I have a working sge setup.
Two ideas:
1 - look in the sge logs on the worker node (on my system they are in
/var/spool...)
2 - maybe a permission problem?
--
Brad Langhorst
New England Biolabs
langhorst@neb.com
On 2/2/12 8:50 AM, "Peter Cock"
p.j.a.cock@googlemail.com wrote:
>Hi all,
>
>I'm trying to configure Galaxy to talk to our SGE cluster via DRMAA.
>I've got jobs submitting, and can verify they are in the queue and then
>run via qstat (from the cluster). However, something isn't right.
>I'm testing with blastp using the following in universe_wsgi.ini
>
>
>[galaxy:tool_runners]
>ncbi_blastp_wrapper = drmaa:///
>...
>
>Job output from run.sh,
>
>galaxy.jobs DEBUG 2012-02-02 11:49:16,707 (25) Working directory for
>job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/25
>galaxy.jobs DEBUG 2012-02-02 11:49:16,710 dispatching job 25 to drmaa
>runner
>galaxy.jobs INFO 2012-02-02 11:49:16,818 job 25 dispatched
>galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:17,174 (25)
>submitting file /mnt/galaxy/galaxy-central/database/pbs/galaxy_25.sh
>galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:17,174 (25) command
>is: blastp -version &>
>/mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_25;
>python /mnt/galaxy/galaxy-central/tools/ncbi_blast_plus/hide_stderr.py
>blastp -query
>"/mnt/galaxy/galaxy-central/database/files/000/dataset_5.dat"
> -subject "/mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat"
>-task blastp -evalue 0.001 -out
>/mnt/galaxy/galaxy-central/database/files/000/dataset_25.dat
>-outfmt 6 -num_threads 8
>galaxy.jobs.runners.drmaa INFO 2012-02-02 11:49:17,178 (25) queued as 223
>galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:18,175 (25/223) state
>change: job is queued and active
>galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:32,176 (25/223) state
>change: job is running
>galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:43,367 (25/223) state
>change: job finished normally
>galaxy.jobs DEBUG 2012-02-02 11:49:43,679 job 25 ended
>galaxy.jobs.runners.drmaa WARNING 2012-02-02 11:49:43,699 Unable to
>cleanup: [Errno 2] No such file or directory:
>'/mnt/galaxy/galaxy-central/database/job_working_directory/000/25/25.drmou
>t'
>galaxy.jobs.runners.drmaa WARNING 2012-02-02 11:49:43,699 Unable to
>cleanup: [Errno 2] No such file or directory:
>'/mnt/galaxy/galaxy-central/database/job_working_directory/000/25/25.drmer
>r'
>
>Interestingly, via the Galaxy interface it does seem to have captured
>stdout (emtpy) and stderr anyway:
>
><quote>
>Error invoking command:
>blastp -query /mnt/galaxy/galaxy-central/database/files/000/dataset_5.dat
>-subject /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat
>-task blastp -evalue 0.001 -out
>/mnt/galaxy/galaxy-central/database/files/000/dataset_25.dat -outfmt 6
>-num_threads 8
>
>[Errno 2] No such file or directory
></quote>
>
>The error in this case is some kind of path problem, which I could
>'fix' by adding 'source ~/.bashrc' to the drm_template defined in
>lib/galaxy/jobs/runners/drmaa.py (although there should be a more
>elegant solution to this!).
>
>Anyway, why is the DRMAA code giving me these warnings about
>missing the stdout and stderr files - even when the run runs fine?
>
>Thanks,
>
>Peter
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