for status FAILED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb,
> processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Sent ack for
> deliveryTag 1
>
> [INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
> :- Experiment status updated to FAILED
>
>
>
> ------------------------------
> *From:* Supun Nakandala [supun.nakandala@gmail.com]
> *Sent:* Monday, June 05, 2017 12:12 PM
> *To:* users@airavata.apache.org
> *Subject:* Re: Running Gaussian on Comet
>
> Jeff,
>
> Basically you need to some setup work in your gateway as the gateway admin
> which includes creating and configuring a storage resource. From the error
> that I see it seems that the storage resource is not properly configured.
> More details on setting up storage resources and other configurations can
> be found here https://cwiki.apache.org/confluence/display/AIRAVATA/
> Tutorial+05+-+PHP+Reference+Gateway+for+Airavata+-+Gateway+Admin+Guide#
> Tutorial05-PHPReferenceGatewayforAiravata-GatewayAdminGuide-TutorialIV-
> RegisterandManageStorageResources
>
> Can you try to setup it following this tutorial? If it still has issues we
> can set up a video call.
>
> On Mon, Jun 5, 2017 at 3:05 PM, Sale, Jeff <es...@ucsd.edu> wrote:
>
>> OK, I made that change and tried again and it looks like I am making
>> progress. Still some errors with data staging. Here are the errors:
>>
>> DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://local
>> host:3306/replica_catalog?autoReconnect=true,Username=
>> airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
>>
>> 1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime -
>> Starting OpenJPA 2.2.0
>>
>> 10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC -
>> Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary"
>> (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java
>> mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5
>> )).
>>
>> [INFO] Message Received with message id 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c'
>> and with message type 'EXPERIMENT' for experimentId:
>> Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>>
>> [INFO] Launching experiment with experimentId:
>> Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id:
>> php_reference_gateway
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid user login
>> name, using gateway computer resource preference login name jsale
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid user login
>> name, using gateway computer resource preference login name jsale
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid user login
>> name, using gateway computer resource preference login name jsale
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid user login
>> name, using gateway computer resource preference login name jsale
>>
>> [WARN] Process compute resource scheduling doesn't have valid scratch
>> location, using gateway computer resource preference scratch
>> location/oasis/scratch/comet/jsale/temp_project/pga/
>>
>> [WARN] Process compute resource scheduling doesn't have valid user login
>> name, using gateway computer resource preference login name jsale
>>
>> [INFO] Validation of org.apache.airavata.orchestrat
>> or.core.validator.impl.BatchQueueValidator is SUCCESSFUL
>>
>> [INFO] Validation of org.apache.airavata.orchestrat
>> or.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, Launched experiment
>>
>> [INFO] Message Received with message id 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
>> and with message type:LAUNCHPROCESS, for processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>>
>> [INFO] Message Received with message id LAUNCHPROCESS and with message
>> type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed event received for status STARTED
>>
>> [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>> :- Experiment status updated to EXECUTING
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> get process cancel data from zookeeper node /experiments/Clone_of_Gaussian
>> _Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/PROCESS_
>> e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed STARTED -> CONFIGURING_WORKSPACE
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed event received for status CONFIGURING_WORKSPACE
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP :
>> Task status changed CREATED -> EXECUTING
>>
>> [INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/
>> comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>>
>> [INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6
>> c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6
>> c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP :
>> Task status changed EXECUTING -> COMPLETED
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :
>> Task status changed CREATED -> EXECUTING
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed event received for status INPUT_DATA_STAGING
>>
>> [INFO] SSH Session validation succeeded, key
>> :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6
>> c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6
>> c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] Transferring from:/var/www/experimentData/j
>> sale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat
>> To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_e2a359f
>> 3-5caa-4ed7-b203-2fde6ce7962c/
>>
>> [INFO] Session validation failed, key :jsale_Comet
>> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [INFO] Initialize a new SSH session for :jsale_Comet
>> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>>
>> [ERROR] JSch initialization error
>>
>> com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet
>> Storage
>>
>> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>>
>> at com.jcraft.jsch.Session.connect(Session.java:215)
>>
>> at com.jcraft.jsch.Session.connect(Session.java:183)
>>
>> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession
>> (HPCRemoteCluster.java:137)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HP
>> CRemoteCluster.java:274)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty
