[Iplant-api-dev] job submit problems

[Rion Dooley]

I Roger,

I got your other email. I’m looking into the issue. It seems that the submit script isn’t being generated for your job. Some combination of settings that don’t line up. I’m tracking it down and adding unit tests to verify it is caught at registration time rather than runtime.

--
Rion




On Jul 24, 2014, at 1:12 PM, Barthelson, Roger A - (rogerab) <rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>> wrote:

I am trying to submit a job for an Agave app that I created and is already registered. I keep getting this response when I run CLI tool, jobs-history for the job:

Job accepted and queued for submission.
Attempt 1 to stage job inputs
Identifying input files for staging
Staging /rogerab/test_dir/gsnap_arab/reads to remote job directory
Copy in progress
Job inputs staged to execution system
Preparing job for submission.
Attempt 1 to submit job
Attempt 1 failed to submit job. Failed to submit job. -----------------------------------------------------------------
-- Welcome to the Lonestar4 Westmere/QDR IB Linux Cluster --
-----------------------------------------------------------------
--> Checking that you specified -V...
--------------------------> Rejecting job <--------------------------
-V is now a required option. Please specify it in your submit script.
---------------------------------------------------------------------
Unable to run job: JSV rejected job.
Exiting.

Attempt 2 to submit job
Attempt 2 failed to submit job. Failed to submit job. -----------------------------------------------------------------
-- Welcome to the Lonestar4 Westmere/QDR IB Linux Cluster --
-----------------------------------------------------------------
--> Checking that you specified -V...
--------------------------> Rejecting job <--------------------------
-V is now a required option. Please specify it in your submit script.
---------------------------------------------------------------------
Unable to run job: JSV rejected job.
Exiting.

Attempt 3 to submit job
Attempt 3 failed to submit job. Failed to submit job. -----------------------------------------------------------------
-- Welcome to the Lonestar4 Westmere/QDR IB Linux Cluster --
-----------------------------------------------------------------
--> Checking that you specified -V...
--------------------------> Rejecting job <--------------------------
-V is now a required option. Please specify it in your submit script.
---------------------------------------------------------------------
Unable to run job: JSV rejected job.
Exiting.

Cleaning up remote work directory.
Completed cleaning up remote work directory.
Unable to submit job after 3 attempts. Job cancelled.

I tried adding a "#$ -V” to the start of my wrapper, but I think this needs to be put in by Agave, since it is creating the header for the submit script. Am I wrong? Any ideas?

Roger

--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>
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