Dear Galaxy-Dev I was hoping to see if anybody had any suggestions to resolve this error.
To summarize, I'm using cloudman/Amazon EC2. I typically batch analyze 20-100 data sets against a workflow. (launched serially using bioblend script) I'm consistently seeing the following error "An error occurred running this job: Job output not returned from cluster" when I launch a large number of samples. If I analyze the same data sets/workflow, but launch 5 at a time, the analysis proceeds smoothly. Any pointers would be appreciated. Thanks Dave On Thu, May 2, 2013 at 1:51 PM, Dave Lin <d...@verdematics.com> wrote: > I am getting similar errors as Brian reported back in March. (Note, we > appear to have the same last name, but no relation) > > An error occurred with this dataset: *Job output not returned from > cluster* > * > * > - Running on Cloudman with 5-6 nodes. (xlarge) > - The error seems to occur consistently when I launch multiple workflows > in batch (using bioblend) > - Probably not relevant, but is failing on a BWA step. > - I am able to run successfully the same workflow against one of the > datasets that failed in batch. > - Change-set is from Feb 8, 2013. 8794:1c7174911392. Stable branch. Prior > to that, I was running different galaxy instances using changesets from > last year and never ran into this problem. > - I'm seeing errors like: > galaxy.jobs.runners.drmaa WARNING 2013-05-02 17:07:51,991 Job output not > returned from cluster: [Errno 2] No such file or directory\ > : '/mnt/galaxyData/tmp/job_working_directory/002/2066/2066.drmec' > - In this example, the /mnt/galaxyData/tmp/job_working_directory/002/2066 > folder and /mnt/galaxyData/tmp/job_working_directory/002/2066/2066.drmec > files do not exist. > > > Any suggestions? Seems like this might be some type of resource contention > issue, but I'm not sure where to investigate next. > > Thanks in advance, > Dave > > > > On Mon, Mar 11, 2013 at 9:04 AM, Brian Lin <brian....@tufts.edu> 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. >> >> From the SGE log, I see these errors: >> >> >> 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 >> cont...@brian-lin.com >> brian....@tufts.edu >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> > >
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