app-C-PAC-brainlife.io v0.1.0 / C-PAC v1.8.0 - default pipeline #17
Comments
shnizzedy
added
debug
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Running *********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {49 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {49 ms}
mri_free -- call killpurge {49 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {49 ms}
mri_killpurge -- check if im==NULL ptr=0x562e5d6d6d80
mri_killpurge -- can't killpurge NULL fname! {49 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {49 ms}
mri_free -- free im {49 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {49 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {49 ms}
mri_free -- call killpurge {49 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {49 ms}
mri_killpurge -- check if im==NULL ptr=0x562e5d6d6e40
mri_killpurge -- can't killpurge NULL fname! {49 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {49 ms}
mri_free -- free im {49 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {49 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {49 ms}
mri_free -- call killpurge {49 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {49 ms}
mri_killpurge -- check if im==NULL ptr=0x562e5d6d6f00
mri_killpurge -- can't killpurge NULL fname! {49 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {49 ms}
mri_free -- free im {49 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {49 ms}
THD_delete_datablock -- free brick_ stuff {49 ms}
THD_delete_datablock -- KILL_KILL {49 ms}
THD_delete_datablock -- free attributes {49 ms}
----THD_delete_datablock [4]: EXIT} (file=thd_delete.c line=122) to THD_delete_3dim_dataset {49 ms}
THD_delete_3dim_dataset -- KILL_KILL {49 ms}
---THD_delete_3dim_dataset [3]: EXIT} (file=thd_delete.c line=179) to 3dECM main {49 ms}
............................................................................
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 bandpassed_demeaned_filtered_trans_flirt.nii.gz
............................................................................
3dECM main
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI compile date = Mar 15 2021
** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
** Program Crash ** |
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If I increase the memory to 2 ( ++ 3dECM: AFNI version=AFNI_20.0.04 (Mar 15 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
++ 49428 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with full method (sparsity=0.001%, thresh=-1.200, scale=1.000, shift=0.000,
max_iter=10000, eps=0.000, binary=0, mem=1946212768)
++ Starting create_sparse_corr_array with a memory allowance of 1946212768
++ The sparse array with 12216 values will take 0.37 MB of memory (budget = 1855.67 MB)
++ Extracting sparse correlation array with threshold = -1.200000 and sparsity = 0.00% (12216)
++ 8 OpenMP threads started
Looping:0Killed |
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Trying *********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {32 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {32 ms}
mri_free -- call killpurge {32 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {32 ms}
mri_killpurge -- check if im==NULL ptr=0x55f33ae02b00
mri_killpurge -- can't killpurge NULL fname! {32 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {32 ms}
mri_free -- free im {32 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {32 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {32 ms}
mri_free -- call killpurge {32 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {32 ms}
mri_killpurge -- check if im==NULL ptr=0x55f33adca580
mri_killpurge -- can't killpurge NULL fname! {32 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {32 ms}
mri_free -- free im {32 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {32 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {32 ms}
mri_free -- call killpurge {32 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {32 ms}
mri_killpurge -- check if im==NULL ptr=0x55f33adca640
mri_killpurge -- can't killpurge NULL fname! {32 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {32 ms}
mri_free -- free im {32 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {32 ms}
THD_delete_datablock -- free brick_ stuff {32 ms}
THD_delete_datablock -- KILL_KILL {32 ms}
THD_delete_datablock -- free attributes {32 ms}
----THD_delete_datablock [4]: EXIT} (file=thd_delete.c line=122) to THD_delete_3dim_dataset {32 ms}
THD_delete_3dim_dataset -- KILL_KILL {32 ms}
---THD_delete_3dim_dataset [3]: EXIT} (file=thd_delete.c line=179) to 3dECM main {32 ms}
............................................................................
