Merge pull request #41 from marcobarilari/marc_update-slurm-files

update slurm files for fmriprep and mriqc

Author: marcobarilari

doc/cpp_fmriprep.slurm

@@ -1,12 +1,12 @@
-#!/bin/bash
+!/bin/bash
 
 #SBATCH --job-name=fMRIprep
 #SBATCH --time=9:00:00 # hh:mm:ss
 
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=4
 #SBATCH --mem-per-cpu=20000 # megabytes
-#SBATCH --partition=batch,debug
+#SBATCH --partition=batch
 
 #SBATCH --mail-user=marco.barilari@uclouvain.be
 #SBATCH --mail-type=ALL
@@ -59,10 +59,9 @@ set -e -x -u -o pipefail
 module --force purge
 
 subjID=$1
-TaskName=$2
 
 # "latest" or procide specific version number
-FMRIPREP_VERSION="24.0.0"
+FMRIPREP_VERSION="25.2.5"
 
 # set username to locate scratch folder
 ceci_username="marcobar"
@@ -71,7 +70,7 @@ ceci_username="marcobar"
 nb_dummy_scans=0
 
 # cluster paths
-path_to_singularity_image="$HOME/tools/containers/images/bids/bids-fmriprep--${FMRIPREP_VERSION}.sing"
+path_to_singularity_image="$HOME/tools/containers/images/bids/bids-fmriprep--${FMRIPREP_VERSION}.sif"
 scratch_dir=$GLOBALSCRATCH
 freesurfer_license_folder="$HOME/tools"
 
@@ -80,7 +79,7 @@ root_dir="$HOME/path-to-project-yoda-fodler"
 bids_dir="$root_dir/inputs/raw"
 output_dir="$root_dir/outputs/derivatives/fmriprep"
 
-# make the scratch folder, here there is no limit space and fmriprep can store stuff in case of crash and do not start from zero again
+# make the scratch folder, here there is no limit space and fmriprep can store temp files in case of crash and it does not start from zero again
 mkdir -p "${scratch_dir}"/work-fmriprep
 
 # create output folder in case it does not exists

doc/cpp_mriqc.slurm

@@ -1,11 +1,11 @@
 #!/bin/bash
 
 #SBATCH --job-name=MRIqc
-#SBATCH --time=4:00:00 # hh:mm:ss
+#SBATCH --time=0:30:00 # hh:mm:ss
 
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=4
-#SBATCH --mem-per-cpu=10000 # megabytes
+#SBATCH --mem-per-cpu=3000 # megabytes
 #SBATCH --partition=batch
 
 #SBATCH --mail-user=marco.barilari@uclouvain.be
@@ -17,7 +17,7 @@
 #export OMP_NUM_THREADS=4
 #export MKL_NUM_THREADS=4
 
-## CPP MRIqc script for CECI cluster v0.3.0
+## CPP MRIqc script for CECI cluster v0.4.0
 #
 # writtent by CPP people
 #
@@ -50,18 +50,18 @@ module --force purge
 subjID=$1
 
 # "latest" or procide specific version number
-MRIQC_VERSION="24.0.0"
+MRIQC_VERSION="24.0.2"
 
 # cluster paths
-path_to_singularity_image="$HOME/tools/containers/images/bids/bids-mriqc--${MRIQC_VERSION}.sing"
+path_to_singularity_image="$HOME/tools/containers/images/bids/bids-mriqc--${MRIQC_VERSION}.sif"
 scratch_dir=$GLOBALSCRATCH
 
 # data paths
 root_dir="$HOME/path-to-project-yoda-fodler"
 bids_dir="$root_dir/inputs/raw"
 output_dir="$root_dir/outputs/derivatives/mriqc"
 
-# make the scratch folder, here there is no limit space and fmriprep can store stuff in case of crash and do not start from zero again
+# make the scratch folder, here there is no space limit and mriqc can store temp files in case of crash and it does not start from zero again
 mkdir -p "${scratch_dir}"/work-mriqc
 
 # create output folder in case it does not exists

doc/cpp_mriqc_group.slurm

@@ -1,11 +1,11 @@
 #!/bin/bash
 
 #SBATCH --job-name=MRIqc
-#SBATCH --time=4:00:00 # hh:mm:ss
+#SBATCH --time=0:30:00 # hh:mm:ss
 
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=4
-#SBATCH --mem-per-cpu=10000 # megabytes
+#SBATCH --mem-per-cpu=3000 # megabytes
 #SBATCH --partition=batch
 
 #SBATCH --mail-user=marco.barilari@uclouvain.be
@@ -17,11 +17,12 @@
 #export OMP_NUM_THREADS=4
 #export MKL_NUM_THREADS=4
 
