Merge pull request #593 from nih-fmrif/pbs

PBS plugin fixes

Author: satra

doc/users/config_file.rst

@@ -95,7 +95,7 @@ Execution
     Perform the hash check on the job submission machine. This option minimizes
     the number of jobs submitted to a cluster engine or a multiprocessing pool
     to only those that need to be rerun. (possible values: ``true`` and
-    ``false``; default value: ``false``)
+    ``false``; default value: ``true``)
 
 *job_finished_timeout*
     When batch jobs are submitted through, SGE/PBS/Condor they could be killed

doc/users/plugins.rst

@@ -114,6 +114,7 @@ Optional arguments::
 
   template: custom template file to use
   qsub_args: any other command line args to be passed to qsub.
+  max_jobname_len: (PBS only) maximum length of the job name.  Default 15.
 
 For example, the following snippet executes the workflow on myqueue with
 a custom template::

nipype/pipeline/plugins/pbs.py

@@ -19,20 +19,27 @@ class PBSPlugin(SGELikeBatchManagerBase):
     - template : template to use for batch job submission
     - qsub_args : arguments to be prepended to the job execution script in the
                   qsub call
+    - max_jobname_len: maximum length of the job name.  Default 15.
 
     """
 
+    # Addtional class variables
+    _max_jobname_len = 15
+    
     def __init__(self, **kwargs):
         template = """
 #PBS -V
         """
         self._retry_timeout = 2
         self._max_tries = 2
+        self._max_jobname_length = 15
         if 'plugin_args' in kwargs and kwargs['plugin_args']:
             if 'retry_timeout' in kwargs['plugin_args']:
                 self._retry_timeout = kwargs['plugin_args']['retry_timeout']
             if  'max_tries' in kwargs['plugin_args']:
                 self._max_tries = kwargs['plugin_args']['max_tries']
+            if  'max_jobname_len' in kwargs['plugin_args']:
+                self._max_jobname_len = kwargs['plugin_args']['max_jobname_len']
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
@@ -71,6 +78,7 @@ def _submit_batchtask(self, scriptfile, node):
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()
         jobname = '.'.join(jobnameitems)
+        jobname = jobname[0:self._max_jobname_len]
         cmd.inputs.args = '%s -N %s %s' % (qsubargs,
                                            jobname,
                                            scriptfile)

nipype/utils/config.py

@@ -36,7 +36,7 @@
 hash_method = timestamp
 job_finished_timeout = 5
 keep_inputs = false
-local_hash_check = false
+local_hash_check = true
 matplotlib_backend = Agg
 plugin = Linear
 remove_node_directories = false