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From Pedro da Silveira <pedro...@gmail.com>
Subject Re: Phonon task
Date Wed, 30 Jan 2013 18:25:17 GMT
Hi Raminder,

Yes. You advice worked. I updated my Firewall and restarted it.

Now, I am getting the following message:

===================================================================================================

[INFO] -----END DATA-----
[INFO] Status is zero
[INFO] Status of job
https://gridftp1.ls4.tacc.utexas.edu:50398/16289811683591668436/8943296923859947437/isPENDING
[INFO] -----DATA-----
[INFO] Status of job
https://gridftp1.ls4.tacc.utexas.edu:50398/16289811683591668436/8943296923859947437/isPENDING
[INFO] -----END DATA-----
[INFO] job
https://gridftp1.ls4.tacc.utexas.edu:50398/16289811683591668436/8943296923859947437/have
same status: PENDING
[INFO] job
https://gridftp1.ls4.tacc.utexas.edu:50398/16289811683591668436/8943296923859947437/have
same status: PENDING
[INFO] job
https://gridftp1.ls4.tacc.utexas.edu:50398/16289811683591668436/8943296923859947437/have
same status: PENDING

===================================================================================================



On Wed, Jan 30, 2013 at 11:43 AM, Raminder Singh
<raminderjsingh@gmail.com>wrote:

> Hi Pedro,
>
> Looks like your machine firewall is blocking the input status socket for
> gram client. Try to following the instructions below to solve this.
>
> 1. Create cog.properties in .globus directory (create directory also if
> not exist)
> vi .globus/cog.properties
>
> tcp.port.range=40000,40100
> GLOBUS_TCP_PORT_RANGE=40000,40100
>
> 2: update the iptables to allow this port range. Eg -A INPUT  -p tcp
> --dport 40000:40100 -j ACCEPT
>
> 3. Restart Airavata server and run the job.
>
> Thanks
> Raminder
>
> On Jan 29, 2013, at 4:31 PM, Pedro da Silveira wrote:
>
> > Hi Raminder,
> >
> > Thanks for your reply. I am exploring the Airavata Client API. I just
> > thought that I should give a try to test my script first using the Xbaya,
> > before I tried the workflow on the API.
> >
> > Thank you
> >
> >
> >
> >
> > On Tue, Jan 29, 2013 at 3:24 PM, Raminder Singh <
> raminderjsingh@gmail.com>wrote:
> >
> >> Gram provider is not able to connect back to your Desktop. Gram client
> >> requires global ip for the client machine as well. I face similar
> problem
> >> when i am running jobs from my home. I have to be connected to IU VPN to
> >> get the job status otherwise its always zero.
> >>
> >> I can help you with getting the outputs. You need to use Airavata API to
> >> make it work. This is not integrated in Xbaya. Please look into [1] for
> API
> >> example class to run and monitor the workflow outside XBaya. You can
> save
> >> your workflow in registry and just pass the workflow name to this
> method to
> >> run the workflow. I have other set of sample code here [2].
> >>
> >> String setOutputNodeName="<name of the workflow node>"; //CABDone_invoke
> >> String setOutputLocation="<local location>";
> >>
> >> ExperimentAdvanceOptions options =
> >> airavataAPI.getExecutionManager().createExperimentAdvanceOptions(
> >>                                workflowName, username, null);
> >>                if(experimentName != null && !experimentName.isEmpty()){
> >>                options.setCustomExperimentId(experimentName);
> >>                }
> >>
> >>
> options.getCustomWorkflowOutputDataSettings().addNewOutputDataSettings(setOutputNodeName,
> >> setOutputLocation,
> >>                                registryURL, false);
> >> String experimentId =
> >> airavataAPI.getExecutionManager().runExperiment(workflowName,
> >> workflowInputs, options);
> >>
> >>
> >> Please let me know if you need more details.
> >>
> >> Thanks
> >> Raminder
> >>
> >> 1.
> >>
> https://svn.apache.org/repos/asf/airavata/trunk/samples/airavata-client/workflow-run/src/main/java/org/apache/airavata/client/samples/RunWorkflow.java
> >> 2.
> >>
> https://ogce.svn.sourceforge.net/svnroot/ogce/gateway-staging/odi-astronomy/airavata-api-client/src/main/java/org/apache/airavata/odi/client/WorkflowSubmission.java
> >>
> >> On Jan 29, 2013, at 4:03 PM, Pedro da Silveira 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
> >>
> >>
>
>

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