Failure to expand arguments when calling sbatch
fsl_sub is setting a series of sbatch options, and several of them appear in square brackets like ['-o', './bet.o%j'], but these are not understood by sbatch (we have slurm 20.11.8). When I remove the quotes and brackets, the command runs fine. It doesn't look like this is an option I can modify in the fsl_sub.yml, and I don't see where this is being set in the fsl_sub python code. I saw there was a recent update to fsl_sub_plugin_slurm 1.4.0 on the FSL gitlab, but I get the same error if I install that (along with fsl_sub 2.6.0). Here's my fsl_sub output
sl_sub -vvv -l . -T 10 -R 2 -N bet bet2 sub-01_ses-test_T1w sub-01_ses-test_T1w_brain METHOD=slurm : TYPE=single : args=bet2 sub-01_ses-test_T1w sub-01_ses-test_T1w_brain Estimated RAM was 2 GBm, runtime was 10 minutes.
Appropriate queue is short slurm_args: --export=ALL,OMP_NUM_THREADS=1,MKL_NUM_THREADS=1,MKL_DOMAIN_NUM_THREADS=1,OPENBLAS_NUM_THREADS=1,GOTO_NUM_THREADS=1,FSLSUB_PARALLEL=1,FSLSUB_JOB_ID_VAR=SLURM_JOB_ID,FSLSUB_ARRAYTASKID_VAR=SLURM_ARRAY_TASK_ID,FSLSUB_ARRAYSTARTID_VAR=SLURM_ARRAY_TASK_MIN,FSLSUB_ARRAYENDID_VAR=SLURM_ARRAY_TASK_MAX,FSLSUB_ARRAYSTEPSIZE_VAR=SLURM_ARRAY_TASK_STEP,FSLSUB_ARRAYCOUNT_VAR=SLURM_ARRAY_TASK_COUNT,FSLSUB_NSLOTS=SLURM_NPROCS ['-o', './bet.o%j'] ['-e', './bet.e%j'] --mem-per-cpu=2G ['-t', 10] --job-name=bet --chdir=/scratch/user/joseph.orr/openneuro_reliability/data/sub-01/ses-test/anat ['-p', 'short'] --parsable --requeue executing single task --export=ALL,OMP_NUM_THREADS=1,MKL_NUM_THREADS=1,MKL_DOMAIN_NUM_THREADS=1,OPENBLAS_NUM_THREADS=1,GOTO_NUM_THREADS=1,FSLSUB_PARALLEL=1,FSLSUB_JOB_ID_VAR=SLURM_JOB_ID,FSLSUB_ARRAYTASKID_VAR=SLURM_ARRAY_TASK_ID,FSLSUB_ARRAYSTARTID_VAR=SLURM_ARRAY_TASK_MIN,FSLSUB_ARRAYENDID_VAR=SLURM_ARRAY_TASK_MAX,FSLSUB_ARRAYSTEPSIZE_VAR=SLURM_ARRAY_TASK_STEP,FSLSUB_ARRAYCOUNT_VAR=SLURM_ARRAY_TASK_COUNT,FSLSUB_NSLOTS=SLURM_NPROCS ['-o', './bet.o%j'] ['-e', './bet.e%j'] --mem-per-cpu=2G ['-t', 10] --job-name=bet --chdir=/scratch/user/joseph.orr/openneuro_reliability/data/sub-01/ses-test/anat ['-p', 'short'] --parsable --requeue Error submitting job - output from submission not understood. Grid output was