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From "Pierce, Marlon" <marpi...@iu.edu>
Subject Re: Trying to Set Up Molecular Dynamics Workflow
Date Mon, 23 May 2016 16:40:16 GMT
OK, to clarify, this script never gets called? What is the difference in your application deployments
between running this and running a simple test (echo) command?  

When you run python, are you uploading the script that you attached? A quick teststhat come
to mind is to run a different command (other than python) that also requires uploading the
input file, like cat.

And you can also look into the Apache logs for any PGA errors.

Marlon


On 5/23/16, 12:02 PM, "Jeff" <jkinniso@nd.edu> wrote:

>I've attached the script here. It actually has a bit of output to 
>stdout, and I've verified that it runs locally, but unfortunately 
>running it through the PGA produces no output whatsoever, not even the 
>autogenerated SLURM submit script, hence why I'm suspicious that it is 
>even running at all. I've set the experiment up to write stdout and 
>stderr to file,and it did this with the echo experiment.
>
>I think these are the relevant parts of the log, as well (after this it 
>just has the logging for auto-refresh):
>
>2016-05-23 11:15:00,387 [pool-15-thread-10] INFO 
>org.apache.airavata.gfac.server.GfacServerHandler  - 
>-----------------------------------7-----------------------------------------
>2016-05-23 11:15:00,387 [pool-15-thread-10] INFO 
>org.apache.airavata.gfac.server.GfacServerHandler  - 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf
>2016-05-23 11:15:00,405 [pool-15-thread-10] INFO 
>org.apache.airavata.gfac.impl.GFacEngineImpl  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf, get process cancel data 
>from zookeeper node 
>/experiments/juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19/PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf/cancelListener
>2016-05-23 11:15:00,912 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.core.context.ProcessContext  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf :- Process status changed 
>STARTED -> CONFIGURING_WORKSPACE
>2016-05-23 11:15:00,961 [pool-19-thread-11] INFO 
>org.apache.airavata.messaging.core.impl.RabbitMQStatusPublisher  - 
>Publishing status to rabbitmq...
>2016-05-23 11:15:00,962 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.core.context.TaskContext  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf, taskId: 
>TASK_b42f5d4e-3b70-4daa-a42f-c5e571cf97c8, type: ENV_SETUP:- Task status 
>changed CREATED -> EXECUTING
>2016-05-23 11:15:00,962 [pool-8-thread-5] INFO 
>org.apache.airavata.orchestrator.server.OrchestratorServerHandler  - 
>expId: juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf :- Process status changed 
>event received for status CONFIGURING_WORKSPACE
>2016-05-23 11:15:01,003 [pool-19-thread-11] INFO 
>org.apache.airavata.messaging.core.impl.RabbitMQStatusPublisher  - 
>Publishing status to rabbitmq...
>2016-05-23 11:15:01,003 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.impl.Factory  - SSH Session validation 
>succeeded, key :jeff_localhost_22
>2016-05-23 11:15:01,006 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.impl.Factory  - Channel creation test 
>succeeded, key :jeff_localhost_22
>2016-05-23 11:15:01,006 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.impl.Factory  - Reuse SSH session for 
>:jeff_localhost_22
>2016-05-23 11:15:01,006 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.impl.HPCRemoteCluster  - Creating directory: 
>localhost:/tmp/PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf
>2016-05-23 11:15:01,010 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.core.context.TaskContext  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf, taskId: 
>TASK_b42f5d4e-3b70-4daa-a42f-c5e571cf97c8, type: ENV_SETUP:- Task status 
>changed EXECUTING -> COMPLETED
>2016-05-23 11:15:01,053 [pool-19-thread-11] INFO 
>org.apache.airavata.messaging.core.impl.RabbitMQStatusPublisher  - 
>Publishing status to rabbitmq...
>2016-05-23 11:15:01,053 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.core.context.ProcessContext  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf :- Process status changed 
>CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING
>2016-05-23 11:15:01,095 [pool-19-thread-11] INFO 
>org.apache.airavata.messaging.core.impl.RabbitMQStatusPublisher  - 
>Publishing status to rabbitmq...
>2016-05-23 11:15:01,095 [pool-19-thread-11] INFO 
>org.apache.airavata.gfac.core.context.TaskContext  - expId: 
>juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf, taskId: 
>TASK_f5028495-bc51-4400-90d3-f56ca06acbde, type: DATA_STAGING:- Task 
>status changed CREATED -> EXECUTING
>2016-05-23 11:15:01,095 [pool-8-thread-6] INFO 
>org.apache.airavata.orchestrator.server.OrchestratorServerHandler  - 
>expId: juhygf_ff4b4196-aaa7-4e05-9dfd-74978e9cfa19, processId: 
>PROCESS_71118aff-fa37-449f-ae7f-fb170243d0bf :- Process status changed 
>event received for status INPUT_DATA_STAGING
>
>
>On 05/23/2016 11:55 AM, Pierce, Marlon wrote:
>> Hi Jeff,
>>
>> What is the script that you are trying to run (see below)?  Can you add some debugging
messages there?
>>
>> Marlon
>>
>>
>> On 5/23/16, 11:47 AM, "Jeff" <jkinniso@nd.edu> wrote:
>>   With my
>>> current setup, I can run jobs that do not require external scripts
>>> (e.g., echo <some string>), but when I try to run any kind of script the
>>> experiment never completes.
>>>
>>
>

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