>> (HPCRemoteCluster.java:173)
>>
>> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDat
>> aStaging(SCPDataStageTask.java:247)
>>
>> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
>> SCPDataStageTask.java:158)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFa
>> cEngineImpl.java:814)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStagin
>> g(GFacEngineImpl.java:604)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskList
>> From(GFacEngineImpl.java:347)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
>> GFacEngineImpl.java:286)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFac
>> Worker.java:227)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>>
>> at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMD
>> C$0(MDCUtil.java:40)
>>
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>> Executor.java:1142)
>>
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>> lExecutor.java:617)
>>
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Caused by: java.net.UnknownHostException: Comet Storage
>>
>> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocket
>> Impl.java:184)
>>
>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>>
>> at java.net.Socket.connect(Socket.java:589)
>>
>> at java.net.Socket.connect(Socket.java:538)
>>
>> at java.net.Socket.<init>(Socket.java:434)
>>
>> at java.net.Socket.<init>(Socket.java:211)
>>
>> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>>
>> ... 18 common frames omitted
>>
>> [ERROR] Data staging failed
>>
>> org.apache.airavata.gfac.core.GFacException: JSch initialization error
>>
>> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession
>> (HPCRemoteCluster.java:137)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HP
>> CRemoteCluster.java:274)
>>
>> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty
>> (HPCRemoteCluster.java:173)
>>
>> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDat
>> aStaging(SCPDataStageTask.java:247)
>>
>> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
>> SCPDataStageTask.java:158)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFa
>> cEngineImpl.java:814)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStagin
>> g(GFacEngineImpl.java:604)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskList
>> From(GFacEngineImpl.java:347)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
>> GFacEngineImpl.java:286)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFac
>> Worker.java:227)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>>
>> at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMD
>> C$0(MDCUtil.java:40)
>>
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>> Executor.java:1142)
>>
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>> lExecutor.java:617)
>>
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException:
>> Comet Storage
>>
>> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>>
>> at com.jcraft.jsch.Session.connect(Session.java:215)
>>
>> at com.jcraft.jsch.Session.connect(Session.java:183)
>>
>> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>>
>> ... 15 common frames omitted
>>
>> Caused by: java.net.UnknownHostException: Comet Storage
>>
>> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocket
>> Impl.java:184)
>>
>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>>
>> at java.net.Socket.connect(Socket.java:589)
>>
>> at java.net.Socket.connect(Socket.java:538)
>>
>> at java.net.Socket.<init>(Socket.java:434)
>>
>> at java.net.Socket.<init>(Socket.java:211)
>>
>> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>>
>> ... 18 common frames omitted
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :
>> Task status changed EXECUTING -> FAILED
>>
>> [ERROR] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
>> taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:-
>> DATA_STAGING failed, reason: Data staging failed
>>
>> [ERROR] GFac Worker throws an exception
>>
>> org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg
>> :Error while executing DATA_STAGING task, actual msg :expId:
>> Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId:
>> PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
>> TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :-
>> DATA_STAGING failed. Reason: Data staging failed
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(G
>> FacEngineImpl.java:628)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStagin
>> g(GFacEngineImpl.java:609)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskList
>> From(GFacEngineImpl.java:347)
>>
>> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
>> GFacEngineImpl.java:286)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFac
>> Worker.java:227)
>>
>> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>>
>> at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMD
>> C$0(MDCUtil.java:40)
>>
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>> Executor.java:1142)
>>
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>> lExecutor.java:617)
>>
>> at java.lang.Thread.run(Thread.java:745)
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed INPUT_DATA_STAGING -> FAILED
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Process status changed event received for status FAILED
>>
>> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276
>> af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>> :- Sent ack for deliveryTag 1
>>
>> [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>> :- Experiment status updated to FAILED
>>
>>
>>
>>
>
>
> --
> Thank you
> Supun Nakandala
> Dept. Computer Science and Engineering
> University of Moratuwa
>
--
Thank You,
Best Regards,
Eroma
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Silly me. I could be wrong but it seems as though I may have named my storage resource incorrectly. The host name was set to 'Comet Storage' when I think it should have been comet.sdsc.edu. So, I deleted it and created a new storage resource but now I get an error when I browse to Gateway Management. Sorry about that (see attached screengrab).
