Make skipping job submissions optional and turned off by default.

Author: chrisgorgo

doc/users/plugins.rst

@@ -136,13 +136,28 @@ particular node might use more resources than other nodes in a workflow.
   this local configuration::
 
      node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}
+	 
+SGEGraph
+~~~~~~~~
+SGEGraph_ is a exuction plugin working with Sun Grid Engine that allows for
+submitting entire graph of dependent jobs at once. This way Nipype does not 
+need to run a monitoring process - SGE takes care of this.
+
+.. note::
+
+  When rerunning unfinished workflows using SGEGraph you may decide not to 
+  submit jobs for Nodes that previously finished running. This can speed up
+  execution, but new or modified inputs that would previously trigger a Node
+  to rerun will be ignored. The following option turns on this functionality::
+
+     workflow.run(plugin='SGEGraph', plugin_args = {'dont_resubmit_completed_jobs': True})
 
 LSF
 ---
 
-Submitting via LSF is almost identical to SGE above:
+Submitting via LSF is almost identical to SGE above::
 
-       workflow.run(plugin='LSF')
+    workflow.run(plugin='LSF')
 
 Optional arguments::
 
@@ -156,7 +171,7 @@ DAGMan
 ~~~~~~
 
 With its DAGMan_ component HTCondor_ (previously Condor) allows for submitting
-entire graphs of dependent jobs at once. With the ``CondorDAGMan`` plug-in
+entire graphs of dependent jobs at once (similar to SGEGraph_). With the ``CondorDAGMan`` plug-in
 Nipype can utilize this functionality to submit complete workflows directly and
 in a single step.  Consequently, and in contrast to other plug-ins, workflow
 execution returns almost instantaneously -- Nipype is only used to generate the

nipype/pipeline/plugins/sgegraph.py

@@ -55,6 +55,10 @@ def __init__(self, **kwargs):
                     self._template = open(self._template).read()
             if 'qsub_args' in plugin_args:
                 self._qsub_args = plugin_args['qsub_args']
+            if 'dont_resubmit_completed_jobs' in plugin_args:
+                self._dont_resubmit_completed_jobs = plugin_args['dont_resubmit_completed_jobs']
+            else:
+                self._dont_resubmit_completed_jobs = False
         super(SGEGraphPlugin, self).__init__(**kwargs)
 
     def _submit_graph(self, pyfiles, dependencies, nodes):
@@ -72,7 +76,7 @@ def make_job_name(jobnumber, nodeslist):
         submitjobsfile = os.path.join(batch_dir, 'submit_jobs.sh')
 
         cache_doneness_per_node = dict()
-        if True: ## A future parameter for controlling this behavior could be added here
+        if self._dont_resubmit_completed_jobs: ## A future parameter for controlling this behavior could be added here
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
                 node_status_done = node_completed_status(node)

nipype/utils/config.py

@@ -48,6 +48,7 @@
 stop_on_unknown_version = false
 write_provenance = false
 parameterize_dirs = true
+sge_dont_resubmit_completed_jobs = false
 
 [check]
 interval = 1209600