Added mandatory args for SLURM, fixed regex for batch job number

Added in several defaults for mandatory arguments to sbatch. Also the
regex that finds the job number was malformed and was returning 'None'
for all batch jobs. That's been fixed and is now returning jobs
correctly.

Author: Chad Cumba

nipype/pipeline/plugins/slurm.py

@@ -35,8 +35,7 @@ class SLURMPlugin(SLURMLikeBatchManagerBase):
 
     def __init__(self, **kwargs):
 
-        template="""
-#!/bin/sh
+        template="""#!/bin/sh
         """
         self._retry_timeout = 2
         self._max_tries = 2
@@ -77,6 +76,12 @@ def _submit_batchtask(self, scriptfile, node):
             sbatch_args = '%s -o %s' % (sbatch_args, path)
         if '-e' not in sbatch_args:
             sbatch_args = '%s -e %s' % (sbatch_args, path)
+        if '-p' not in sbatch_args:
+            sbatch_args = '%s -p normal' % (sbatch_args)
+        if '-n' not in sbatch_args:
+            sbatch_args = '%s -n 16' % (sbatch_args)
+        if '-t' not in sbatch_args:
+            sbatch_args = '%s -t 48:00:00' % (sbatch_args)
         if node._hierarchy:
             jobname = '.'.join((os.environ.data['LOGNAME'],
                                 node._hierarchy,
@@ -110,7 +115,7 @@ def _submit_batchtask(self, scriptfile, node):
         iflogger.setLevel(oldlevel)
         # retrieve sge taskid
         lines = [line for line in result.runtime.stdout.split('\n') if line]
-        taskid = int(re.match("Your job ([0-9]*) .* has been submitted",
+        taskid = int(re.match("Submitted batch job ([0-9]*)",
                               lines[-1]).groups()[0])
         self._pending[taskid] = node.output_dir()
         logger.debug('submitted sbatch task: %d for node %s' % (taskid, node._id))