Jeff
________________________________
From: Sale, Jeff [esale@ucsd.edu]
Sent: Monday, June 12, 2017 10:44 AM
To: users@airavata.apache.org
Subject: RE: Running Gaussian on Comet
Supun,
I believe I configured my storage resource settings for Comet correctly but I am still getting errors. However, the job is at least able to open a directory on Comet in the path that I specified as my scratch. Unfortunately the directory is empty. The directory name is:
PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
The same thing happened back on June 5 the last time I tried, but it was also empty.
The errors I am getting appear to be related to ssh authentication. My Data Movement Protocol is set to SCP using SSH Keys. I assume this is correct, even though the instructions are not specific about these details. I used the testdrive.airavata.org for some guidance. I believe I have added my Comet Storage resource to the pga_config.php file correctly, i.e. as follows:
/**
* Gateway data store resource id
*/
'gateway-data-store-resource-id' => 'CometStorage_efa7abdf-ade7-4adc-b97c-49f81d4dbcf0',
Here are the errors I am still getting.
[INFO] Started Gfac Server on Port 8950 ...
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/replica_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
0 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - Starting OpenJPA 2.2.0
16 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )).
[INFO] Message Received with message id 'LAUNCH.EXP-6956f6ca-3237-4f27-b0fd-5f085f24f4e5' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8 and with message type:LAUNCHPROCESS, for processId:PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, expId:Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb :- Experiment status updated to EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, get process cancel data from zookeeper node /experiments/Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb/PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7/cancelListener
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed STARTED -> CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status changed CREATED -> EXECUTING
[INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/comet/jsale/temp_project/pga/PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
[INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status changed EXECUTING -> COMPLETED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task status changed CREATED -> EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status INPUT_DATA_STAGING
[INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Transferring from:/var/www/experimentData/jsale37/GaussianonComet/Clone_of_Gaussian_Job_51497288328/water_opt_8c.dat To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7/
[INFO] Session validation failed, key :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[ERROR] JSch initialization error
com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[ERROR] Data staging failed
org.apache.airavata.gfac.core.GFacException: JSch initialization error
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
... 15 common frames omitted
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task status changed EXECUTING -> FAILED
[ERROR] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b type: DATA_STAGING,:- DATA_STAGING failed, reason: Data staging failed
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error while executing DATA_STAGING task, actual msg :expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING :- DATA_STAGING failed. Reason: Data staging failed
at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed INPUT_DATA_STAGING -> FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Sent ack for deliveryTag 1
[INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb :- Experiment status updated to FAILED
________________________________
From: Supun Nakandala [supun.nakandala@gmail.com]
Sent: Monday, June 05, 2017 12:12 PM
To: users@airavata.apache.org
Subject: Re: Running Gaussian on Comet
Jeff,
Basically you need to some setup work in your gateway as the gateway admin which includes creating and configuring a storage resource. From the error that I see it seems that the storage resource is not properly configured. More details on setting up storage resources and other configurations can be found here https://cwiki.apache.org/confluence/display/AIRAVATA/Tutorial+05+-+PHP+Reference+Gateway+for+Airavata+-+Gateway+Admin+Guide#Tutorial05-PHPReferenceGatewayforAiravata-GatewayAdminGuide-TutorialIV-RegisterandManageStorageResources
Can you try to setup it following this tutorial? If it still has issues we can set up a video call.
On Mon, Jun 5, 2017 at 3:05 PM, Sale, Jeff <es...@ucsd.edu>> wrote:
OK, I made that change and tried again and it looks like I am making progress. Still some errors with data staging. Here are the errors:
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/replica_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - Starting OpenJPA 2.2.0
10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )).
