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 <[email protected]> Authored: Sat Jul 26 09:22:23 2014 -0400 Committer: lahiru <[email protected]> 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());
