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CoBrALab / antsRegistration-MAGeT

A reimplementation of MAGeTbrain using only ANTs tools.
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Job dependencies with multiatlas #82

Closed cbedetti closed 6 years ago

cbedetti commented 7 years ago

It seems the job dependencies is not working with multiatlas stages. atlas-template registrations were complete during first run. multiatlas resample labels were complete during second run. I'm on the master branch.

First run:

(antsRegistration-MAGeT)cbedetti@gpc-f102n002-ib0:~/scratch/antsmaget/hippocampus-subfields_simplified
$ mb.sh -- multiatlas
2017-05-17 21:25:37 UTC [  warning] Even number of templates detected, use an odd number to avoid tie label votes
2017-05-17 21:25:37 UTC [     info] Found:
2017-05-17 21:25:37 UTC [     info]   5 atlases in input/atlas
2017-05-17 21:25:37 UTC [     info]   1 labels per atlas in input/atlas
2017-05-17 21:25:37 UTC [     info]   32 templates in input/template
2017-05-17 21:25:37 UTC [     info]   32 subjects in input/subject
2017-05-17 21:25:37 UTC [     info]   0 models in input/models
2017-05-17 21:25:37 UTC [     info] Progress:
2017-05-17 21:25:37 UTC [     info]   0 of 160 atlas-template registrations completed
2017-05-17 21:25:37 UTC [     info]   0 of 992 template-subject registrations completed
2017-05-17 21:25:37 UTC [     info]   0 of 5120 resample labels completed
2017-05-17 21:25:37 UTC [     info]   0 of 32 voted labels completed
2017-05-17 21:25:37 UTC [     info] Checking Resolution of First Atlas
2017-05-17 21:26:17 UTC [     info]   Found 206977724 voxels
2017-05-17 21:26:17 UTC [     info] Checking Resolution of First Template
2017-05-17 21:26:17 UTC [     info]   Found 3817380 voxels
2017-05-17 21:26:17 UTC [     info] Checking Resolution of First Subject
2017-05-17 21:26:17 UTC [     info]   Found 3817380 voxels
2017-05-17 21:26:17 UTC [   notice] MAGeTbrain estimates walltime and memory based on files with the largest file size, if some files are uncompressed, this estimate may be incorrect
2017-05-17 21:26:18 UTC [     info] Submitting template jobs to 32GB nodes
2017-05-17 21:26:18 UTC [     info] Submitting subject jobs to 16GB nodes, two commands in parallel
2017-05-17 21:26:18 UTC [     info] Computing Atlas to Template Registrations
42201042[].gpc-sched-ib0
42201043[].gpc-sched-ib0
42201044[].gpc-sched-ib0
42201045[].gpc-sched-ib0
42201046[].gpc-sched-ib0
42201047[].gpc-sched-ib0
42201048[].gpc-sched-ib0
42201049[].gpc-sched-ib0
42201050[].gpc-sched-ib0
42201051[].gpc-sched-ib0
42201052[].gpc-sched-ib0
42201053[].gpc-sched-ib0
42201054[].gpc-sched-ib0
42201055[].gpc-sched-ib0
42201056[].gpc-sched-ib0
42201057[].gpc-sched-ib0
42201058[].gpc-sched-ib0
42201059[].gpc-sched-ib0
42201060[].gpc-sched-ib0
42201061[].gpc-sched-ib0
42201062[].gpc-sched-ib0
42201063[].gpc-sched-ib0
42201064[].gpc-sched-ib0
42201065[].gpc-sched-ib0
42201066[].gpc-sched-ib0
42201068[].gpc-sched-ib0
42201069[].gpc-sched-ib0
42201070[].gpc-sched-ib0
42201071[].gpc-sched-ib0
42201072[].gpc-sched-ib0
42201073[].gpc-sched-ib0
42201074[].gpc-sched-ib0
2017-05-17 21:26:24 UTC [     info] Computing Multiatlas/Template Label Resamples
42201075.gpc-sched-ib0
2017-05-17 21:26:25 UTC [     info] Computing Multiatlas/Template Votes
/home/s/sbramba/cbedetti/local/antsRegistration-MAGeT/bin/stages.sh: line 150: subjectname: unbound variable
No jobs to submit, exiting
2017-05-17 21:26:25 UTC [     info] Cleaning up. Done

Second Run:

