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. >>> >> >
