setup for compute canada

sct-pipeline · Aug 13, 2024 · 9511c21 · 9511c21
1 parent c849a24
commit 9511c21
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Showing 4 changed files with 15 additions and 3 deletions.
diff --git a/config_sct_run_batch_cc.yml b/config_sct_run_batch_cc.yml
@@ -0,0 +1,10 @@
+# config file for sct_run_batch
+path_data: /home/sabeda/scratch/data-multi-subject
+path_output: /home/sabeda/scratch/results_csa-atrophy_t2-all
+script: /home/sabeda/csa-atrophy/process_data.sh
+script_args: /home/sabeda/csa-atrophy/config_script.yml
+jobs: -1
+batch_log: sct_run_batch_log.txt
+continue_on_error: 1
+subject_prefix: sub-
+zip: true
diff --git a/job_template.sh b/job_template.sh
@@ -3,7 +3,7 @@
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=32    # number of OpenMP processes
 #SBATCH --mem=128G
-#SBATCH --mail-user=paul.bautin@polymtl.ca
+#SBATCH --mail-user=sandrine.bedard@polymtl.ca
 #SBATCH --mail-type=ALL
 export OMP_NUM_THREADS=1
 export MKL_NUM_THREADS=1

diff --git a/requirements.txt → requirements_cc.txt b/requirements.txt → requirements_cc.txt
@@ -5,9 +5,9 @@ matplotlib
 scikit-image
 nibabel
 ruamel.yaml
-yaml-1.3
 argparse
 setuptools
 PyYAML
 coloredlogs
-
+networkx
+yaml-1.3
diff --git a/requirements_manual_pip.txt b/requirements_manual_pip.txt
@@ -0,0 +1,2 @@
+networkx==3.2.1
+yaml-1.3