Hi,
I am using fmriprep on Sherlock.
The pathway to my dataset : /scratch/PI/aetkin/redwan/framing/sourcedata/
My dataset in on BIDS format according the BIDS validator online
On sherlock I use the following command lines :
module load singularity
sbatch framing.sbatch
My framing sbatch is like that :
#!/bin/bash
#
#all commands that start with SBATCH contain commands that are just used by SLURM for scheduling
#################
#set a job name
#SBATCH --job-name=Framing
#################
#a file for job output, you can check job progress, append the job ID with %j to make it unique
#SBATCH --output=Framing.%j.out
#################
# a file for errors from the job
#SBATCH --error=Framing.%j.err
#################
#time you think you need; default is 2 hours
#format could be dd-hh:mm:ss, hh:mm:ss, mm:ss, or mm
#SBATCH --time=8:00:00
#################
#Quality of Service (QOS); think of it as job priority, there is also --qos=long for with a max job length of 7 days, qos normal is 48 h
ours.
# REMOVE "normal" and set to "long" if you want your job to run longer than 48 hours,
# NOTE- in the hns partition the default max run time is 7 days , so you wont need to include qos
#SBATCH --qos=normal
# We are submitting to the dev partition, there are several on sherlock: normal, gpu, owners, hns, bigmem (jobs requiring >64Gigs RAM)
# The more partitions you can submit to the less time you will wait, you can submit to multiple partitions with -p at once in comma sepa
rated format.
#SBATCH -p normal
#################
#number of nodes you are requesting, the more you ask for the longer you wait
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#################
# --mem is memory per node; default is 4000 MB per CPU, remember to ask for enough mem to match your CPU request, since
# sherlock automatically allocates 8 Gigs of RAM/CPU, if you ask for 8 CPUs you will need 32 Gigs of RAM, so either
# leave --mem commented out or request >= to the RAM needed for your CPU request.
#SBATCH --mem=16000
#################
# Have SLURM send you an email when the job ends or fails, careful, the email could end up in your clutter folder
# Also, if you submit hundreds of jobs at once you will get hundreds of emails.
#SBATCH --mail-type=END,FAIL # notifications for job done & fail
# Remember to change this to your email
#SBATCH --mail-user=rmaatoug@stanford.edu
#now run normal batch commands
# note the "CMD BATCH is an specific command
module load singularity
# You can use srun if your job is parallel
singularity run /share/PI/russpold/singularity_images/poldracklab_fmriprep_0.3.1-2017-03-25-c38ac0136e8c.img /scratch/PI/aetkin/redwan/framing/sourcedata/ /scratch/PI/aetkin/redwan/preprocessed/ participant -–participant_label sub-01
(the error file from Sherlock seems to say that there is a mistake in my syntax with “participant” but I have tried many different ways without any success.
I would really appreciate any help
Thank you,
Redwan