3dECM main
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -thresh 0.999 bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI compile date = Mar 15 2021
** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
** Program Crash **Trying *********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {31 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {31 ms}
mri_free -- call killpurge {31 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {31 ms}
mri_killpurge -- check if im==NULL ptr=0x5654cee58b90
mri_killpurge -- can't killpurge NULL fname! {31 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {31 ms}
mri_free -- free im {31 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {31 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {31 ms}
mri_free -- call killpurge {31 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {31 ms}
mri_killpurge -- check if im==NULL ptr=0x5654cee58c50
mri_killpurge -- can't killpurge NULL fname! {31 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {31 ms}
mri_free -- free im {31 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {31 ms}
+++++mri_free [5]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {31 ms}
mri_free -- call killpurge {31 ms}
++++++mri_killpurge [6]: {ENTRY (file=mri_purger.c line=259) from mri_free {31 ms}
mri_killpurge -- check if im==NULL ptr=0x5654cee58d10
mri_killpurge -- can't killpurge NULL fname! {31 ms}
------mri_killpurge [6]: EXIT} (file=mri_purger.c line=270) to mri_free {31 ms}
mri_free -- free im {31 ms}
-----mri_free [5]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {31 ms}
THD_delete_datablock -- free brick_ stuff {31 ms}
THD_delete_datablock -- KILL_KILL {31 ms}
THD_delete_datablock -- free attributes {31 ms}
----THD_delete_datablock [4]: EXIT} (file=thd_delete.c line=122) to THD_delete_3dim_dataset {31 ms}
THD_delete_3dim_dataset -- KILL_KILL {31 ms}
---THD_delete_3dim_dataset [3]: EXIT} (file=thd_delete.c line=179) to 3dECM main {31 ms}
............................................................................
3dECM main
** Command line was:
3dECM -automask -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI compile date = Mar 15 2021
** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
** Program Crash ** |
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To report here - I ran this with the same data, but on an AFNI version of 3dECM with compile date Jan 3 2017. I see above that yours got killed right after the Looping: bit shows up. Mine gets a little farther, and then crashes with a bit more information to terminal:
Here's the crash log:
Note:
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Just confirmed, same behavior in Singularity on AWS. 210415-21:25:48,370 nipype.workflow WARNING:
[Node] Error on "cpac_sub-SBJ01_ses-1.afni_centrality_eigenvector_centrality_274.afni_centrality" (/media/ebs/brainlife/out_2021-04-13/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality)
210415-21:25:48,374 nipype.workflow ERROR:
Node afni_centrality.a0 failed to run on host ip-172-31-79-78.
210415-21:25:48,440 nipype.workflow ERROR:
Saving crash info to /media/ebs/brainlife/out_2021-04-13/log/crash-20210415-212548-ubuntu-afni_centrality.a0-d542083b-5a2d-426d-a8bf-d1f1ed04f7b2.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 125, in _run_interface
runtime, correct_return_codes
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife/out_2021-04-13/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
Standard output:
Standard error:
++ 3dECM: AFNI version=AFNI_20.0.04 (Mar 15 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /media/ebs/brainlife/out_2021-04-13/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
Fatal Signal 11 (SIGSEGV) received
3dECM main
Bottom of Debug Stack
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife/out_2021-04-13/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI version = AFNI_20.0.04 Compile date = Mar 15 2021
** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/ubuntu/.afni.crashlog
Return code: 1Next I will try in Docker on AWS. |
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Same result in Docker: 210416-04:46:16,949 nipype.workflow INFO:
[Node] Setting-up "cpac_sub-SBJ01_ses-1.afni_centrality_eigenvector_centrality_274.afni_centrality" in "/media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvect
or_centrality_274/_scan_rest/afni_centrality".
210416-04:46:16,955 nipype.workflow INFO:
[Node] Running "afni_centrality" ("nipype.interfaces.afni.preprocess.ECM"), a CommandLine Interface with command:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-
1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
210416-04:46:17,251 nipype.interface INFO:
stderr 2021-04-16T04:46:17.251403:++ 3dECM: AFNI version=AFNI_20.0.04 (Mar 15 2021) [64-bit]
210416-04:46:17,277 nipype.interface INFO:
stderr 2021-04-16T04:46:17.277298:** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274
/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
210416-04:46:17,277 nipype.interface INFO:
stderr 2021-04-16T04:46:17.277298: Warnings of this type will be muted for this session.
