Merge pull request #1458 from FCP-INDI/enh/memory-estimates

⚡️ Increase memory estimates for some overrunning Nodes
FCP-INDI · Mar 10, 2021 · 1287ee9 · 1287ee9
2 parents 4c8193b + 543d29a
commit 1287ee9
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Showing 5 changed files with 11 additions and 9 deletions.
diff --git a/CPAC/anat_preproc/ants.py b/CPAC/anat_preproc/ants.py
@@ -17,7 +17,7 @@
 from packaging.version import parse as parseversion, Version
 
 # nipype
-from nipype.pipeline import engine as pe
+from CPAC.pipeline.nipype_pipeline_engine import engine as pe
 from nipype.interfaces import utility as niu
 from nipype.interfaces.fsl.maths import ApplyMask
 from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos, MultiplyImages

diff --git a/CPAC/pipeline/nipype_pipeline_engine/__init__.py b/CPAC/pipeline/nipype_pipeline_engine/__init__.py
@@ -4,9 +4,9 @@
 See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
 for Nipype's documentation.'''  # noqa E501
 from nipype.pipeline import engine as pe
-# import __all__ from nipype.pipeline.engine
+# import everything in nipype.pipeline.engine.__all__
 from nipype.pipeline.engine import *  # noqa F401
-# import DEFAULT_MEM_GB and override Node, MapNode
+# import our DEFAULT_MEM_GB and override Node, MapNode
 from .engine import DEFAULT_MEM_GB, Node, MapNode
 
 __all__ = [

diff --git a/CPAC/registration/registration.py b/CPAC/registration/registration.py
@@ -2272,7 +2272,8 @@ def warp_timeseries_to_T1template(wf, cfg, strat_pool, pipe_num, opt=None):
 
     apply_xfm = apply_transform(f'warp_ts_to_T1template_{pipe_num}', reg_tool,
                                 time_series=True, num_cpus=num_cpus,
-                                num_ants_cores=num_ants_cores)
+                                num_ants_cores=num_ants_cores,
+                                mem_gb=2.5)
 
     if reg_tool == 'ants':
         apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[
@@ -2486,9 +2487,10 @@ def warp_timeseries_to_EPItemplate(wf, cfg, strat_pool, pipe_num, opt=None):
 
     num_ants_cores = cfg.pipeline_setup['system_config']['num_ants_threads']
 
-    apply_xfm = apply_transform('warp_ts_to_EPItemplate', reg_tool,
+    apply_xfm = apply_transform(f'warp_ts_to_EPItemplate_{pipe_num}', reg_tool,
                                 time_series=True, num_cpus=num_cpus,
-                                num_ants_cores=num_ants_cores)
+                                num_ants_cores=num_ants_cores,
+                                mem_gb=2.5)
 
     if reg_tool == 'ants':
         apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[

diff --git a/CPAC/seg_preproc/seg_preproc.py b/CPAC/seg_preproc/seg_preproc.py
@@ -575,8 +575,7 @@ def tissue_seg_fsl_fast(wf, cfg, strat_pool, pipe_num, opt=None):
     #  'probability_maps' output is a list of individual probability maps
     #      triggered by 'probability_maps' boolean input (-p)
 
-    segment = pe.Node(interface=fsl.FAST(), name=f'segment_{pipe_num}',
-                      mem_gb=1.5)
+    segment = pe.Node(interface=fsl.FAST(), name=f'segment_{pipe_num}')
     segment.inputs.img_type = 1
     segment.inputs.segments = True
     segment.inputs.probability_maps = True

diff --git a/CPAC/vmhc/vmhc.py b/CPAC/vmhc/vmhc.py
@@ -81,7 +81,8 @@ def warp_timeseries_to_sym_template(wf, cfg, strat_pool, pipe_num, opt=None):
 
     apply_xfm = apply_transform(f'warp_ts_to_sym_template_{pipe_num}',
                                 reg_tool, time_series=True, num_cpus=num_cpus,
-                                num_ants_cores=num_ants_cores)
+                                num_ants_cores=num_ants_cores,
+                                mem_gb=2.5)
 
     if reg_tool == 'ants':
         apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[