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tsalotsalo
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Give workbench more memory.
1 parent 64500f4 commit 85fa4f0

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4 files changed

+22
-26
lines changed

4 files changed

+22
-26
lines changed

‎xcp_d/workflows/anatomical/parcellation.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -139,7 +139,7 @@ def init_parcellate_surfaces_wf(files_to_parcellate, name='parcellate_surfaces_w
139139
]) # fmt:skip
140140

141141
parcellate_surface_wf = init_parcellate_cifti_wf(
142-
mem_gb={'bold': 2},
142+
mem_gb={'bold': 2, 'volume': 1},
143143
compute_mask=True,
144144
name=f'parcellate_{file_to_parcellate}_wf',
145145
)

‎xcp_d/workflows/bold/cifti.py‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -213,12 +213,10 @@ def init_postprocess_cifti_wf(
213213
name='outputnode',
214214
)
215215

216-
mem_gbx = mem_gb
217-
218216
downcast_data = pe.Node(
219217
ConvertTo32(),
220218
name='downcast_data',
221-
mem_gb=mem_gbx['bold'],
219+
mem_gb=mem_gb['bold'],
222220
)
223221

224222
workflow.connect([
@@ -233,7 +231,7 @@ def init_postprocess_cifti_wf(
233231
TR=TR,
234232
exact_scans=exact_scans,
235233
head_radius=head_radius,
236-
mem_gb=mem_gbx,
234+
mem_gb=mem_gb,
237235
)
238236

239237
workflow.connect([
@@ -249,7 +247,7 @@ def init_postprocess_cifti_wf(
249247
]),
250248
]) # fmt:skip
251249

252-
denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gbx)
250+
denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gb)
253251

254252
workflow.connect([
255253
(prepare_confounds_wf, denoise_bold_wf, [
@@ -264,7 +262,7 @@ def init_postprocess_cifti_wf(
264262
]) # fmt:skip
265263

266264
if despike:
267-
despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gbx)
265+
despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gb)
268266

269267
workflow.connect([
270268
(prepare_confounds_wf, despike_wf, [
@@ -288,7 +286,7 @@ def init_postprocess_cifti_wf(
288286
skip_alff = (not bandpass_filter) or ('alff' in config.workflow.skip_outputs)
289287

290288
if not skip_alff:
291-
alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gbx)
289+
alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gb)
292290

293291
workflow.connect([
294292
(inputnode, alff_wf, [
@@ -306,7 +304,7 @@ def init_postprocess_cifti_wf(
306304
# Skip ReHo calculation if requested
307305
skip_reho = 'reho' in config.workflow.skip_outputs
308306
if not skip_reho:
309-
reho_wf = init_reho_cifti_wf(name_source=bold_file, mem_gb=mem_gbx)
307+
reho_wf = init_reho_cifti_wf(name_source=bold_file, mem_gb=mem_gb)
310308

311309
workflow.connect([
312310
(inputnode, reho_wf, [
@@ -321,7 +319,7 @@ def init_postprocess_cifti_wf(
321319
qc_report_wf = init_qc_report_wf(
322320
TR=TR,
323321
head_radius=head_radius,
324-
mem_gb=mem_gbx,
322+
mem_gb=mem_gb,
325323
name='qc_report_wf',
326324
)
327325

@@ -392,7 +390,7 @@ def init_postprocess_cifti_wf(
392390

393391
if config.execution.atlases:
394392
connectivity_wf = init_functional_connectivity_cifti_wf(
395-
mem_gb=mem_gbx,
393+
mem_gb=mem_gb,
396394
exact_scans=exact_scans,
397395
has_multiple_runs=has_multiple_runs,
398396
skip_reho=skip_reho,
@@ -450,7 +448,7 @@ def init_postprocess_cifti_wf(
450448
preproc_nifti=run_data['nifti_file'],
451449
t1w_available=t1w_available,
452450
t2w_available=t2w_available,
453-
mem_gb=mem_gbx,
451+
mem_gb=mem_gb,
454452
)
455453
workflow.connect([
456454
(inputnode, execsummary_functional_plots_wf, [

‎xcp_d/workflows/bold/nifti.py‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -221,12 +221,10 @@ def init_postprocess_nifti_wf(
221221
name='outputnode',
222222
)
223223

224-
mem_gbx = mem_gb
225-
226224
downcast_data = pe.Node(
227225
ConvertTo32(),
228226
name='downcast_data',
229-
mem_gb=mem_gbx['bold'],
227+
mem_gb=mem_gb['bold'],
230228
)
231229