[INFO] Message Received with message id 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529 and with message type:LAUNCHPROCESS, for processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, get process cancel data from zookeeper node /experiments/Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed STARTED -> CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed CREATED -> EXECUTING
[INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
[INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed EXECUTING -> COMPLETED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed CREATED -> EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status INPUT_DATA_STAGING
[INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Transferring from:/var/www/experimentData/jsale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/
[INFO] Session validation failed, key :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[ERROR] JSch initialization error
com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.UnknownHostException: Comet Storage
at java.net<http://java.net>.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[ERROR] Data staging failed
org.apache.airavata.gfac.core.GFacException: JSch initialization error
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
... 15 common frames omitted
Caused by: java.net.UnknownHostException: Comet Storage
at java.net<http://java.net>.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed EXECUTING -> FAILED
[ERROR] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:- DATA_STAGING failed, reason: Data staging failed
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error while executing DATA_STAGING task, actual msg :expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :- DATA_STAGING failed. Reason: Data staging failed
at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed INPUT_DATA_STAGING -> FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Sent ack for deliveryTag 1
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to FAILED
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Supun,
I believe I configured my storage resource settings for Comet correctly but I am still getting errors. However, the job is at least able to open a directory on Comet in the path that I specified as my scratch. Unfortunately the directory is empty. The directory name is:
PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
The same thing happened back on June 5 the last time I tried, but it was also empty.
The errors I am getting appear to be related to ssh authentication. My Data Movement Protocol is set to SCP using SSH Keys. I assume this is correct, even though the instructions are not specific about these details. I used the testdrive.airavata.org for some guidance. I believe I have added my Comet Storage resource to the pga_config.php file correctly, i.e. as follows:
/**
* Gateway data store resource id
*/
'gateway-data-store-resource-id' => 'CometStorage_efa7abdf-ade7-4adc-b97c-49f81d4dbcf0',
Here are the errors I am still getting.
[INFO] Started Gfac Server on Port 8950 ...
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/replica_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
0 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - Starting OpenJPA 2.2.0
16 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )).
[INFO] Message Received with message id 'LAUNCH.EXP-6956f6ca-3237-4f27-b0fd-5f085f24f4e5' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8 and with message type:LAUNCHPROCESS, for processId:PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, expId:Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-7a545822-c32b-43a1-87b2-2496b59da9a8
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb :- Experiment status updated to EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, get process cancel data from zookeeper node /experiments/Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb/PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7/cancelListener
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed STARTED -> CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status changed CREATED -> EXECUTING
[INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/comet/jsale/temp_project/pga/PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7
[INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_fb013659-b4c4-427a-967f-e5e5b4be0c8a, type: ENV_SETUP : Task status changed EXECUTING -> COMPLETED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task status changed CREATED -> EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status INPUT_DATA_STAGING
[INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Transferring from:/var/www/experimentData/jsale37/GaussianonComet/Clone_of_Gaussian_Job_51497288328/water_opt_8c.dat To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7/
[INFO] Session validation failed, key :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[ERROR] JSch initialization error
com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[ERROR] Data staging failed
org.apache.airavata.gfac.core.GFacException: JSch initialization error
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
... 15 common frames omitted
Caused by: java.net.UnknownHostException: Comet Storage
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING : Task status changed EXECUTING -> FAILED
[ERROR] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b type: DATA_STAGING,:- DATA_STAGING failed, reason: Data staging failed
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error while executing DATA_STAGING task, actual msg :expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7, taskId: TASK_f3129550-e851-4699-8b09-e8909d17168b, type: DATA_STAGING :- DATA_STAGING failed. Reason: Data staging failed
at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed INPUT_DATA_STAGING -> FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Process status changed event received for status FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb, processId: PROCESS_7a041582-fd6a-4d68-9237-3ff1f5d059e7 :- Sent ack for deliveryTag 1
[INFO] expId : Clone_of_Gaussian_Job_5_849cde15-5a1b-4b14-adec-f3b5af2c48cb :- Experiment status updated to FAILED
________________________________
From: Supun Nakandala [supun.nakandala@gmail.com]
Sent: Monday, June 05, 2017 12:12 PM
To: users@airavata.apache.org
Subject: Re: Running Gaussian on Comet
Jeff,
Basically you need to some setup work in your gateway as the gateway admin which includes creating and configuring a storage resource. From the error that I see it seems that the storage resource is not properly configured. More details on setting up storage resources and other configurations can be found here https://cwiki.apache.org/confluence/display/AIRAVATA/Tutorial+05+-+PHP+Reference+Gateway+for+Airavata+-+Gateway+Admin+Guide#Tutorial05-PHPReferenceGatewayforAiravata-GatewayAdminGuide-TutorialIV-RegisterandManageStorageResources
Can you try to setup it following this tutorial? If it still has issues we can set up a video call.
