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From Jeff <jkinn...@nd.edu>
Subject Re: Trying to Set Up Molecular Dynamics Workflow
Date Mon, 23 May 2016 16:02:33 GMT
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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