1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/6fe91b7bfe6e/ changeset: 6fe91b7bfe6e user: Scott McManus date: 2012-06-20 19:02:16 summary: PBS runner now writes and reads an exit code for each command affected #: 1 file
diff -r 663e03e40c86ffa0766dd6638ea7c0886632117d -r 6fe91b7bfe6e4bdcf62299ae88a6206fcb50d3f1 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -33,6 +33,8 @@
__all__ = [ 'PBSJobRunner' ]
+# The last two lines execute the command and then retrieve the command's +# exit code ($?) and write it to a file. pbs_template = """#!/bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then @@ -45,8 +47,11 @@ %s cd %s %s +echo $? > %s """
+# The last two lines execute the command and then retrieve the command's +# exit code ($?) and write it to a file. pbs_symlink_template = """#!/bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then @@ -65,6 +70,7 @@ %s cd %s %s +echo $? > %s """
# From pbs' job.h @@ -93,6 +99,7 @@ self.job_file = None self.ofile = None self.efile = None + self.ecfile = None self.runner_url = None self.check_count = 0 self.stop_job = False @@ -233,6 +240,7 @@ # define job attributes ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id) efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id) + ecfile = "%s/%s.ec" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
output_fnames = job_wrapper.get_output_fnames()
@@ -273,12 +281,15 @@ self.app.config.pbs_stage_path, job_wrapper.get_env_setup_clause(), exec_dir, - command_line ) + command_line, + ecfile ) + else: script = pbs_template % ( job_wrapper.galaxy_lib_dir, job_wrapper.get_env_setup_clause(), exec_dir, - command_line ) + command_line, + ecfile ) job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id) fh = file(job_file, "w") fh.write(script) @@ -289,7 +300,7 @@ log.debug( "Job %s deleted by user before it entered the PBS queue" % job_wrapper.job_id ) pbs.pbs_disconnect(c) if self.app.config.cleanup_job in ( "always", "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) + self.cleanup( ( ofile, efile, ecfile, job_file ) ) job_wrapper.cleanup() return
@@ -321,6 +332,7 @@ pbs_job_state.job_id = job_id pbs_job_state.ofile = ofile pbs_job_state.efile = efile + pbs_job_state.ecfile = ecfile pbs_job_state.job_file = job_file pbs_job_state.old_state = 'N' pbs_job_state.running = False @@ -510,27 +522,35 @@ """ ofile = pbs_job_state.ofile efile = pbs_job_state.efile + ecfile = pbs_job_state.ecfile job_file = pbs_job_state.job_file # collect the output try: ofh = file(ofile, "r") efh = file(efile, "r") + ecfh = file(ecfile, "r") stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) + # This should be an 8-bit exit code, but read ahead anyway: + exit_code = ecfh.read(32) except: stdout = '' stderr = 'Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.' + # By default, the exit code is 0, which usually indicates success + # (although clearly some error happened). + exit_code = 0 log.debug(stderr) + log.debug( "Job exit code: " + exit_code )
try: - pbs_job_state.job_wrapper.finish( stdout, stderr ) + pbs_job_state.job_wrapper.finish( stdout, stderr, exit_code ) except: log.exception("Job wrapper finish method failed") pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True)
# clean up the pbs files if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) + self.cleanup( ( ofile, efile, ecfile, job_file ) )
def fail_job( self, pbs_job_state ): """ @@ -594,6 +614,7 @@ pbs_job_state = PBSJobState() pbs_job_state.ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id) + pbs_job_state.ecfile = "%s/%s.ec" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_id = str( job.job_runner_external_id ) pbs_job_state.runner_url = job_wrapper.get_job_runner()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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