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 <[email protected]>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 < > [email protected]>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 > >> > >> > >