210416-04:46:17,278 nipype.interface INFO:
stderr 2021-04-16T04:46:17.277298: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
210416-04:46:17,311 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:
210416-04:46:17,311 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:Fatal Signal 11 (SIGSEGV) received
210416-04:46:17,312 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404: 3dECM main
210416-04:46:17,312 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404: Bottom of Debug Stack
210416-04:46:17,312 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** Command line was:
210416-04:46:17,312 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife
/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
210416-04:46:17,313 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** AFNI version = AFNI_20.0.04 Compile date = Mar 15 2021
210416-04:46:17,313 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
210416-04:46:17,313 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** Program Death **
210416-04:46:17,313 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** If you report this crash to the AFNI message board,
210416-04:46:17,314 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** please copy the error messages EXACTLY, and give
210416-04:46:17,314 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** the command line you used to run the program, and
210416-04:46:17,314 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** any other information needed to repeat the problem.
210416-04:46:17,314 nipype.interface INFO:
stderr 2021-04-16T04:46:17.311404:** You may later be asked to upload data to help debug.
210416-04:46:17,315 nipype.interface INFO:
stderr 2021-04-16T04:46:17.315104:** Crash log is appended to file /root/.afni.crashlog
210416-04:46:17,547 nipype.workflow WARNING:
Storing result file without outputs
210416-04:46:17,548 nipype.workflow WARNING:
[Node] Error on "cpac_sub-SBJ01_ses-1.afni_centrality_eigenvector_centrality_274.afni_centrality" (/media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality)
210416-04:46:17,553 nipype.workflow ERROR:
Node afni_centrality.a0 failed to run on host d1708d22d5c5.
210416-04:46:17,555 nipype.workflow ERROR:
Saving crash info to /media/ebs/brainlife/out_2021-04-15/log/crash-20210416-044617-root-afni_centrality.a0-683396c6-1455-41d4-9da4-cd3d363910fd.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 125, in _run_interface
runtime, correct_return_codes
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
Standard output:
Standard error:
++ 3dECM: AFNI version=AFNI_20.0.04 (Mar 15 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
Fatal Signal 11 (SIGSEGV) received
3dECM main
Bottom of Debug Stack
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 /media/ebs/brainlife/out_2021-04-15/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI version = AFNI_20.0.04 Compile date = Mar 15 2021
** [[Precompiled binary linux_ubuntu_16_64: Mar 15 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /root/.afni.crashlog
Return code: 1 |
|
Also with a newer version of AFNI: ++ 3dECM: AFNI version=AFNI_21.0.18 (Mar 14 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Downloads/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
munmap_chunk(): invalid pointer
Fatal Signal 6 (SIGABRT) received
3dECM main
Bottom of Debug Stack
** Command line was:
3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 1.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.001000 bandpassed_demeaned_filtered_trans_flirt.nii.gz
** AFNI version = AFNI_21.0.18 Compile date = Mar 14 2021
** [[Precompiled binary linux_openmp_64: Mar 14 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /root/.afni.crashlog |
|
, Saturday, Apr 17, 2021 11:38 AM
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With the newer 3dECM, I still get a crash ( 3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 5.000000 -prefix eigenvector_centrality_merged.nii.gz -sparsity 0.100000 bandpassed_demeaned_filtered_trans_flirt.nii.gz
Standard output:
opened input dataset /output/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz
Standard error:
++ 3dECM cc mods: AFNI version=AFNI_21.1.02 (Apr 16 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /output/working/cpac_sub-SBJ01_ses-1/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ 49428 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with full method (sparsity=0.100%,
thresh=-1.200, scale=1.000, shift=0.000, max_iter=10000, eps=0.000,
binary=0, mem=5167438240)
++ Starting create_sparse_corr_array with a memory allowance of 5167438240
++ The sparse array with 1221539 values will take 37.28 MB of memory (budget = 4927.67 MB)
++ Extracting sparse correlation array with threshold = -1.200000 and sparsity = 0.10% (1221539)
++ 1 OpenMP threads started
Looping:012�[7m*+ WARNING:�[0m Could not allocate a new node!
