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From Jeff <jkinn...@nd.edu>
Subject Re: Trying to Set Up Molecular Dynamics Workflow
Date Mon, 23 May 2016 17:20:01 GMT
As I've set it up, the line that gets generated should look something like:

/path/to/my/python alasim.py ala.pdb

where ala.pdb is my model. My echo command was simply /bin/echo 
<string>. So the difference is that I'm trying to call python on a 
python script and another input file, whereas with the simple echo app 
I'm directly calling echo with the necessary input. I tried something 
similar with a script that sleeps for 10 seconds and then runs echo, 
with the same result. It was called like

/bin/bash echoscript.sh

One thing to note is that the uploaded files do actually get moved to 
/var/www/experimentData, so the upload is actually occurring.

Unfortunately, the apache error logs don't show anything relevant 
(missing favicon errors), and the job is actually submitting just not 
completing, so I don't think it's an error with the PGA.

Best,
Jeff K.


On 05/23/2016 12:40 PM, Pierce, Marlon wrote:
> 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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