232230
workflow.connect([
@@ -246,7 +244,7 @@ def init_postprocess_nifti_wf(
246244
TR=TR,
247245
exact_scans=exact_scans,
248246
head_radius=head_radius,
249-
mem_gb=mem_gbx,
247+
mem_gb=mem_gb,
250248
)
251249

252250
workflow.connect([
@@ -262,7 +260,7 @@ def init_postprocess_nifti_wf(
262260
]),
263261
]) # fmt:skip
264262

265-
denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gbx)
263+
denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gb)
266264

267265
workflow.connect([
268266
(downcast_data, denoise_bold_wf, [('bold_mask', 'inputnode.mask')]),
@@ -278,7 +276,7 @@ def init_postprocess_nifti_wf(
278276
]) # fmt:skip
279277

280278
if despike:
281-
despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gbx)
279+
despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gb)
282280

283281
workflow.connect([
284282
(prepare_confounds_wf, despike_wf, [
@@ -302,7 +300,7 @@ def init_postprocess_nifti_wf(
302300
skip_alff = (not bandpass_filter) or ('alff' in config.workflow.skip_outputs)
303301

304302
if not skip_alff:
305-
alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gbx)
303+
alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gb)
306304

307305
workflow.connect([
308306
(downcast_data, alff_wf, [('bold_mask', 'inputnode.bold_mask')]),
@@ -317,7 +315,7 @@ def init_postprocess_nifti_wf(
317315
# Skip ReHo calculation if requested
318316
skip_reho = 'reho' in config.workflow.skip_outputs
319317
if not skip_reho:
320-
reho_wf = init_reho_nifti_wf(name_source=bold_file, mem_gb=mem_gbx)
318+
reho_wf = init_reho_nifti_wf(name_source=bold_file, mem_gb=mem_gb)
321319

322320
workflow.connect([
323321
(downcast_data, reho_wf, [('bold_mask', 'inputnode.bold_mask')]),
@@ -329,7 +327,7 @@ def init_postprocess_nifti_wf(
329327
qc_report_wf = init_qc_report_wf(
330328
TR=TR,
331329
head_radius=head_radius,
332-
mem_gb=mem_gbx,
330+
mem_gb=mem_gb,
333331
name='qc_report_wf',
334332
)
335333

@@ -407,7 +405,7 @@ def init_postprocess_nifti_wf(
407405
if config.execution.atlases:
408406
connectivity_wf = init_functional_connectivity_nifti_wf(
409407
has_multiple_runs=has_multiple_runs,
410-
mem_gb=mem_gbx,
408+
mem_gb=mem_gb,
411409
skip_reho=skip_reho,
412410
skip_alff=skip_alff,
413411
)
@@ -458,7 +456,7 @@ def init_postprocess_nifti_wf(
458456
preproc_nifti=bold_file,
459457
t1w_available=t1w_available,
460458
t2w_available=t2w_available,
461-
mem_gb=mem_gbx,
459+
mem_gb=mem_gb,
462460
)
463461
workflow.connect([
464462
# Use inputnode for executive summary instead of downcast_data

‎xcp_d/workflows/parcellation.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -250,7 +250,7 @@ def init_parcellate_cifti_wf(
250250
from xcp_d.workflows.parcellation import init_parcellate_cifti_wf
251251
252252
with mock_config():
253-
wf = init_parcellate_cifti_wf(mem_gb={"bold": 2})
253+
wf = init_parcellate_cifti_wf(mem_gb={"bold": 2, "volume": 1})
254254
255255
Parameters
256256
----------
@@ -409,7 +409,7 @@ def init_parcellate_cifti_wf(
409409
),
410410
name='threshold_coverage',
411411
iterfield=['data'],
412-
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
412+
mem_gb=2 * mem_gb['volume'],
413413
)
414414
workflow.connect([(coverage_buffer, threshold_coverage, [('coverage_cifti', 'data')])])
415415

@@ -418,7 +418,7 @@ def init_parcellate_cifti_wf(
418418
CiftiMask(),
419419
name='mask_parcellated_data',
420420
iterfield=['in_file', 'mask'],
421-
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
421+
mem_gb=2 * mem_gb['volume'],
422422
)
423423
workflow.connect([
424424
(parcellate_data, mask_parcellated_data, [('out_file', 'in_file')]),

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