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source $SLURM_TMPDIR/env/bin/activate; | source $SLURM_TMPDIR/env/bin/activate; | ||
export OMP_NUM_THREADS=1 | export OMP_NUM_THREADS=1 | ||
# srun exports the current env, which contains $VIRTUAL_ENV and $PATH variables | # srun exports the current env, which contains $VIRTUAL_ENV and $PATH variables | ||
Revision as of 21:05, 2 May 2024
Dedalus est un cadre flexible pour résoudre des équations aux dérivées partielles à l'aide de méthodes spectrales modernes.
Versions disponibles
Sur nos grappes, les versions de Dedalus sobnt des wheels Python. Pour connaître les versions disponibles, lancez avail_wheels.
[name@server ~]$ avail_wheels dedalus --all-versions
$ avail_wheels dedalus
name version python arch
------- --------- -------- ---------
dedalus 3.0.2 cp311 x86-64-v3
dedalus 3.0.2 cp310 x86-64-v3
Installation dans un environnement virtuel Python
1. Chargez les dépendances d'exécution pour Dedalus.
[name@server ~]$ module load StdEnv/2023 gcc openmpi mpi4py/3.1.4 fftw-mpi/3.3.10 hdf5-mpi/1.14.2 python/3.11
2. Créez et activez un environnement virtuel Python.
[name@server ~]$ virtualenv --no-download ~/dedalus_env
[name@server ~]$ source ~/dedalus_env/bin/activate
3. Installez une version de Dedalus et ses dépendances Python.
(dedalus_env) [name@server ~] pip install --no-index --upgrade pip
(dedalus_env) [name@server ~] pip install --no-index dedalus==X.Y.Z
où X.Y.Z est la version choisie (par exemple 3.0.2).
Si aucun numéro n'est indiqué, la plus récente version sera installée.
4. Validez.
(dedalus_env) [name@server ~] python -c 'import dedalus'
5. Gelez l'environnement et les éléments requis.
(dedalus_env) [name@server ~] pip freeze --local > ~/dedalus-3.0.2-requirements.txt
6. Supprimez l'environnement virtuel local.
(dedalus_env) [name@server ~] deactivate && rm -r ~/dedalus_env
Exécution
Dedalus peut être exécuté en mode distribué sur plusieurs nœuds ou cœurs. Pour plus d'information, voir
1. Préparez le script.
File : submit-dedalus-distributed.sh
#!/bin/bash
#SBATCH --account=def-someprof # adjust this to match the accounting group you are using to submit jobs
#SBATCH --time=08:00:00 # adjust this to match the walltime of your job
#SBATCH --ntasks=4 # adjust this to match the number of tasks/processes to run
#SBATCH --mem-per-cpu=4G # adjust this according to the memory you need per process
# Run on cores accross the system : https://docs.alliancecan.ca/wiki/Advanced_MPI_scheduling#Few_cores,_any_number_of_nodes
# Load modules dependencies.
module load StdEnv/2023 gcc openmpi mpi4py/3.1.4 fftw-mpi/3.3.10 hdf5-mpi/1.14.2 python/3.11
# create the virtual environment on each allocated node:
srun --ntasks $SLURM_NNODES --tasks-per-node=1 bash << EOF
virtualenv --no-download $SLURM_TMPDIR/env
source $SLURM_TMPDIR/env/bin/activate
pip install --no-index --upgrade pip
pip install --no-index -r dedalus-3.0.2-requirements.txt
EOF
# activate only on main node
source $SLURM_TMPDIR/env/bin/activate;
export OMP_NUM_THREADS=1
# srun exports the current env, which contains $VIRTUAL_ENV and $PATH variables
srun python $SCRATCH/myscript.py;
File : submit-dedalus-whole-nodes.sh
#!/bin/bash
#SBATCH --account=def-someprof # adjust this to match the accounting group you are using to submit jobs
#SBATCH --time=08:00:00 # adjust this to match the walltime of your job
#SBATCH --nodes=2 # adjust this to match the number of whole node
#SBATCH --ntasks-per-node=4 # adjust this to match the number of tasks/processes to run per node
#SBATCH --mem-per-cpu=4G # adjust this according to the memory you need per process
# Run on N whole nodes : https://docs.alliancecan.ca/wiki/Advanced_MPI_scheduling#Whole_nodes
# Load modules dependencies.
module load StdEnv/2023 gcc openmpi mpi4py/3.1.4 fftw-mpi/3.3.10 hdf5-mpi/1.14.2 python/3.11
# create the virtual environment on each allocated node:
srun --ntasks $SLURM_NNODES --tasks-per-node=1 bash << EOF
virtualenv --no-download $SLURM_TMPDIR/env
source $SLURM_TMPDIR/env/bin/activate
pip install --no-index --upgrade pip
pip install --no-index -r dedalus-3.0.2-requirements.txt
EOF
# activate only on main node
source $SLURM_TMPDIR/env/bin/activate;
export OMP_NUM_THREADS=1
# srun exports the current env, which contains $VIRTUAL_ENV and $PATH variables
srun python $SCRATCH/myscript.py;
2. Soumettez la tâche à l'ordonnaceur.
Before submitting your job, it is important to test that your submission script will start without errors. You can do a quick test in an interactive job.
[name@server ~]$ sbatch submit-dedalus.sh