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Posted to issues@airavata.apache.org by "Eroma (JIRA)" <ji...@apache.org> on 2017/08/01 13:55:00 UTC
[jira] [Created] (AIRAVATA-2498) Transfered job output has file
size 0. Where as the actual file has content
Eroma created AIRAVATA-2498:
-------------------------------
Summary: Transfered job output has file size 0. Where as the actual file has content
Key: AIRAVATA-2498
URL: https://issues.apache.org/jira/browse/AIRAVATA-2498
Project: Airavata
Issue Type: Bug
Components: Airavata System
Affects Versions: 0.17
Environment: https://ultrascan.scigap.org/
Reporter: Eroma
Assignee: Supun Chathuranga Nakandala
Fix For: 0.18
1. Experiment launched and job got completed.
2. 3 output files exists for trasnfer.
3. Transfer of the analysis-results.tar file failed with errors [1]
4. Other two, stderr and stdout transferred successfully.
5. When tried to download, a 0 byte file downloads for analysis-results.tar
6. Although the log clearly has all the errors in [1]
7. Both job and experiment statuses are COMPLETED.
8. exp ID: US3-AIRA_d8c1e7a9-0f77-414c-8137-fdeacdfa5c4b ran in LS5
[1]
2017-07-30 12:40:04,282 [pool-9-thread-1361] ERROR o.a.a.gfac.impl.SSHUtils - Error transfering the file content
2017-07-30 12:40:04,283 [pool-9-thread-1361] ERROR o.a.a.gfac.impl.SSHUtils - Error transfering the file content
java.lang.Exception: Error transfering the file content
at org.apache.airavata.gfac.impl.SSHUtils.scpThirdParty(SSHUtils.java:402)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:175)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.outputDataStaging(SCPDataStageTask.java:257)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:163)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:355)
at org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721)
at org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2017-07-30 12:40:04,283 [pool-9-thread-1361] ERROR o.a.a.g.impl.HPCRemoteCluster - Issue with jsch, Retry transferring from:/scratch/01623/us3/airavata-workingdirs/PROCESS_970223dc-89dc-4154-b5e9-c9070bd06b0c/output/analysis-results.tar To: /srv/www/htdocs/uslims3/uslims3_data/f73e3606-e55b-5e84-9da2-13dbcbd71a75/analysis-results.tar
com.jcraft.jsch.JSchException: Error transfering the file content
at org.apache.airavata.gfac.impl.SSHUtils.scpThirdParty(SSHUtils.java:413)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:175)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.outputDataStaging(SCPDataStageTask.java:257)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:163)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:355)
at org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721)
at org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Second attempt
2017-07-30 12:40:12,750 [pool-9-thread-1361] ERROR o.a.a.gfac.impl.SSHUtils - session is down
com.jcraft.jsch.JSchException: session is down
at com.jcraft.jsch.Session.openChannel(Session.java:853)
at org.apache.airavata.gfac.impl.SSHUtils.scpThirdParty(SSHUtils.java:286)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:175)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.outputDataStaging(SCPDataStageTask.java:257)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:163)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:355)
at org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721)
at org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2017-07-30 12:40:12,751 [pool-9-thread-1361] ERROR o.a.a.g.impl.HPCRemoteCluster - Issue with jsch, Retry transferring from:/scratch/01623/us3/airavata-workingdirs/PROCESS_970223dc-89dc-4154-b5e9-c9070bd06b0c/output/analysis-results.tar To: /srv/www/htdocs/uslims3/uslims3_data/f73e3606-e55b-5e84-9da2-13dbcbd71a75/analysis-results.tar
com.jcraft.jsch.JSchException: session is down
at org.apache.airavata.gfac.impl.SSHUtils.scpThirdParty(SSHUtils.java:413)
at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty(HPCRemoteCluster.java:175)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.outputDataStaging(SCPDataStageTask.java:257)
at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute(SCPDataStageTask.java:163)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
at org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766)
at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:355)
at org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721)
at org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196)
at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
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