-## CPP MRIqc script for CECI cluster v0.3.0
+## CPP MRIqc script for CECI cluster v0.4.0
 #
 # writtent by CPP people
 #
 # Submission command for Lemaitre4 after running mriqc for each participant
+# !!! to run from within `raw` folder
 #
 # sbatch cpp_mriqc_group.slurm
 
@@ -37,19 +38,19 @@ set -e -x -u -o pipefail
 
 module --force purge
 
-# "latest" or procide specific version number
-MRIQC_VERSION="24.0.0"
+# "latest" or provide specific version number
+MRIQC_VERSION="24.0.2"
 
 # cluster paths
-path_to_singularity_image="$HOME/tools/containers/images/bids/bids-mriqc--${MRIQC_VERSION}.sing"
+path_to_singularity_image="$HOME/tools/containers/images/bids/bids-mriqc--${MRIQC_VERSION}.sif"
 scratch_dir=$GLOBALSCRATCH
 
 # data paths
 root_dir="$HOME/path-to-project-yoda-fodler"
 bids_dir="$root_dir/inputs/raw"
 output_dir="$root_dir/outputs/derivatives/mriqc"
 
-# make the scratch folder, here there is no limit space and fmriprep can store stuff in case of crash and do not start from zero again
+# make the scratch folder, here there is no space limit and mriqc can store temp files in case of crash and it does not start from zero again
 mkdir -p "${scratch_dir}"/work-mriqc
 
 # create mriqc output folder in case they don't exist
@@ -62,6 +63,6 @@ singularity run --cleanenv \
     "${path_to_singularity_image}" \
     /bids_dir \
     /output \
-    --work-dir /scratch_dir/work-mriqc/"${subjID}" \
+    --work-dir /scratch_dir/work-mriqc/group \
     --verbose-reports \
     group

doc/run_fmriprep.md

@@ -20,14 +20,14 @@ To contribute see [here](https://cpp-lln-lab.github.io/CPP_HPC/contributing/)
 - install datalad on your user (see [here](https://github.com/cpp-lln-lab/CPP_HPC/install_datalad))
 - get the fmriprep singularity image as follow:
 
-here the example is with `fmriprp version 24.0.0` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
+here the example is with `fmriprp version 25.2.5` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
 
 ```bash
 datalad install -s https://github.com/ReproNim/containers.git ~/tools/containers
 
 cd tools/containers
 
-datalad get images/bids/bids-fmriprep--24.0.0.sing
+datalad get images/bids/bids-fmriprep--25.2.5.sif
 ```
 
 In case you have installed the repo a while a ago and you want to use a new version of fmriprep., update the `containers` repo via:
@@ -42,7 +42,7 @@ datald update --merge
 Depending on the cluster “unlock” is needed or not. No need for `lemaitre4`.
 
 ```bash
-datalad unlock containers/images/bids/bids-fmriprep--24.0.0.sing
+datalad unlock containers/images/bids/bids-fmriprep--25.2.5.sif
 ```
 
 ## Submit a fmriprep job via a `slurm` script

doc/run_mriqc.md

@@ -16,18 +16,18 @@ To contribute see [here](https://cpp-lln-lab.github.io/CPP_HPC/contributing/)
 
 ## Prepare to run MRIqc on the cluster
 
-- have your data on the cluster and unlock them if they are managed by datalad
+- have your data on the cluster and unlock them if they are managed by datalad (for MRIqc v24.0.2 data should not need to be unlocked)
 - install datalad on your user (see [here](https://github.com/cpp-lln-lab/CPP_HPC/install_datalad))
 - get the fmriprep singularity image as follow:
 
-here the example is with `MRIqc version 24.0.0` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
+here the example is with `MRIqc version 24.0.2` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
 
 ```bash
 datalad install https://github.com/ReproNim/containers.git
 
 cd containers
 
-datalad get images/bids/bids-mriqc--24.0.0.sing
+datalad get images/bids/bids-mriqc--24.0.2.sif
 ```
 
 In case you have installe the repo a while a ago and you want to use a new version of fmriprep., update the `containers` repo via:
@@ -116,6 +116,16 @@ sbatch cpp_mriqc_group.slurm
 
 ## TIPS
 
+### Troubleshooting
+
+- ERROR: `OSError: [Errno 30] Read-only file system: '/home/mriqc/.cache'`
+
+add this flag to the singulairy inputs 
+
+```bash
+    -B "$HOME/tools/containers/images/bids":/home/mriqc \
+```
+
 ### check your job
 
 see [here](https://github.com/cpp-lln-lab.github.io/CPP_HPC/cluster_code_snippets/#check-your-running-jobs)