Peter:

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
-- 
Brad Langhorst
New England Biolabs
langho...@neb.com

 





On 2/2/12 8:50 AM, "Peter Cock" <p.j.a.c...@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
>___________________________________________________________
>Please keep all replies on the list by using "reply all"
>in your mail client.  To manage your subscriptions to this
>and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to