How to run antsMultivariateTemplateConstruction2.sh in SLURM

[Marjola89]

Hi,
I was wondering how you run any ANTs script in SLURM?
I am trying to run antsMultivariateTemplateConstruction2.sh using the following slurm script:

#!/bin/bash
#SBATCH -N 1              # Number of nodes
#SBATCH -n 1              # Number of tasks
#SBATCH -c 7              # Number of cores
#SBATCH --mem=15000       # Memory in MB
#SBATCH --output=slurm_out/slurm_%j.out  # Output file
#SBATCH --error=slurm_out/slurm_%j.err   # Error file
#SBATCH -t 24:00:00       # Time requested in HH:MM:SS
#SBATCH [email protected]
#SBATCH --mail-type=END,FAIL

export ANTSPATH=/home/install/bin/
export PATH=${ANTSPATH}:$PATH

ANTSPATH=/home/install/bin

inputPath=/home/template
outputPath=/home/template_test/

"${ANTSPATH}"/antsMultivariateTemplateConstruction2.sh \
  -d 3 \
  -o ${outputPath}T_ \
  -i 4 \
  -g 0.2 \
  -c 5 \
  -k 1 \
  -y 1 \
  -w 1 \
  -q 100x70x50x10 \
  -n 0 \
  -r 1 \
  -m MI \
  -t BSplineSyN \
  ${inputPath}/*/analysis/organ.nii.gz

It reads the data ok:

$ cat slurm_out/slurm_3033309.out
....
reading /home/template_test/initialCOM0_299_organ.nii.gz
 writing output
Sharpening method none

--------------------------------------------------------------------------------------
 Starting ANTS rigid registration on SLURM cluster. Submitted 300 jobs
--------------------------------------------------------------------------------------
  Waiting for 1 jobs:  3033310 3033311 3033312 3033313 3033314 3033315 3033316 3033317 3033318 3033319 3033320 3033321 3033322 3033323 3033324 3033325 3033326 3033327 3033328 3033329 3033330 3033331 303333>
  No more jobs in queue


Building rigid template from /home/template_test/rigid0_0_organ.nii.gz ...

but I get error:

$ cat slurm_out/slurm_3033309.err
squeue: error: Unrecognized option: 3033311
 Cannot read input file: /home/template_test/rigid0_0_organ.nii.gz
 file /home/template_test/T_template0.nii.gz does not exist . 
terminate called after throwing an instance of 'itk::ExceptionObject'

and inside the individual jobs I get this error:

$ cat slurm-3033310.out
/var/spool/slurmd/job3033310/slurm_script: 3: antsRegistration: not found
/var/spool/slurmd/job3033310/slurm_script: 4: antsApplyTransforms: not found

So, I am not sure if it has to do with the way I run this using SLURM or there is anything else I am missing.
I have tried to run ANTs scripts using CPU cores and have run other ANTs functions inside SLURM but I do not get any errors regarding the script not found.
I would really appreciate your suggestions on this.

Thank you,
Maria

[cookpa]

It looks like the jobs don't have ANTs on the PATH. You can try to fix this globally, or edit the script to set QSUBOPTS="PATH=${PATH}"

ANTs/Scripts/antsMultivariateTemplateConstruction2.sh

Line 574 in 5434f28

QSUBOPTS="" # EDIT THIS