3456789,0123456789,0123456789,0123456789,0123456789,.
�[7m** ERROR:�[0m Memory budget (4928.053131 MB) exceeded, consider using a higher correlation or lower sparsity threshold
�[7m*+ WARNING:�[0m Error getting sparse weight array.
�[7m** FATAL ERROR:�[0m Eigen vector calculation failed!
** Program compile date = Apr 16 2021) if I leave the default threshold ( 3dECM -mask /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz -memory 5.000000 -prefix eigenvector_centrality_merged.nii.gz -thresh 0.999 bandpassed_demeaned_filtered_trans_flirt.nii.gz
++ 3dECM cc mods: AFNI version=AFNI_21.1.02 (Apr 16 2021) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /Downloads/bandpassed_demeaned_filtered_trans_flirt.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
opened input dataset bandpassed_demeaned_filtered_trans_flirt.nii.gz
++ 49428 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with full method (sparsity=100.000%,
thresh=0.999, scale=1.000, shift=0.000, max_iter=10000, eps=0.000,
binary=0, mem=5167438240)
++ Starting create_sparse_corr_array with a memory allowance of 5167438240
*+ WARNING: Cannot pre-calculate the memory required for a sparse matrix when only a correlation threshold is used. Instead the mem is tracked and if we exceed what would be used by the non-sparse array, the operation will be aborted.
++ Extracting sparse correlation array with threshold = 0.999000 and sparsity = 100.00% (0)
++ 8 OpenMP threads started
Looping:0123456789,0123456789,0123456789,0123456789,0123456789,.
** ERROR: No correlations exceeded threshold, consider using a lower correlation threshold
*+ WARNING: Error getting sparse weight array.
** FATAL ERROR: Eigen vector calculation failed!
** Program compile date = Apr 16 2021). However, if I set ++ Finished iter 10000: Verr 0.000, Vnorm 1.000
*+ WARNING: Power iteration did not converge (0.000 >= 0.000)
in 10000 iterations. You might consider increase max_iters, or
epsilon. For now we are writing out the obtained solution,
which may or may not be good enough.
creating output bucket(eigenvector_centrality_merged.nii.gz)
+ creating output dataset in memory
++ Done..
++ Writing output dataset to disk [1,086,532 bytes]
++ Output dataset ./eigenvector_centrality_merged.nii.gz. All this 👆 is pre-addition of the variance filter. |
C-PAC Run Info
T1W: 256 × 256 × 192
CPAC run errorcrash-20210408-011807-user-afni_centrality.a0-801f0be8-89c0-4f18-a142-ab8a64e47b5e.txt
tail of
pypeline.log(before run summary)tail of
slurm-18050.err(before run summary)/output/working/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/command.txt/output/working/afni_centrality_eigenvector_centrality_274/_scan_rest/afni_centrality/_report/report.rstInclude:
(excerpt)
{ "t1": "../606dedb98ccc6fc85b37e154/6069f9d5b0f2b975dfdbb48c/t1.nii.gz", "bold": "../606dedb98ccc6fc85b37e154/6069fb20b0f2b971c1dbc79f/bold.nii.gz", "events": "../606dedb98ccc6fc85b37e154/6069fb20b0f2b971c1dbc79f/events.tsv", "events_json": "../606dedb98ccc6fc85b37e154/6069fb20b0f2b971c1dbc79f/events.json", "preconfig": "", "_app": "5f3593e84615e04651bf9364", }Pipeline Config: cpac_pipeline_config_2021-04-07T17-40-30Z.yml
Data Config: cpac_data_config_2021-04-07T17-40-30Z.yml
Developers only:
Default Pipeline Diff: cpac_pipeline_config_2021-04-07T17-40-30Z_min.yml
Node timing information:
sorted_node_times.txt
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