(antsRegistration-MAGeT)cbedetti@gpc-f104n084-ib0:~/scratch/antsmaget/hippocampus-subfields_simplified
$ mb.sh -- multiatlas
2017-05-21 23:43:00 UTC [  warning] Even number of templates detected, use an odd number to avoid tie label votes
2017-05-21 23:43:01 UTC [     info] Found:
2017-05-21 23:43:01 UTC [     info]   5 atlases in input/atlas
2017-05-21 23:43:01 UTC [     info]   1 labels per atlas in input/atlas
2017-05-21 23:43:01 UTC [     info]   32 templates in input/template
2017-05-21 23:43:01 UTC [     info]   32 subjects in input/subject
2017-05-21 23:43:01 UTC [     info]   0 models in input/models
2017-05-21 23:43:01 UTC [     info] Progress:
2017-05-21 23:43:01 UTC [     info]   160 of 160 atlas-template registrations completed
2017-05-21 23:43:01 UTC [     info]   0 of 992 template-subject registrations completed
2017-05-21 23:43:01 UTC [     info]   0 of 5120 resample labels completed
2017-05-21 23:43:01 UTC [     info]   0 of 32 voted labels completed
2017-05-21 23:43:01 UTC [     info]   0 of 160 multiatlas resample labels completed
2017-05-21 23:43:01 UTC [     info]   0 of 32 multiatlas voted labels completed
2017-05-21 23:43:01 UTC [     info] Checking Resolution of First Atlas
2017-05-21 23:43:37 UTC [     info]   Found 206977724 voxels
2017-05-21 23:43:37 UTC [     info] Checking Resolution of First Template
2017-05-21 23:43:37 UTC [     info]   Found 3817380 voxels
2017-05-21 23:43:37 UTC [     info] Checking Resolution of First Subject
2017-05-21 23:43:37 UTC [     info]   Found 3817380 voxels
2017-05-21 23:43:37 UTC [   notice] MAGeTbrain estimates walltime and memory based on files with the largest file size, if some files are uncompressed, this estimate may be incorrect
2017-05-21 23:43:37 UTC [     info] Submitting template jobs to 32GB nodes
2017-05-21 23:43:37 UTC [     info] Submitting subject jobs to 16GB nodes, two commands in parallel
2017-05-21 23:43:37 UTC [     info] Computing Atlas to Template Registrations
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
2017-05-21 23:43:42 UTC [     info] Computing Multiatlas/Template Label Resamples
42306209.gpc-sched-ib0
2017-05-21 23:43:44 UTC [     info] Computing Multiatlas/Template Votes
/home/s/sbramba/cbedetti/local/antsRegistration-MAGeT/bin/stages.sh: line 150: subjectname: unbound variable
No jobs to submit, exiting
2017-05-21 23:43:44 UTC [     info] Cleaning up. Done

Third run:

(antsRegistration-MAGeT)cbedetti@gpc-f102n002-ib0:~/scratch/antsmaget/hippocampus-subfields_simplified
$ mb.sh -- multiatlas
2017-05-23 14:12:13 UTC [  warning] Even number of templates detected, use an odd number to avoid tie label votes
2017-05-23 14:12:14 UTC [     info] Found:
2017-05-23 14:12:14 UTC [     info]   5 atlases in input/atlas
2017-05-23 14:12:14 UTC [     info]   1 labels per atlas in input/atlas
2017-05-23 14:12:14 UTC [     info]   32 templates in input/template
2017-05-23 14:12:14 UTC [     info]   32 subjects in input/subject
2017-05-23 14:12:14 UTC [     info]   0 models in input/models
2017-05-23 14:12:14 UTC [     info] Progress:
2017-05-23 14:12:14 UTC [     info]   160 of 160 atlas-template registrations completed
2017-05-23 14:12:14 UTC [     info]   0 of 992 template-subject registrations completed
2017-05-23 14:12:14 UTC [     info]   0 of 5120 resample labels completed
2017-05-23 14:12:14 UTC [     info]   0 of 32 voted labels completed
2017-05-23 14:12:14 UTC [     info]   160 of 160 multiatlas resample labels completed
2017-05-23 14:12:14 UTC [     info]   0 of 32 multiatlas voted labels completed
2017-05-23 14:12:14 UTC [     info] Checking Resolution of First Atlas
2017-05-23 14:12:55 UTC [     info]   Found 206977724 voxels
2017-05-23 14:12:55 UTC [     info] Checking Resolution of First Template
2017-05-23 14:12:55 UTC [     info]   Found 3817380 voxels
2017-05-23 14:12:55 UTC [     info] Checking Resolution of First Subject
2017-05-23 14:12:55 UTC [     info]   Found 3817380 voxels
2017-05-23 14:12:55 UTC [   notice] MAGeTbrain estimates walltime and memory based on files with the largest file size, if some files are uncompressed, this estimate may be incorrect
2017-05-23 14:12:56 UTC [     info] Submitting template jobs to 32GB nodes
2017-05-23 14:12:56 UTC [     info] Submitting subject jobs to 16GB nodes, two commands in parallel
2017-05-23 14:12:56 UTC [     info] Computing Atlas to Template Registrations
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
No jobs to submit, exiting
2017-05-23 14:13:01 UTC [     info] Computing Multiatlas/Template Label Resamples
No jobs to submit, exiting
2017-05-23 14:13:02 UTC [     info] Computing Multiatlas/Template Votes
/home/s/sbramba/cbedetti/local/antsRegistration-MAGeT/bin/stages.sh: line 150: subjectname: unbound variable
No jobs to submit, exiting
2017-05-23 14:13:02 UTC [     info] Cleaning up. Done
gdevenyi commented 7 years ago

not a dependencies issue, clearly a coding error:

/home/s/sbramba/cbedetti/local/antsRegistration-MAGeT/bin/stages.sh: line 150: subjectname: unbound variable

looking into it

gdevenyi commented 7 years ago

replace subject with template in these lines https://github.com/CobraLab/antsRegistration-MAGeT/blob/master/bin/stages.sh#L150-L152

gdevenyi commented 6 years ago

Fixed