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Posted to commits@airavata.apache.org by la...@apache.org on 2014/07/26 15:22:49 UTC
git commit: fixing bigred 2 monitoring issues
Repository: airavata
Updated Branches:
refs/heads/master d9f4dc0ef -> 1a2411d2e
fixing bigred 2 monitoring issues
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/1a2411d2
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/1a2411d2
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/1a2411d2
Branch: refs/heads/master
Commit: 1a2411d2e70e2138aad5b5e8508e53a5bd1a3665
Parents: d9f4dc0
Author: lahiru <la...@apache.org>
Authored: Sat Jul 26 09:22:23 2014 -0400
Committer: lahiru <la...@apache.org>
Committed: Sat Jul 26 09:22:23 2014 -0400
----------------------------------------------------------------------
.../apache/airavata/client/tools/DocumentCreatorNew.java | 2 +-
.../store/credential/impl/ssh/SSHCredential.java | 2 ++
.../gfac/gsissh/provider/impl/GSISSHProvider.java | 1 -
.../apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java | 2 +-
.../airavata/gfac/ssh/provider/impl/SSHProvider.java | 2 +-
.../airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java | 10 +++++-----
.../org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java | 2 +-
7 files changed, 11 insertions(+), 10 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java
----------------------------------------------------------------------
diff --git a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java
index 895736d..5dd487c 100644
--- a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java
+++ b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java
@@ -658,7 +658,7 @@ public class DocumentCreatorNew {
Map<JobManagerCommand, String> commands = new HashMap<JobManagerCommand, String>();
- commands.put(JobManagerCommand.SUBMISSION, "aprun -n 1");
+ commands.put(JobManagerCommand.SUBMISSION, "aprun -n");
ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.UGE, "/opt/torque/torque-4.2.3.1/bin/", commands, null);
SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
sshJobSubmission.setResourceJobManager(resourceJobManager);
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/credential-store-service/credential-store/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java
----------------------------------------------------------------------
diff --git a/modules/credential-store-service/credential-store/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java b/modules/credential-store-service/credential-store/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java
index 87b32ec..d41af21 100644
--- a/modules/credential-store-service/credential-store/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java
+++ b/modules/credential-store-service/credential-store/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java
@@ -50,6 +50,7 @@ public class SSHCredential extends Credential implements Serializable {
this.passphrase = passphrase;
this.gateway = gateway;
this.username = username;
+ this.setPortalUserName(username);
}
public byte[] getPrivateKey() {
@@ -83,4 +84,5 @@ public class SSHCredential extends Credential implements Serializable {
public void setGateway(String gateway) {
this.gateway = gateway;
}
+
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
index 8d311bc..9ea284b 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
@@ -94,7 +94,6 @@ public class GSISSHProvider extends AbstractRecoverableProvider {
String jobID = cluster.submitBatchJob(jobDescriptor);
jobExecutionContext.setJobDetails(jobDetails);
- jobID = null; // todo should remove this line
if (jobID == null) {
jobDetails.setJobID("none");
GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
index 4c93024..aca1155 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
@@ -113,7 +113,7 @@ public class GFACGSISSHUtils {
jobDescriptor.setStandardErrorFile(app.getStandardError());
Random random = new Random();
int i = random.nextInt(Integer.MAX_VALUE); // We always set the job name
- jobDescriptor.setJobName(String.valueOf(i));
+ jobDescriptor.setJobName(String.valueOf(i+99999999));
jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());
List<String> inputValues = new ArrayList<String>();
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
index ad26286..ab268df 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
@@ -164,7 +164,7 @@ public class SSHProvider extends AbstractProvider {
}
// This installed path is a mandetory field, because this could change based on the computing resource
JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, app, cluster);
-
+ jobDetails.setJobName(jobDescriptor.getJobName());
log.info(jobDescriptor.toXML());
jobDetails.setJobDescription(jobDescriptor.toXML());
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
index c820751..afa43f5 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java
@@ -148,12 +148,12 @@ public class TokenizedSSHAuthInfo implements SSHPublicKeyFileAuthentication {
public SSHCredential getDefaultCredentials() throws GFacException, ApplicationSettingsException {
Properties configurationProperties = ServerSettings.getProperties();
String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
- String sshPrivateKey = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
- String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
- String sshPassword = configurationProperties.getProperty(Constants.SSH_PASSWORD);
- String sshPublicKey = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
this.getRequestData().setRequestUser(sshUserName);
- return new SSHCredential(sshPrivateKey.getBytes(), sshPublicKey.getBytes(), sshPrivateKeyPass, requestData.getGatewayId(), sshUserName);
+ this.privateKeyFile = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
+ this.publicKeyFile = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
+ this.passPhrase = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
+ this.getRequestData().setRequestUser(sshUserName);
+ return new SSHCredential(null, null, null, requestData.getGatewayId(), sshUserName);
}
public CredentialReader getCredentialReader() {
http://git-wip-us.apache.org/repos/asf/airavata/blob/1a2411d2/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index f0f5c50..3753f97 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@ -101,7 +101,7 @@ public class GFACSSHUtils {
jobDescriptor.setStandardErrorFile(app.getStandardError());
Random random = new Random();
int i = random.nextInt(Integer.MAX_VALUE);
- jobDescriptor.setJobName(String.valueOf(i));
+ jobDescriptor.setJobName(String.valueOf(i+99999999));
jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());