1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f2f1cce4678c/ Changeset: f2f1cce4678c User: jmchilton Date: 2013-11-06 03:47:21 Summary: Attept to improve user feedback for pbs jobs which hit max walltime. Working with Dan Sullivan on this. Affected #: 1 file diff -r 8213c75972b3dd478c6448af9ce266fd57c82cf4 -r f2f1cce4678cf1eb188d9611b05f00706afc8897 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -34,6 +34,8 @@ __all__ = [ 'PBSJobRunner' ] +CLUSTER_ERROR_MESSAGE = "Job cannot be completed due to a cluster error, please retry it later: %s" + # The last two lines execute the command and then retrieve the command's # exit code ($?) and write it to a file. pbs_symlink_template = """ @@ -80,7 +82,7 @@ -6: "job aborted on MOM init, chkpt, ok migrate", -7: "job restart failed", -8: "exec() of user command failed", - -11: "job maximum walltime exceeded", + -11: "job maximum walltime exceeded", # Added by John, not from job.h. } @@ -413,8 +415,10 @@ assert int( status.exit_status ) == 0 log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) ) except AssertionError: - pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error, please retry it later' - log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) ) + exit_status = int( status.exit_status ) + error_message = JOB_EXIT_STATUS.get( exit_status, 'Unknown error: %s' % status.exit_status ) + pbs_job_state.fail_message = CLUSTER_ERROR_MESSAGE % error_message + log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, error_message ) ) pbs_job_state.stop_job = False self.work_queue.put( ( self.fail_job, pbs_job_state ) ) continue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.