I'm receiving Fatal Signal 11 (SIGSEGV) when I run 3dTrackID PROB in parallel.
It works fine when I run one subject at a time or even a for loop, however I much prefer to run them in parallel to save time.
I have run all commands leading up to this (e.g. 3dDWItoDT and 3dDWUncert) in parallel with no problem, therefore I believe the error is related to AFNI. Any ideas what might be causing this? My command and the error (example from one subject, though it happened for all) are pasted below. Thank you!

find SPN01* -type f | nohup parallel 'dtipath="/home/eji/newdata/projects/spins/dwi" && cd {} && mkdir tract && cd tract && 3dTrackID -mode PROB -uncert $dtipath/{}/uncert/Uncert+orig. -netrois $dtipath/{}/parc318.nii.gz -mask $dtipath/{}/T1_dwspace_mask.nii.gz -prefix prob -dti_in $dtipath/{}/tensors/DT_ -alg_Thresh_FA 0.2 -alg_Nmonte 1000 -alg_Nseed_Vox 5 -alg_Thresh_Frac 0.1 -nifti -dump_rois AFNI -no_indipair_out -overwrite' ::: * > nohup_tractography.out &

++ Tracking mode: PROB
++ Number of ROIs in netw[0] = 318
++ No refset labeltable for naming things.
++ SEARCHING for vector files with prefix '/home/eji/newdata/projects/spins/dwi/SPN01_MRP_0105_01/tensors/DT_*':
FINDING: 'V1' 'V2' 'V3'
++ SEARCHING for scalar files with prefix '/home/eji/newdata/projects/spins/dwi/SPN01_MRP_0105_01/tensors/DT_*':
FINDING: not:'DT' 'FA' 'L1' not:'L2' not:'L3' 'MD' 'RD'
++ Done with scalar search, found: 4 parameters
--> so will have 15 output data matrices.
++ Effective Monte iterations: 5000. Fraction threshold set: 0.10000
--> Ntrack voxel threshold: 500.

Fatal Signal 11 (SIGSEGV) received
Bottom of Debug Stack
** AFNI version = AFNI_20.3.03 Compile date = Dec 7 2020
** [[Precompiled binary linux_ubuntu_16_64: Dec 7 2020]]
** 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/eji/.afni.crashlog


********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
mri_killpurge -- check if im==NULL ptr=0x21ba600
mri_killpurge -- can't killpurge NULL fname! {17729 ms}
----mri_killpurge [4]: EXIT} (file=mri_purger.c line=270) to mri_free {17729 ms}
mri_free -- free im {17729 ms}
---mri_free [3]: EXIT} (file=mri_free.c line=67) to EDIT_substitute_brick {17729 ms}
--EDIT_substitute_brick [2]: EXIT} (file=edt_substbrick.c line=69) to Bottom of Debug Stack {17729 ms}
++THD_delete_3dim_dataset [2]: {ENTRY (file=thd_delete.c line=131) from Bottom of Debug Stack {17731 ms}
+++THD_delete_datablock [3]: {ENTRY (file=thd_delete.c line=27) from THD_delete_3dim_dataset {17731 ms}
THD_delete_datablock -- call purge {17731 ms}
++++THD_purge_datablock [4]: {ENTRY (file=thd_purgedblk.c line=15) from THD_delete_datablock {17731 ms}
THD_purge_datablock -- MEM_MALLOC: clearing sub-bricks {17731 ms}
+++++mri_killpurge [5]: {ENTRY (file=mri_purger.c line=259) from THD_purge_datablock {17731 ms}
mri_killpurge -- check if im==NULL ptr=0x21b62b0
mri_killpurge -- can't killpurge NULL fname! {17731 ms}
-----mri_killpurge [5]: EXIT} (file=mri_purger.c line=270) to THD_purge_datablock {17731 ms}
----THD_purge_datablock [4]: EXIT} (file=thd_purgedblk.c line=39) to THD_delete_datablock {17731 ms}
THD_delete_datablock -- destroy imarr {17731 ms}
++++mri_free [4]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {17731 ms}
mri_free -- call killpurge {17731 ms}
+++++mri_killpurge [5]: {ENTRY (file=mri_purger.c line=259) from mri_free {17731 ms}
mri_killpurge -- check if im==NULL ptr=0x21b62b0
mri_killpurge -- can't killpurge NULL fname! {17731 ms}
-----mri_killpurge [5]: EXIT} (file=mri_purger.c line=270) to mri_free {17731 ms}
mri_free -- free im {17731 ms}
----mri_free [4]: EXIT} (file=mri_free.c line=67) to THD_delete_datablock {17731 ms}
THD_delete_datablock -- free brick_ stuff {17731 ms}
THD_delete_datablock -- KILL_KILL {17731 ms}
THD_delete_datablock -- free attributes {17731 ms}
---THD_delete_datablock [3]: EXIT} (file=thd_delete.c line=122) to THD_delete_3dim_dataset {17731 ms}
THD_delete_3dim_dataset -- KILL_KILL {17731 ms}
--THD_delete_3dim_dataset [2]: EXIT} (file=thd_delete.c line=179) to Bottom of Debug Stack {17731 ms}

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
++TrackItP_NEW_M [2]: {ENTRY (file=DoTrackit.c line=1322) from Bottom of Debug Stack {853714 ms}
--TrackItP_NEW_M [2]: EXIT} (file=DoTrackit.c line=1555) to Bottom of Debug Stack {853714 ms}
............................................................................
** AFNI compile date = Dec 7 2020
** [[Precompiled binary linux_ubuntu_16_64: Dec 7 2020]]
** Program Crash **



Edited 2 time(s). Last edit at 03/02/2021 07:58AM by eji.