On Mon, Jun 5, 2017 at 3:05 PM, Sale, Jeff <es...@ucsd.edu>> wrote:
OK, I made that change and tried again and it looks like I am making progress. Still some errors with data staging. Here are the errors:
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/replica_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - Starting OpenJPA 2.2.0
10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )).
[INFO] Message Received with message id 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c' and with message type 'EXPERIMENT' for experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id: php_reference_gateway
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[WARN] Process compute resource scheduling doesn't have valid scratch location, using gateway computer resource preference scratch location/oasis/scratch/comet/jsale/temp_project/pga/
[WARN] Process compute resource scheduling doesn't have valid user login name, using gateway computer resource preference login name jsale
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator is SUCCESSFUL
[INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator is SUCCESSFUL
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, Launched experiment
[INFO] Message Received with message id 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529 and with message type:LAUNCHPROCESS, for processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
[INFO] Message Received with message id LAUNCHPROCESS and with message type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status STARTED
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, get process cancel data from zookeeper node /experiments/Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed STARTED -> CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status CONFIGURING_WORKSPACE
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed CREATED -> EXECUTING
[INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
[INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status changed EXECUTING -> COMPLETED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed CREATED -> EXECUTING
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status INPUT_DATA_STAGING
[INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Transferring from:/var/www/experimentData/jsale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/
[INFO] Session validation failed, key :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[INFO] Initialize a new SSH session for :jsale_Comet Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
[ERROR] JSch initialization error
com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.UnknownHostException: Comet Storage
at java.net<http://java.net>.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[ERROR] Data staging failed
org.apache.airavata.gfac.core.GFacException: JSch initialization error
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:137)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:274)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:173)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(SCPDataStageTask.java:247)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:158)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:604)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
at com.jcraft.jsch.Util.createSocket(Util.java:349)
at com.jcraft.jsch.Session.connect(Session.java:215)
at com.jcraft.jsch.Session.connect(Session.java:183)
at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
... 15 common frames omitted
Caused by: java.net.UnknownHostException: Comet Storage
at java.net<http://java.net>.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.jcraft.jsch.Util.createSocket(Util.java:343)
... 18 common frames omitted
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task status changed EXECUTING -> FAILED
[ERROR] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:- DATA_STAGING failed, reason: Data staging failed
[ERROR] GFac Worker throws an exception
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error while executing DATA_STAGING task, actual msg :expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :- DATA_STAGING failed. Reason: Data staging failed
at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed INPUT_DATA_STAGING -> FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status changed event received for status FAILED
[INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Sent ack for deliveryTag 1
[INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 :- Experiment status updated to FAILED
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Running Gaussian on Comet
Posted by Supun Nakandala <su...@gmail.com>.
Jeff,
Basically you need to some setup work in your gateway as the gateway admin
which includes creating and configuring a storage resource. From the error
that I see it seems that the storage resource is not properly configured.
More details on setting up storage resources and other configurations can
be found here
https://cwiki.apache.org/confluence/display/AIRAVATA/Tutorial+05+-+PHP+Reference+Gateway+for+Airavata+-+Gateway+Admin+Guide#Tutorial05-PHPReferenceGatewayforAiravata-GatewayAdminGuide-TutorialIV-RegisterandManageStorageResources
Can you try to setup it following this tutorial? If it still has issues we
can set up a video call.
On Mon, Jun 5, 2017 at 3:05 PM, Sale, Jeff <es...@ucsd.edu> wrote:
> OK, I made that change and tried again and it looks like I am making
> progress. Still some errors with data staging. Here are the errors:
>
> DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://
> localhost:3306/replica_catalog?autoReconnect=true,
> Username=airavata,Password=airavata,validationQuery=SELECT 1 from
> CONFIGURATION
>
> 1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime -
> Starting OpenJPA 2.2.0
>
> 10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC -
> Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary"
> (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java
> mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5
> )).
