ENH: Modifications to address freesurfer running envirionment.

matsuij · Apr 18, 2012 · cd3d052 · cd3d052
1 parent 1007fc1
commit cd3d052
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Showing 2 changed files with 20 additions and 8 deletions.
diff --git a/AutoWorkup/WorkupT1T2.py b/AutoWorkup/WorkupT1T2.py
@@ -755,7 +755,7 @@ def printFullPath(outFileFullPath):
         ## Make deformed Atlas image space
         if processingLevel > 2:
 
-            many_cpu_sge_options_dictionary={'qsub_args': '-S /bin/bash -q UI -pe smp1 6-12 -l mem_free=5000M -o /dev/null -e /dev/null ', 'overwrite': True}
+            many_cpu_sge_options_dictionary={'qsub_args': '-S /bin/bash -q all.q -pe smp1 4-12 -l mem_free=5000M -o /dev/null -e /dev/null ', 'overwrite': True}
             print("""
             Run ANTS Registration at processingLevel={0}
             """.format(processingLevel) )
@@ -769,7 +769,7 @@ def printFullPath(outFileFullPath):
             baw200.connect( BAtlas,'template_t1',    ComputeAtlasToSubjectTransform,"moving_T2_image")
             baw200.connect(BLI,'outputTransformFilename',ComputeAtlasToSubjectTransform,'initialTransform')
 
-        #if processingLevel == -123:
+        if processingLevel == -123:
             WarpAtlas = pe.Node(interface=WarpAllAtlas(), name = "19_WarpAtlas")
             WarpAtlas.inputs.moving_atlas = atlas_fname_wpath
             WarpAtlas.inputs.deformed_atlas = "./template_t2.nii.gz"
@@ -779,14 +779,15 @@ def printFullPath(outFileFullPath):
             baw200.connect( SplitAvgBABC,'avgBABCT1', WarpAtlas, 'reference_image')
 
 
-        #if processingLevel > 3:
-        if processingLevel == -123:
+        if processingLevel > 3:
             print("""
             Run Freesurfer ReconAll at processingLevel={0}
             """.format(processingLevel) )
             subj_id = os.path.basename(os.path.dirname(os.path.dirname(baw200.base_dir)))
             scan_id = os.path.basename(os.path.dirname(baw200.base_dir))
             reconall = pe.Node(interface=ReconAll(),name="41_FS510")
+            freesurfer_sge_options_dictionary={'qsub_args': '-S /bin/bash -q all.q -pe smp1 1 -l mem_free=3100M -o /dev/null -e /dev/null ', 'overwrite': True}
+            reconall.plugin_args=freesurfer_sge_options_dictionary
             reconall.inputs.subject_id = subj_id+'_'+scan_id
             reconall.inputs.directive = 'all'
             reconall.inputs.subjects_dir = '.'

diff --git a/AutoWorkup/baw_exp.py b/AutoWorkup/baw_exp.py
@@ -13,9 +13,14 @@
 import sys
 
 ##############################################################################
-def get_global_sge_script(pythonPathsList,binPathsList):
+def get_global_sge_script(pythonPathsList,binPathsList,customEnvironment={}):
     """This is a wrapper script for running commands on an SGE cluster
 so that all the python modules and commands are pathed properly"""
+
+    custEnvString=""
+    for key,value in customEnvironment.items():
+        custEnvString+=key+"="+value+"\n"
+
     PYTHONPATH=":".join(pythonPathsList)
     BASE_BUILDS=":".join(binPathsList)
     GLOBAL_SGE_SCRIPT="""#!/bin/bash
@@ -25,8 +30,11 @@ def get_global_sge_script(pythonPathsList,binPathsList):
 export PYTHONPATH={PYTHONPATH}
 echo "With PYTHONPATH={PYTHONPATH}"
 echo "With PATH={BINPATH}"
+echo "With custom environment:"
+echo {CUSTENV}
+{CUSTENV}
 ## NOTE:  nipype inserts the actaul commands that need running below this section.
-""".format(PYTHONPATH=PYTHONPATH,BINPATH=BASE_BUILDS)
+""".format(PYTHONPATH=PYTHONPATH,BINPATH=BASE_BUILDS,CUSTENV=custEnvString)
     return GLOBAL_SGE_SCRIPT
 
 def main(argv=None):
@@ -85,6 +93,8 @@ def main(argv=None):
     #    Define workup common reference data sets
     ATLASPATH=expConfig.get(input_arguments.processingEnvironment,'ATLASPATH')
     BCDMODELPATH=expConfig.get(input_arguments.processingEnvironment,'BCDMODELPATH')
+    CUSTOM_ENVIRONMENT=expConfig.get(input_arguments.processingEnvironment,'CUSTOM_ENVIRONMENT')
+    CUSTOM_ENVIRONMENT=eval(CUSTOM_ENVIRONMENT)
 
     print "Configuring Pipeline"
     import WorkupT1T2 ## NOTE:  This needs to occur AFTER the PYTHON_AUX_PATHS has been modified
@@ -98,10 +108,11 @@ def main(argv=None):
 
     ## Create the shell wrapper script for ensuring that all jobs running on remote hosts from SGE
     #  have the same environment as the job submission host.
-    JOB_SCRIPT=get_global_sge_script(sys.path,PROGRAM_PATHS)
+    JOB_SCRIPT=get_global_sge_script(sys.path,PROGRAM_PATHS,CUSTOM_ENVIRONMENT)
+    print JOB_SCRIPT
     if input_arguments.wfrun == 'helium_all.q':
         baw200.run(plugin='SGE',
-            plugin_args=dict(template=JOB_SCRIPT,qsub_args="-S /bin/bash -q UI -pe smp1 2-4 -o /dev/null -e /dev/null "))
+            plugin_args=dict(template=JOB_SCRIPT,qsub_args="-S /bin/bash -q all.q -pe smp1 2-4 -o /dev/null -e /dev/null "))
     elif input_arguments.wfrun == 'ipl_OSX':
         baw200.run(plugin='SGE',
             plugin_args=dict(template=JOB_SCRIPT,qsub_args="-S /bin/bash -q OSX -pe smp1 2-4 -o /dev/null -e /dev/null "))