Yes. I can try again. I would like to try my script where I can run "pw.x" and later "ph.x". Do you know what should I modify on my script, since both executable are working fine?
What do I have to do to transfer one output file "Text File" from Lonestar back to my Desktop? Thank you, On Tue, Jan 29, 2013 at 3:16 PM, Lahiru Gunathilake <[email protected]>wrote: > Hi Pedro, > > I think this is due to connection to the server has lost, if you get the > same error again this could be an issue, but I think this is due to some > connection failure to lonestar .. can you try again. > > Lahiru > > On Tue, Jan 29, 2013 at 4:03 PM, Pedro da Silveira <[email protected] > >wrote: > > > Hi All, > > > > I ran a task on Lonestar using Apache Airavata that took approximately 15 > > hour to finish. In the end it finishes successfully. > > > > I noticed on the log of Apache Airavata that it was constantly printing, > > while I was hanging waiting the task to finish. It looks fine, since the > > job was taking some time to finish. > > > > ============================= > > [INFO] Status is zero > > [INFO] Status is zero > > [INFO] Job proxy expired. Trying to renew proxy > > org.globus.gsi.gssapi.GlobusGSSCredentialImpl@19d00552 > > [INFO] Proxy file renewed to > > /tmp/x509up_uogce8653d6c7-7eed-4628-abf3-816fb122c8d6 for the user ogce > > with 3600 lifetime. > > [INFO] Myproxy renewed > > [INFO] Status is zero > > [INFO] Status is zero > > ============================================ > > > > In the end, my task completed nicely, but at the Xbaya I had this screen: > > > > http://i50.tinypic.com/208h08p.jpg > > > > <ns:description>The connection to the server failed (check host and port) > > [Caused by: Connection refused]: > > org.apache.airavata.core.gfac.exception.JobSubmissionFault: The > connection > > to the server failed (check host and port) [Caused by: Connection > > refused]</ns:description> > > > > > > At the Airavata-Server log, I had: > > > > ================================================================= > > > > [INFO] Job proxy expired. Trying to renew proxy > > org.globus.gsi.gssapi.GlobusGSSCredentialImpl@ef61e4a > > [INFO] Proxy file renewed to > > /tmp/x509up_uogce6ce97bd7-650c-46fb-8dea-b6f537fecd13 for the user ogce > > with 3600 lifetime. > > [ERROR] Context passed was NULL. > > java.lang.RuntimeException: Context passed was NULL. > > at > > > > > org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:496) > > at > > > > > org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:485) > > at > > > > > org.apache.airavata.core.gfac.notification.impl.WorkflowTrackingNotification.executionFail(WorkflowTrackingNotification.java:108) > > at > > > > > org.apache.airavata.core.gfac.notification.impl.DefaultNotifier.executionFail(DefaultNotifier.java:135) > > at > > > > > org.apache.airavata.core.gfac.exception.JobSubmissionFault.sendFaultNotification(JobSubmissionFault.java:52) > > at > > > > > org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:231) > > at > > > > > org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69) > > at > > > > > org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118) > > at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140) > > at > > > > > org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382) > > at java.lang.Thread.run(Thread.java:680) > > [INFO] -----DATA----- > > [INFO] lonestar4.tacc.teragrid.org,&( queue = "normal" )( stdout = > > > > > "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stdout" > > )( count = "64" )( executable = > > "/scratch/01437/ogce/Vlab/Phonon/executePhonon.sh" )( stderr = > > > > > "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stderr" > > )( maxwalltime = "1440" )( hostCount = "8" )( minmemory = "10240" )( > > project = "TG-STA110014S" )( jobtype = "mpi" )( environment = ( > "inputData" > > > > > "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData" > > ) ( "outputData" > > > > > "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/outputData" > > ) )( proxy_timeout = "1" )( arguments = > > > > > "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Pwscf_Input" > > > > > "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Cd_PON_sp_LDA.vdb" > > > > > "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Te_PON_LDA.vdb" > > > > > "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Phonon_Input" > > )( directory = > > > > > "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4" > > )( maxmemory = "15360" ) > > [INFO] -----END DATA----- > > [ERROR] The connection to the server failed (check host and port) [Caused > > by: Connection refused] > > org.apache.airavata.core.gfac.exception.JobSubmissionFault: The > connection > > to the server failed (check host and port) [Caused by: Connection > refused] > > at > > > > > org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229) > > at > > > > > org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69) > > at > > > > > org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118) > > at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140) > > at > > > > > org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382) > > at java.lang.Thread.run(Thread.java:680) > > Caused by: org.globus.gram.GramException: The connection to the server > > failed (check host and port) [Caused by: Connection refused] > > at org.globus.gram.Gram.renew(Gram.java:595) > > at org.globus.gram.GramJob.renew(GramJob.java:329) > > at org.globus.gram.GramJob.renew(GramJob.java:315) > > at > > > > > org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72) > > at > > > > > org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206) > > ... 11 more > > Exception in thread "Thread-42" > > org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException: > > org.apache.airavata.workflow.model.exceptions.WorkflowException: The > > connection to the server failed (check host and port) [Caused by: > > Connection refused] > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:392) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382) > > at java.lang.Thread.run(Thread.java:680) > > Caused by: > org.apache.airavata.workflow.model.exceptions.WorkflowException: > > The connection to the server failed (check host and port) [Caused by: > > Connection refused] > > at > > > > > org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:321) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218) > > at > > > > > org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389) > > ... 3 more > > Caused by: org.apache.airavata.core.gfac.exception.JobSubmissionFault: > The > > connection to the server failed (check host and port) [Caused by: > > Connection refused] > > at > > > > > org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229) > > at > > > > > org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69) > > at > > > > > org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118) > > at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140) > > at > > > > > org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256) > > ... 7 more > > Caused by: org.globus.gram.GramException: The connection to the server > > failed (check host and port) [Caused by: Connection refused] > > at org.globus.gram.Gram.renew(Gram.java:595) > > at org.globus.gram.GramJob.renew(GramJob.java:329) > > at org.globus.gram.GramJob.renew(GramJob.java:315) > > at > > > > > org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72) > > at > > > > > org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206) > > ... 11 more > > > > ================================================================= > > > > My questions: > > > > Is there anything that I should do to avoid this error to happen? > > What do I have to do transfer one output file "Text File" from Lonestar > > back to my Desktop? > > > > Thank you, > > > > Pedro da Silveira > > > > > > -- > System Analyst Programmer > PTI Lab > Indiana University >
