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" <[email protected]> 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" <[email protected]> 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.