>
> [INFO] Message Received with message id 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c'
> and with message type 'EXPERIMENT' for experimentId:
> Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>
> [INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_
> f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id: php_reference_gateway
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [WARN] Process compute resource scheduling doesn't have valid scratch
> location, using gateway computer resource preference scratch
> location/oasis/scratch/comet/jsale/temp_project/pga/
>
> [WARN] Process compute resource scheduling doesn't have valid user login
> name, using gateway computer resource preference login name jsale
>
> [INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator
> is SUCCESSFUL
>
> [INFO] Validation of org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator
> is SUCCESSFUL
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> Launched experiment
>
> [INFO] Message Received with message id 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
> and with message type:LAUNCHPROCESS, for processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c,
> expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
>
> [INFO] Message Received with message id LAUNCHPROCESS and with message
> type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed event received for status STARTED
>
> [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
> :- Experiment status updated to EXECUTING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, get process
> cancel data from zookeeper node /experiments/Clone_of_
> Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/
> PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed STARTED -> CONFIGURING_WORKSPACE
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed event received for status CONFIGURING_WORKSPACE
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status
> changed CREATED -> EXECUTING
>
> [INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/
> comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c
>
> [INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status
> changed EXECUTING -> COMPLETED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task
> status changed CREATED -> EXECUTING
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed event received for status INPUT_DATA_STAGING
>
> [INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_
> c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Transferring from:/var/www/experimentData/
> jsale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat
> To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_
> e2a359f3-5caa-4ed7-b203-2fde6ce7962c/
>
> [INFO] Session validation failed, key :jsale_Comet
> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [INFO] Initialize a new SSH session for :jsale_Comet
> Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115
>
> [ERROR] JSch initialization error
>
> com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage
>
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>
> at com.jcraft.jsch.Session.connect(Session.java:215)
>
> at com.jcraft.jsch.Session.connect(Session.java:183)
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(
> HPCRemoteCluster.java:137)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(
> HPCRemoteCluster.java:274)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(
> HPCRemoteCluster.java:173)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(
> SCPDataStageTask.java:247)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
> SCPDataStageTask.java:158)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(
> GFacEngineImpl.java:814)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:604)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: java.net.UnknownHostException: Comet Storage
>
> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:
> 184)
>
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>
> at java.net.Socket.connect(Socket.java:589)
>
> at java.net.Socket.connect(Socket.java:538)
>
> at java.net.Socket.<init>(Socket.java:434)
>
> at java.net.Socket.<init>(Socket.java:211)
>
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>
> ... 18 common frames omitted
>
> [ERROR] Data staging failed
>
> org.apache.airavata.gfac.core.GFacException: JSch initialization error
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(
> HPCRemoteCluster.java:137)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(
> HPCRemoteCluster.java:274)
>
> at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(
> HPCRemoteCluster.java:173)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging(
> SCPDataStageTask.java:247)
>
> at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(
> SCPDataStageTask.java:158)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(
> GFacEngineImpl.java:814)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:604)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException:
> Comet Storage
>
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
>
> at com.jcraft.jsch.Session.connect(Session.java:215)
>
> at com.jcraft.jsch.Session.connect(Session.java:183)
>
> at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
>
> ... 15 common frames omitted
>
> Caused by: java.net.UnknownHostException: Comet Storage
>
> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:
> 184)
>
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
>
> at java.net.Socket.connect(Socket.java:589)
>
> at java.net.Socket.connect(Socket.java:538)
>
> at java.net.Socket.<init>(Socket.java:434)
>
> at java.net.Socket.<init>(Socket.java:211)
>
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
>
> ... 18 common frames omitted
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task
> status changed EXECUTING -> FAILED
>
> [ERROR] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:-
> DATA_STAGING failed, reason: Data staging failed
>
> [ERROR] GFac Worker throws an exception
>
> org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg
> :Error while executing DATA_STAGING task, actual msg :expId:
> Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId:
> PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId:
> TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :-
> DATA_STAGING failed. Reason: Data staging failed
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(
> GFacEngineImpl.java:628)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(
> GFacEngineImpl.java:609)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:347)
>
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(
> GFacEngineImpl.java:286)
>
> at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(
> GFacWorker.java:227)
>
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>
> at org.apache.airavata.common.logging.MDCUtil.lambda$
> wrapWithMDC$0(MDCUtil.java:40)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed INPUT_DATA_STAGING -> FAILED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status
> changed event received for status FAILED
>
> [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8,
> processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Sent ack for
> deliveryTag 1
>
> [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8
> :- Experiment status updated to FAILED
>
>
>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
RE: Running Gaussian on Comet
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Supun,
I did not do that step. I see a line in the pga_config.php file that looks like where I specify that. Here's what I did:
/**
* Gateway data store resource id
*/
'gateway-data-store-resource-id' => 'CometStorage_efa7abdf-ade7-4adc-b97c-49f81d4dbcf0',
Is there anything else I need to do? Do I set the Data Movement Protocol to SCP and the Security Protocol to SSH_KEYS?
