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⚡️ Increase memory estimates for some overrunning Nodes #1458

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Merged
merged 2 commits into from
Mar 10, 2021
Merged

⚡️ Increase memory estimates for some overrunning Nodes #1458

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47fe8a4
:zap: Set default mem_gb estimate to 2.0 (from 0.2)
shnizzedy Mar 4, 2021
543d29a
:zap: Increase memory estimates by 0.5GB on overrunning nodes
shnizzedy Mar 4, 2021
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2 changes: 1 addition & 1 deletion CPAC/anat_preproc/ants.py
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions CPAC/pipeline/nipype_pipeline_engine/__init__.py
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Expand Up @@ -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__ = [
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8 changes: 5 additions & 3 deletions CPAC/registration/registration.py
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Expand Up @@ -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[
Expand Down Expand Up @@ -2487,9 +2488,10 @@ 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[
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3 changes: 1 addition & 2 deletions CPAC/seg_preproc/seg_preproc.py
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Expand Up @@ -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
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3 changes: 2 additions & 1 deletion CPAC/vmhc/vmhc.py
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Expand Up @@ -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[
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