Merge pull request #140 from university-of-york/quickFix

Quick fix
university-of-york · Dec 5, 2023 · 683d130 · 683d130
2 parents 203bd99 + 232b677
commit 683d130
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diff --git a/docs/source/applications/voxfe.rst b/docs/source/applications/voxfe.rst
@@ -8,36 +8,33 @@ VOX-FE
     $ module load module load {MOD_VOXFE}
 
 
-An example job script can be found here. This script takes 40 CPUs, 1 GB of memory and 2 hours. Remember to update the account code and email address provided to ``slurm`` to your own details.
+An example job script can be found here. This script described using a whole node with 96 cores exclusively for two hours. Remember to update the account code and email address provided to ``slurm`` to your own details and be sure to substitute ``Script.txt`` with the path to your script.
 
 .. code-block:: bash
 
     {SHEBANG}
     #SBATCH --job-name=VOX-FE_CPU_example       # Job name
     #SBATCH --mail-type=BEGIN,END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
     #SBATCH [email protected]       # Where to send mail to
-    #SBATCH --ntasks=40
-    #SBATCH --cpus-per-task=1
-    #SBATCH --nodes=1
-    #SBATCH --ntasks-per-node=40
-    #SBATCH --ntasks-per-socket=20
-    #SBATCH --mem-per-cpu=1gb
-    #SBATCH --time=02:00:00
-    #SBATCH --output=logs/VOX-FE_CPU_example-node-%j.log
+    #SBATCH --nodes=1                           # Number of nodes
+    #SBATCH --exclusive                         # Exclusively use the whole node
+    #SBATCH --time=02:00:00                     # Time of the job in HH:MM:SS
+    #SBATCH --output=VOX-FE_CPU_example-%j.log  # Output file
     #SBATCH --account=dept-proj-year            # Project account to use
 
     # Abort if any command fails
     set -e
 
     module purge                                # purge any loaded modules
+    module load OpenMPI/4.1.4-GCC-12.2.0
     module load module load {MOD_VOXFE}
 
-    echo "Running small-vox-fe on $SLURM_NTASKS CPU cores"
+    echo "Running small-vox-fe on $SLURM_JOB_CPUS_PER_NODE CPU cores"
     echo "Nodes allocated to job: " $SLURM_JOB_NUM_NODES "(" $SLURM_JOB_NODELIST ")"
     echo
 
     date
-    mpirun -np $SLURM_NTASKS PARA_BMU Script.txt
+    mpirun -np $SLURM_JOB_CPUS_PER_NODE voxfe_solver Script.txt
     date
 
 .. note::

diff --git a/docs/source/replacements.py b/docs/source/replacements.py
@@ -28,7 +28,7 @@ def variableReplace(app, docname, source):
     "{MOD_GAUSSIAN}": "Gaussian/G16a03",
     "{MOD_MATLAB}": "MATLAB/2023b",
     "{MOD_MONGODB}": "MongoDB/4.2.3",
-    "{MOD_VOXFE}": "VOX-FE/2.0.1-foss-2022b",
+    "{MOD_VOXFE}": "VOX-FE/2.0.1-foss-2022b",  # need to update the OpenMPI on same page
     "{MOD_RELION}": "RELION/4.0.1-foss-2021a",
     "{MOD_ALPHAFOLD_CPU}": "AlphaFold/2.3.1-foss-2022a",
     "{MOD_ALPHAFOLD_GPU}": "AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0",