On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
Renaming the file to replace the colon with (say) an underscore allows a manual qsub to work fine with UGE. I've edited Galaxy to avoid the colons (patch below) but the submission still fails.
Hi Peter,
After seeing your email I now wonder if the problem I described here[1] and didn't get any answer about it is related to your findings while trying UGE.
[1]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-t...
I noticed the only mayor different I can notice between jobs submission with and without tasked option enabled is a colon in the name. See the relevant output from "qstat -f JOBID" below.
Without tasked: Error_Path = /local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmerr Output_Path = /local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmout
Job finishes and galaxy is able to collect drmerr and drmout files.
With tasked: Error_Path = /local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr Output_Path = /local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout
sched_hint = Post job file processing error; job 40.head.local on host node01.local/7+node01.local/6+node01.local/5+node01.local/4+node01.local/3+node01.local/2+node01.local/1+node01.brel.local/0
Unable to copy file /var/spool/torque/spool/40.head.local.OU to galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/40.head.local.OU
Unable to copy file /var/spool/torque/spool/40.head.local.ER to galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/40.head.local.ER
Job finishes, galaxy is not able to collect drmerr and drmout files and job turns green in the history panels but includes partial information about not being able to collect drmerr and drmout files.
I will try to see if switching from using colon to underscore could help in this situation also. Although I'm also worry about "galaxy@" in the file path. I don't understand why is there.
I'm using latest Galaxy Dist, Torque 4.1.4, Maui 3.3.1 and pbs-drmaa 1.0.12. I tried using pbs-python but that failed for me. I also tried libdrmaa from this Torque version with the same exact results.
Best, Carlos