Managed to fix this by adding job manager commands in client code
ResourceJobManager resourceJobManager = RegisterSampleApplicationsUtils.
createResourceJobManager(ResourceJobManagerType.FORK, null, null, null);
resourceJobManager.setJobManagerBinPath("/bin/");
Map<JobManagerCommand, String> jobManagerCommandStringMap = new
HashMap<JobManagerCommand, String>();
jobManagerCommandStringMap.put(JobManagerCommand.SUBMISSION, "sh");
resourceJobManager.setJobManagerCommands(jobManagerCommandStringMap);
LOCALSubmission submission = new LOCALSubmission();
submission.setSecurityProtocol(SecurityProtocol.LOCAL);
submission.setResourceJobManager(resourceJobManager);
Thanks
Dimuthu
On Fri, Dec 15, 2017 at 10:36 PM, DImuthu Upeksha <
dimuthu.upeks...@gmail.com> wrote:
> Hi Suresh,
>
> I'm getting following error when launching the experiment
>
> [ERROR] Thread Thread[pool-41-thread-13,5,main] died
> java.lang.NullPointerException: null
> at org.apache.airavata.gfac.impl.job.ForkJobConfiguration.
> getSubmitCommand(ForkJobConfiguration.java:85)
> at org.apache.airavata.gfac.impl.LocalRemoteCluster.submitBatchJob(
> LocalRemoteCluster.java:60)
> at org.apache.airavata.gfac.impl.task.LocalJobSubmissionTask.execute(
> LocalJobSubmissionTask.java:89)
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(
> GFacEngineImpl.java:814)
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeJobSubmission(
> GFacEngineImpl.java:510)
> at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(
> GFacEngineImpl.java:386)
> 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$0(MDCUtil.java:40)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1149)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
>
> Code point that emits NPE is
>
> @Override
> public RawCommandInfo getSubmitCommand(String workingDirectory, String
> forkFilePath) {
> return new RawCommandInfo(this.installedPath +
> jobManagerCommands.get(JobManagerCommand.SUBMISSION).trim() + " " +
> workingDirectory + File.separator +
> FilenameUtils.getName(forkFilePath));
> }
>
> When I debug, there was no job manager command for SUBMISSION type.
>
> This is the client code that I'm working on [1]. Please let me know if I
> have to add any other configuration when creating these resources.
>
> [1] https://gist.github.com/DImuthuUpe/3e31f1a5b64cf258bb6129ee848d1991
>
> Thanks
> Dimuthu
>
> On Fri, Dec 15, 2017 at 10:19 PM, Suresh Marru <sma...@apache.org> wrote:
>
>> Hi Dimuthu,
>>
>> Since Airavata supports different type of computational resources from
>> simple local executions to batch systems to cloud, the Resource Job Manager
>> specifies the types of job submissions executed on a given resource, the
>> protocol used and so forth [2].
>>
>> The job manager commands are particularly relevant to batch schedulers
>> [1] on HPC clusters [3]. These envelop basic commands to interact with the
>> scheduler to queue jobs, check job statuses, cancel jobs and so forth.
>> Different schedulers have different commands to interact and these structs
>> help capture them.
>>
>> Not sure if this what you are looking for. If you have any particular
>> question related to these within GFac, may be I can point to those
>> implementations and elaborate.
>>
>> Suresh
>>
>> [1] - https://github.com/apache/airavata/blob/master/thrift-inte
>> rface-descriptions/data-models/resource-catalog-models/
>> compute_resource_model.thrift#L85-L92
>> [2] - https://github.com/apache/airavata/blob/master/thrift-inte
>> rface-descriptions/data-models/resource-catalog-models/
>> compute_resource_model.thrift#L113-L118
>> [3] - https://en.wikipedia.org/wiki/Job_scheduler#Batch_queuing_
>> for_HPC_clusters
>>
>>
>> On Dec 15, 2017, at 11:31 AM, DImuthu Upeksha <dimuthu.upeks...@gmail.com>
>> wrote:
>>
>> Hi Folks,
>>
>> While I was trying to update the java sample clients for the Airavata,
>> there were some unclear areas that I came across. I'll use this thread to
>> get them clarified.
>>
>> What is the role of Resource Job Manager and Job Manager Command?
>>
>> Thanks
>> Dimuthu
>>
>>
>>
>
