From 000c1cff8443ff36909d4a3b725e1ae1c1c8a319 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 1 Dec 2023 15:49:47 +0000 Subject: [PATCH 1/3] amend vox-fe jobscript --- docs/source/applications/voxfe.rst | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/source/applications/voxfe.rst b/docs/source/applications/voxfe.rst index d453022..49e46fb 100644 --- a/docs/source/applications/voxfe.rst +++ b/docs/source/applications/voxfe.rst @@ -8,7 +8,7 @@ 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 takes 96 CPU cores, 1 GB of memory and 2 hours. Remember to update the account code and email address provided to ``slurm`` to your own details. .. code-block:: bash @@ -16,11 +16,10 @@ An example job script can be found here. This script takes 40 CPUs, 1 GB of memo #SBATCH --job-name=VOX-FE_CPU_example # Job name #SBATCH --mail-type=BEGIN,END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=abc123@york.ac.uk # 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 --ntasks=96 + #SBATCH --cpus-per-task=1 + #SBATCH --ntasks-per-node=96 #SBATCH --mem-per-cpu=1gb #SBATCH --time=02:00:00 #SBATCH --output=logs/VOX-FE_CPU_example-node-%j.log From 5e523cdd6ebc78e6411d4f562d8044762d7e631e Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Mon, 4 Dec 2023 10:34:11 +0000 Subject: [PATCH 2/3] update vox-fe jobscript --- docs/source/applications/voxfe.rst | 16 +++++++--------- docs/source/replacements.py | 2 +- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/docs/source/applications/voxfe.rst b/docs/source/applications/voxfe.rst index 49e46fb..73ecce6 100644 --- a/docs/source/applications/voxfe.rst +++ b/docs/source/applications/voxfe.rst @@ -8,7 +8,7 @@ VOX-FE $ module load module load {MOD_VOXFE} -An example job script can be found here. This script takes 96 CPU cores, 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. .. code-block:: bash @@ -16,12 +16,9 @@ An example job script can be found here. This script takes 96 CPU cores, 1 GB of #SBATCH --job-name=VOX-FE_CPU_example # Job name #SBATCH --mail-type=BEGIN,END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=abc123@york.ac.uk # Where to send mail to - #SBATCH --nodes=1 - #SBATCH --ntasks=96 - #SBATCH --cpus-per-task=1 - #SBATCH --ntasks-per-node=96 - #SBATCH --mem-per-cpu=1gb - #SBATCH --time=02:00:00 + #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=logs/VOX-FE_CPU_example-node-%j.log #SBATCH --account=dept-proj-year # Project account to use @@ -29,14 +26,15 @@ An example job script can be found here. This script takes 96 CPU cores, 1 GB of 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 PARA_BMU Script.txt date .. note:: diff --git a/docs/source/replacements.py b/docs/source/replacements.py index 42e0394..9a6e877 100644 --- 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", From 232b677f6950e7e9c83ed9836982662ab5f20255 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Tue, 5 Dec 2023 15:44:18 +0000 Subject: [PATCH 3/3] update jobscript --- docs/source/applications/voxfe.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/applications/voxfe.rst b/docs/source/applications/voxfe.rst index 73ecce6..e2d9a9c 100644 --- a/docs/source/applications/voxfe.rst +++ b/docs/source/applications/voxfe.rst @@ -8,7 +8,7 @@ VOX-FE $ module load module load {MOD_VOXFE} -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. +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 @@ -19,7 +19,7 @@ An example job script can be found here. This script described using a whole nod #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=logs/VOX-FE_CPU_example-node-%j.log + #SBATCH --output=VOX-FE_CPU_example-%j.log # Output file #SBATCH --account=dept-proj-year # Project account to use # Abort if any command fails @@ -34,7 +34,7 @@ An example job script can be found here. This script described using a whole nod echo date - mpirun -np $SLURM_JOB_CPUS_PER_NODE PARA_BMU Script.txt + mpirun -np $SLURM_JOB_CPUS_PER_NODE voxfe_solver Script.txt date .. note::