[
https://issues.apache.org/jira/browse/AIRAVATA-2624?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16330572#comment-16330572
]
Eroma commented on AIRAVATA-2624:
---------------------------------
Tested the issue in [https://dev.seagrid.org|https://dev.seagrid.org/]
Test cases
# Submit a job to Stampede2 cluster development queue. Job should get launched
and queued in Stampede2. Once execution completed job status should get
updated. Tested with AutoDock_Vina - PASS
# Submit a job to Stampede2 cluster normal queue. Job should get launched and
queued in Stampede2. Once execution completed job status should get updated.
Tested with AutoDock_Vina - PASS
# Cancel a job in Stampede2 cluster development queue. Job should get
CANCELLED in Stampede2 and status update in gateway. Tested with AutoDock_Vina
- PASS
# Cancel a job in Stampede2 cluster normal queue. Job should get CANCELLED in
Stampede2 and status update in gateway. Tested with AutoDock_Vina - PASS
# Submit another test job to a different SLURM machine using SSH submission.
Tested with Comet. - PASS
# Cancel another test job to a different SLURM machine using SSH submission.
Tested with Comet. - PASS
# Submit another test job to a PBS machine using SSH submission. Tested with
bigred2 CPU queue individual cluster login. - PASS
# Cancel another test job to a different PBS machine using SSH submission.
Tested with bigred2 CPU queue individual cluster login. - PASS
# Submit another test job to a PBS machine using SSH submission. Tested with
bigred2 GPU queue community cluster login. - PASS
# Cancel another test job to a different PBS machine using SSH submission.
Tested with bigred2 GPU queue community cluster login. - PASS
> Stampede2 cluster SSH connectivity issue
> ----------------------------------------
>
> Key: AIRAVATA-2624
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2624
> Project: Airavata
> Issue Type: Bug
> Components: Airavata System, GFac
> Affects Versions: 0.18
> Environment: https://seagrid.org
> Reporter: Eroma
> Assignee: Dimuthu Upeksha
> Priority: Major
> Fix For: 0.18
>
>
> Job submission fails at env creation due to JSch initialization error.
> Error messages
> 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR
> o.a.a.gfac.core.GFacException
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - JSch initialization error
> com.jcraft.jsch.JSchException: Auth fail
> at com.jcraft.jsch.Session.connect(Session.java:512)
> 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:138)
> at
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> 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:748)
> 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR
> o.a.a.g.i.t.EnvironmentSetupTask
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - Error while environment setup
> 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:138)
> at
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> 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:748)
> Caused by: com.jcraft.jsch.JSchException: Auth fail
> at com.jcraft.jsch.Session.connect(Session.java:512)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> ... 14 common frames omitted
> 2018-01-09 09:46:10,786 [pool-7-thread-15] INFO
> o.a.a.g.c.context.TaskContext
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - expId:
> Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, processId:
> PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, taskId:
> TASK_03ea62e9-55c0-4d9f-bfc9-af26c9c45aa0, type: ENV_SETUP : Task status
> changed EXECUTING -> FAILED
> 2018-01-09 09:46:10,793 [pool-7-thread-15] ERROR
> o.a.a.gfac.impl.GFacEngineImpl
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - expId:
> Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, processId:
> PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, taskId:
> TASK_03ea62e9-55c0-4d9f-bfc9-af26c9c45aa0 type: ENV_SETUP,:- Input staging
> failed, reason: Error while environment setup
> 2018-01-09 09:46:10,803 [pool-7-thread-15] ERROR o.a.a.gfac.impl.GFacWorker
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - GFac Worker throws an exception
> org.apache.airavata.gfac.core.GFacException: Error while environment setup
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:572)
> at
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> 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:748)
> 2018-01-09 09:46:10,803 [pool-7-thread-15] INFO o.a.a.g.c.c.ProcessContext
> process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37,
> token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b,
> experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990,
> gateway_id=seagrid - expId:
> Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, processId:
> PROCESS_650014f6-fcb6-4680-90ea-898bee373f37 :- Process status changed
> CONFIGURING_WORKSPACE -> FAILE
--
This message was sent by Atlassian JIRA
(v7.6.3#76005)