Jeff
________________________________
From: Supun Nakandala [supun.nakandala@gmail.com]
Sent: Monday, June 05, 2017 11:21 AM
To: users@airavata.apache.org
Subject: Re: Running Gaussian on Comet
Jeff,
I assume that you have registered a storage resource for your gateway. After registering a storage resource you need to add that storage resource id in your pga_config.php file in the PGA.
On Mon, Jun 5, 2017 at 2:19 PM, Sale, Jeff <es...@ucsd.edu>> wrote:
Supun,
Should I still share my airavata-server.properties file with you? I see there is a section containing the following commented lines. Is this what I should be modifying?
################# ---------- For ssh key pair sshKeyAuthentication ------------------- ################
#ssh.public.key=/path to public key for ssh
#ssh.private.key=/path to private key file for ssh
#ssh.keypass=passphrase for the private key
#ssh.username=username for ssh connection
## If you set "yes" for ssh.strict.hostKey.checking, then you must provide known hosts file path
#ssh.strict.hostKey.checking=yes/no
#ssh.known.hosts.file=/path to known hosts file
### Incase of password sshKeyAuthentication.
#ssh.password=Password for ssh connection
Jeff
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Running Gaussian on Comet
Posted by Supun Nakandala <su...@gmail.com>.
Jeff,
I assume that you have registered a storage resource for your gateway.
After registering a storage resource you need to add that storage resource
id in your pga_config.php file in the PGA.
On Mon, Jun 5, 2017 at 2:19 PM, Sale, Jeff <es...@ucsd.edu> wrote:
> Supun,
>
> Should I still share my airavata-server.properties file with you? I see
> there is a section containing the following commented lines. Is this what I
> should be modifying?
>
> ################# ---------- For ssh key pair sshKeyAuthentication
> ------------------- ################
>
> #ssh.public.key=/path to public key for ssh
>
> #ssh.private.key=/path to private key file for ssh
>
> #ssh.keypass=passphrase for the private key
>
> #ssh.username=username for ssh connection
>
> ## If you set "yes" for ssh.strict.hostKey.checking, then you must provide
> known hosts file path
>
> #ssh.strict.hostKey.checking=yes/no
>
> #ssh.known.hosts.file=/path to known hosts file
>
> ### Incase of password sshKeyAuthentication.
>
> #ssh.password=Password for ssh connection
>
>
> Jeff
>
>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa
Re: Running Gaussian on Comet
Posted by Supun Nakandala <su...@gmail.com>.
Can you share the airavata-server.properties file(Please mask any sensitive
passwords that you have in the file)?
On Mon, Jun 5, 2017 at 10:51 AM, Sale, Jeff <es...@ucsd.edu> wrote:
> Supun,
>
> Thanks. It turns out there was no CREDENTIALS table in the
> credential_store database to DROP (perhaps not a surprise), but I did
> manage to create one. Unfortunately we are still getting the "Unknown
> column 'DESCRIPTION' in 'field list' " error.
>
> I see there is also a database named airavata_credentialstore which also
> includes a CREDENTIALS table but has no DESCRIPTION field, but that's
> probably irrelevant. Just thought I'd mention it.
>
> I still get the "Error occurred while registering SSH Credential. More
> info : Error occurred while saving SSH Credentials." in the browser.
> Below is the error and below that are some SQL queries to confirm that the
> table was built and contains the DESCRIPTION field. I restarted everything
> including mysql just to be safe, but still no luck.
>
> Jeff
>
>
>
>
> [ERROR] Error persisting credentials. gateway - php_reference_gateway
> token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
>
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column
> 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> [ERROR] Error occurred while saving SSH Credentials.
>
> org.apache.airavata.credential.store.store.CredentialStoreException:
> Error persisting credentials. gateway - php_reference_gateway token id -
> 4eefe6f0-a9e3-4110-98c5-dc947d3268a6
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:121)
>
> at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.
