Question: Amazon Ec2: An Error Occurred Running This Job: Job Output Not Returned From Cluster
0
Brian Lin • 10 wrote:
Hi guys, I'm running a galaxy cloudman instance and running the usual
tophat->cufflinks->cuffdiff workflow from RNAseq data.
I am using a m2.4xlarge as a master node, and autoscaling from 0-4
workers
of the m2.xlarge type.
I have gotten the error: An error occurred running this job: *Job
output
not returned from cluster*
when running fasta groomer, tophat, and now cufflinks.
Following up troubleshooting from other people in the mailing list, I
have
set a new line in universe_wsgi.ini of retry_job_output_collection=30
Unfortunately, this does not seem to have fixed the problem.
The stdout is blank, and stderr gives Job output not returned from
cluster
Under manage jobs in the admin panel, it lists 4 out of the 6 jobs as
currently running. What is confusing is that of the 4 "running," one
has
already returned the error in the user dataset panel and yet is still
listed as running.
03/11/2013 14:32:52|worker|ip-10-159-47-223|W|job 42.1 failed on host
ip-10-30-130-84.ec2.internal before writing exit_status because:
shepherd exited with exit status 19: before writing exit_status
03/11/2013 14:32:52|worker|ip-10-159-47-223|W|job 43.1 failed on host
ip-10-30-130-84.ec2.internal before writing exit_status because:
shepherd exited with exit status 19: before writing exit_status
03/11/2013 14:39:41|worker|ip-10-159-47-223|E|adminhost
"ip-10-30-130-84.ec2.internal" already exists
03/11/2013 14:40:07|worker|ip-10-159-47-223|E|exechost
"ip-10-30-130-84.ec2.internal" already exists
03/11/2013 14:50:54|worker|ip-10-159-47-223|E|adminhost
"ip-10-30-130-84.ec2.internal" already exists
03/11/2013 14:50:55|worker|ip-10-159-47-223|E|exechost
"ip-10-30-130-84.ec2.internal" already exists
Does anyone have any idea how to solve this error? It has removed my
ability to use workflows completely and I still have not been able to
run a
single analysis to completion due to it.
Thanks for any insight anyone provide!
Brian
--
Brian Lin
contact@brian-lin.com
brian.lin@tufts.edu