-
Notifications
You must be signed in to change notification settings - Fork 4
Open
Description
Hello, I'm trying to use the containerized GIFT BIDS app on our HPC but running into an issue when specifying the configuration file:
[seeles01@li03c04 gift]$ cat 136018476.err
Error using icatb_eval_script
More than one configuration file provided.
Error in groupica (line 74)
[seeles01@li03c04 gift]$ cat 136018476.out
Sender: LSF System <lsfadmin@lh06c11>
Subject: Job 136018476: <gift> in cluster <chimera> Exited
Job <gift> was submitted from host <li03c04.chimera.hpc.mssm.edu> by user <seeles01> in cluster <chimera> at Fri Aug 2 11:25:13 2024
Job was executed on host(s) <lh06c11>, in queue <express>, as user <seeles01> in cluster <chimera> at Fri Aug 2 11:25:21 2024
</hpc/users/seeles01> was used as the home directory.
</hpc/users/seeles01/minerva/gift> was used as the working directory.
Started at Fri Aug 2 11:25:21 2024
Terminated at Fri Aug 2 11:25:45 2024
Results reported at Fri Aug 2 11:25:45 2024
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
#!/bin/bash
#BSUB -J gift #job name
#BSUB -P acc_federa03a #project allocation number
#BSUB -q express #queue to run on
#BSUB -n 1 #1 job slot
#BSUB -R affinity[core(1)] #with 1 cores
#BSUB -R rusage[mem=16000] #with 16GB memory dynamically allocated across cores
#BSUB -a openmp #use openmp multithreading
#BSUB -W 1:00 #wall time
#BSUB -o %J.out #output file to t.out
#BSUB -e %J.err #error file to t.err`
module purge
module load singularity
singularity run --cleanenv \
-B /sc/arion/scratch/seeles01:/tmp \
-B /sc/arion/scratch/seeles01:/var/tmp \
-B /sc/arion/projects/psychres/WTC_resilience_imaging/data/BIDS_data/derivatives/fmriprep/:/data \
-B /sc/arion/projects/psychres/WTC_resilience_imaging/data/BIDS_data/derivatives/gift/:/output \
-B /hpc/users/seeles01/minerva/gift/cfg/:/cfg \
/hpc/users/seeles01/gift-bids_v4.0.5.3.sif \
/data /output participant --participant_label 002 \
config --config /cfg/config_nwtc.m \
validate --skip-bids-validator
------------------------------------------------------------
Exited with exit code 249.
Resource usage summary:
CPU time : 15.80 sec.
Max Memory : 353 MB
Average Memory : 183.93 MB
Total Requested Memory : 16000.00 MB
Delta Memory : 15647.00 MB
Max Swap : -
Max Processes : 5
Max Threads : 42
Run time : 23 sec.
Turnaround time : 32 sec.
The output (if any) follows:
PS:
Read file <136018476.err> for stderr output of this job.
I've confirmed that -B /hpc/users/seeles01/minerva/gift/cfg/:/cfg is working as expected.
If I don't mount the cfg directory and remove the --config argument (just for troubleshooting purposes), then I get this error:
Error using icatb_eval_script No default configuration file found for "participants" level. Error in groupica (line 74)
I'm not sure where to go from here - any ideas for further troubleshooting?
Reactions are currently unavailable
Metadata
Metadata
Assignees
Labels
No labels