> writeCredentials(SSHCredentialWriter.java:64)
>
> at org.apache.airavata.credential.store.server.
> CredentialStoreServerHandler.addSSHCredential(
> CredentialStoreServerHandler.java:102)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1160)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> Processor$addSSHCredential.getResult(CredentialStoreService.java:1144)
>
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
>
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
>
> at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(
> TThreadPoolServer.java:286)
>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'DESCRIPTION' in 'field list'
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
>
> at com.mysql.jdbc.Util.getInstance(Util.java:408)
>
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
>
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
>
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2501)
>
> at com.mysql.jdbc.PreparedStatement.executeInternal(
> PreparedStatement.java:1858)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2079)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(
> PreparedStatement.java:2013)
>
> at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(
> PreparedStatement.java:5104)
>
> at com.mysql.jdbc.PreparedStatement.executeUpdate(
> PreparedStatement.java:1998)
>
> at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.
> addCredentials(CredentialsDAO.java:112)
>
> ... 10 common frames omitted
>
> [ERROR] Error occurred while registering SSH Credential
>
> org.apache.airavata.credential.store.exception.CredentialStoreException:
> Error occurred while saving SSH Credentials.
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3719)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result$addSSHCredential_resultStandardScheme.read(
> CredentialStoreService.java:3697)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$
> addSSHCredential_result.read(CredentialStoreService.java:3639)
>
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> recv_addSSHCredential(CredentialStoreService.java:210)
>
> at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.
> addSSHCredential(CredentialStoreService.java:197)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler.
> generateAndRegisterSSHKeys(AiravataServerHandler.java:528)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$a0d31de2.CGLIB$generateAndRegisterSSHKeys$
> 167(<generated>)
>
> at org.apache.airavata.api.server.handler.AiravataServerHandler$$
> EnhancerByGuice$$a0d31de2$$FastClassByGuice$$4a3820fa.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:56)
>
> 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$$
> EnhancerByGuice$$a0d31de2.generateAndRegisterSSHKeys(<generated>)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16585)
>
> at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.
> getResult(Airavata.java:16569)
>
> 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)
>
>
> mysql> show databases;
>
> +--------------------------+
>
> | Database |
>
> +--------------------------+
>
> | airavata_credentialstore |
>
> | app_catalog |
>
> | credential_store |
>
> | experiment_catalog |
>
> | information_schema |
>
> | mysql |
>
> | performance_schema |
>
> | replica_catalog |
>
> | sharing_catalog |
>
> | test |
>
> | workflow_catalog |
>
> +--------------------------+
>
> 11 rows in set (0.04 sec)
>
>
> mysql> use credential_store;
>
> Reading table information for completion of table and column names
>
> You can turn off this feature to get a quicker startup with -A
>
>
> Database changed
>
> mysql> show tables;
>
> +----------------------------+
>
> | Tables_in_credential_store |
>
> +----------------------------+
>
> | CREDENTIALS |
>
> +----------------------------+
>
> 1 row in set (0.00 sec)
>
> mysql> show fields from CREDENTIALS;
>
> +-----------------------+--------------+------+-----+-------
> ------------+-------+
>
> | Field | Type | Null | Key | Default |
> Extra |
>
> +-----------------------+--------------+------+-----+-------
> ------------+-------+
>
> | GATEWAY_ID | varchar(100) | NO | PRI | NULL
> | |
>
> | TOKEN_ID | varchar(100) | NO | PRI | NULL
> | |
>
> | CREDENTIAL | blob | NO | | NULL
> | |
>
> | PORTAL_USER_ID | varchar(256) | NO | | NULL
> | |
>
> | TIME_PERSISTED | timestamp | NO | | CURRENT_TIMESTAMP
> | |
>
> | DESCRIPTION | varchar(500) | YES | | NULL
> | |
>
> | CREDENTIAL_OWNER_TYPE | varchar(10) | NO | | GATEWAY
> | |
>
> +-----------------------+--------------+------+-----+-------
> ------------+-------+
>
> 7 rows in set (0.01 sec)
>
>
>
>
--
Thank you
Supun Nakandala
Dept. Computer Science and Engineering
University of Moratuwa