hw3 first submission

kjm14009 · Feb 27, 2020 · 231c66c · 231c66c
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commit 231c66c
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diff --git a/error_3110850_4294967294.log b/error_3110850_4294967294.log
@@ -0,0 +1,2 @@
+[33mWARNING:[0m skipping mount of /gpfs/scratchfs1/amw17004/hw3/$/scratch/hw3/out: no such file or directory
+[31mFATAL:  [0m container creation failed: mount /gpfs/scratchfs1/amw17004/hw3/$/scratch/hw3/out->/out error: while mounting /gpfs/scratchfs1/amw17004/hw3/$/scratch/hw3/out: mount source /gpfs/scratchfs1/amw17004/hw3/$/scratch/hw3/out doesn't exist
diff --git a/error_3110981_4294967294.log b/error_3110981_4294967294.log
@@ -0,0 +1,2 @@
+[33mWARNING:[0m skipping mount of /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/out: no such file or directory
+[31mFATAL:  [0m container creation failed: mount /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/out->/out error: while mounting /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/out: mount source /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/out doesn't exist
diff --git a/error_3111011_4294967294.log b/error_3111011_4294967294.log
@@ -0,0 +1,2 @@
+[33mWARNING:[0m skipping mount of /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/mriqc: no such file or directory
+[31mFATAL:  [0m container creation failed: mount /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/mriqc->/out error: while mounting /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/mriqc: mount source /gpfs/scratchfs1/amw17004/hw3/$/scratch/amw17004/hw3/mriqc doesn't exist
diff --git a/error_3130832_4294967294.log b/error_3130832_4294967294.log
diff --git a/output_3110850_4294967294.log b/output_3110850_4294967294.log
diff --git a/output_3110981_4294967294.log b/output_3110981_4294967294.log
diff --git a/output_3111011_4294967294.log b/output_3111011_4294967294.log
diff --git a/output_3130832_4294967294.log b/output_3130832_4294967294.log
diff --git a/sbatch_mriqc.sh b/sbatch_mriqc.sh
@@ -2,5 +2,24 @@
 
 # Add your SLURM options here
 
+#SBATCH --cpus-per-task=8 # Number of cores to use
+#SBATCH --mem=16gb # Memory limit
+#SBATCH --time=02:00:00 # Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log # Standard error
+#SBATCH -o output_%A_%a.log # Standard output
+#SBATCH --job-name=mriqc # Descriptive job name
+#SBATCH --partition=serial # Use a serial partition 24 cores/7days
+
+
+##### load required modules
+
+module load singularity
+
 # Add commands needed to run mriqc
 
+singularity run --cleanenv \
+--bind /scratch/psyc5171/exercises/mbdata/bids:/data \
+--bind /scratch/amw17004/hw3/out:/out \
+/scratch/psyc5171/containers/mriqc_latest.sif \
+/data /out participant
+