diff --git a/2-resources.ipynb b/2-resources.ipynb index 2579895..f310d2c 100644 --- a/2-resources.ipynb +++ b/2-resources.ipynb @@ -55,7 +55,7 @@ "#SBATCH --mem-per-cpu=1000M\n", "#SBATCH --time=0-00:10\n", "\n", - "module load gcc/9.3.0 &> /dev/null\n", + "module load StdEnv/2023 gcc/12.3\n", "\n", "mpirun printenv HOSTNAME OMPI_COMM_WORLD_RANK OMPI_COMM_WORLD_SIZE\n", "```\n", diff --git a/90-exercises.ipynb b/90-exercises.ipynb index 6e34091..e1316c9 100644 --- a/90-exercises.ipynb +++ b/90-exercises.ipynb @@ -35,7 +35,7 @@ "* Analyse avec Python, Pandas et Numpy dans le script [`scripts/inv-mat-pred.py`](https://github.com/calculquebec/cip201-serveurs-calcul/blob/main/scripts/inv-mat-pred.py) :\n", "\n", "```Bash\n", - "module load gcc python scipy-stack\n", + "module load StdEnv/2023 gcc/12.3 python/3.11 scipy-stack\n", "\n", "cat scripts/inv-mat-pred.py\n", "python scripts/inv-mat-pred.py temps_inv.csv\n", diff --git a/extra/estimer-mem.ipynb b/extra/estimer-mem.ipynb index 8762eff..d670cf5 100644 --- a/extra/estimer-mem.ipynb +++ b/extra/estimer-mem.ipynb @@ -65,7 +65,7 @@ " * **8 octets** : ~18 trillions de valeurs de 0 à $(2^{64}-1)$ ou de $-(2^{63}-1)$ à $(2^{63}-1)$\n", "\n", "```Bash\n", - "module load python scipy-stack\n", + "module load StdEnv/2023 python/3.11 scipy-stack\n", "python\n", "```\n", "\n", diff --git a/scripts/blastn-array.sh b/scripts/blastn-array.sh index d9dda1e..e93deb9 100644 --- a/scripts/blastn-array.sh +++ b/scripts/blastn-array.sh @@ -9,7 +9,7 @@ if [ "$(basename $PWD)" = "scripts" ]; then fi cd data -module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0 +module load StdEnv/2023 gcc/12.3 blast+/2.14.1 seqkit/2.5.1 UNKNOWNS=(M N O P Q R) UNK_X="${UNKNOWNS[$SLURM_ARRAY_TASK_ID]}" diff --git a/scripts/blastn-gen-seq.sh b/scripts/blastn-gen-seq.sh index 09c7f67..e3423e2 100644 --- a/scripts/blastn-gen-seq.sh +++ b/scripts/blastn-gen-seq.sh @@ -3,7 +3,7 @@ #SBATCH --mem-per-cpu=1000M #SBATCH --time=0-00:10 -module load gcc/9.3.0 python/3.8.10 blast+/2.12.0 seqkit/0.15.0 +module load StdEnv/2023 gcc/12.3 python/3.11 blast+/2.14.1 seqkit/2.5.1 if [ "$(basename $PWD)" = "scripts" ]; then cd .. diff --git a/scripts/blastn-glost.sh b/scripts/blastn-glost.sh index 0063e0b..8ce70a6 100644 --- a/scripts/blastn-glost.sh +++ b/scripts/blastn-glost.sh @@ -8,7 +8,7 @@ if [ "$(basename $PWD)" = "scripts" ]; then fi cd donnees -module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0 glost/0.3.1 +module load StdEnv/2023 gcc/12.3 blast+/2.14.1 seqkit/2.5.1 glost/0.3.1 mkdir -p $SCRATCH/res_glost diff --git a/scripts/blastn-meta.sh b/scripts/blastn-meta.sh index 9d1bff3..092dc5e 100644 --- a/scripts/blastn-meta.sh +++ b/scripts/blastn-meta.sh @@ -2,7 +2,7 @@ #SBATCH --mem-per-cpu=2000M #SBATCH --time=0-00:20 -module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0 glost/0.3.1 meta-farm/1.0.2 +module load StdEnv/2023 gcc/12.3 blast+/2.14.1 seqkit/2.5.1 glost/0.3.1 meta-farm/1.0.2 mkdir -p $SCRATCH/res_meta diff --git a/scripts/blastn-parallel.sh b/scripts/blastn-parallel.sh index 6612ca7..98ae0ab 100644 --- a/scripts/blastn-parallel.sh +++ b/scripts/blastn-parallel.sh @@ -8,7 +8,7 @@ if [ "$(basename $PWD)" = "scripts" ]; then fi cd data -module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0 +module load StdEnv/2023 gcc/12.3 blast+/2.14.1 seqkit/2.5.1 mkdir -p res_prll diff --git a/scripts/crunch-sbatch-1gpu.sh b/scripts/crunch-sbatch-1gpu.sh index 0ce50df..9cf5bee 100644 --- a/scripts/crunch-sbatch-1gpu.sh +++ b/scripts/crunch-sbatch-1gpu.sh @@ -4,11 +4,11 @@ #SBATCH --time=0:9:0 #SBATCH --gres=gpu:1 -module load gcc/9.3.0 cuda/11.4 python/3.8.10 +module load StdEnv/2023 gcc/12.3 cuda/12.2 python/3.11 virtualenv --no-download $SLURM_TMPDIR/venv_cupy source $SLURM_TMPDIR/venv_cupy/bin/activate -pip install --no-index numpy==1.24.2 cupy==11.2.0 +pip install --no-index numpy==1.26.4 cupy==12.2.0 time -p python scripts/crunch.py -n 672 --gpu > tg.log & sleep 2 diff --git a/scripts/crunch.sh b/scripts/crunch.sh index 04f55ae..c32f193 100644 --- a/scripts/crunch.sh +++ b/scripts/crunch.sh @@ -20,22 +20,22 @@ if [ "$1" = '--cpu' ]; then exit fi - module load gcc/9.3.0 python/3.8.10 &> /dev/null + module load StdEnv/2023 gcc/12.3 python/3.11 virtualenv --no-download $SLURM_TMPDIR/venv_numpy source $SLURM_TMPDIR/venv_numpy/bin/activate - pip install --no-index numpy==1.24.2 + pip install --no-index numpy==1.26.4 export OMP_NUM_THREADS=$2 time -p python $(dirname $0)/crunch.py -n 672 --cpu > t$2.log & echo "It is running!" elif [ "$1" = '--gpu' ]; then - module load gcc/9.3.0 cuda/11.4 python/3.8.10 &> /dev/null + module load StdEnv/2023 gcc/12.3 cuda/12.2 python/3.11 virtualenv --no-download $SLURM_TMPDIR/venv_cupy source $SLURM_TMPDIR/venv_cupy/bin/activate - pip install --no-index numpy==1.24.2 cupy==11.2.0 + pip install --no-index numpy==1.26.4 cupy==12.2.0 time -p python $(dirname $0)/crunch.py -n 672 --gpu > tg.log & echo "It is running!" diff --git a/scripts/extra/b5D-glost.sh b/scripts/extra/b5D-glost.sh index 33c7382..d96cff8 100644 --- a/scripts/extra/b5D-glost.sh +++ b/scripts/extra/b5D-glost.sh @@ -3,7 +3,7 @@ #SBATCH --mem-per-cpu=2000M #SBATCH --time=0-00:20 -module load gcc/9.3.0 &> /dev/null +module load StdEnv/2023 gcc/12.3 cd $SLURM_TMPDIR cp $HOME/cq-formation-benchmark5D/solutions/b5D.omp ./ diff --git a/scripts/extra/b5D-parallel.sh b/scripts/extra/b5D-parallel.sh index d551ece..7a9769d 100644 --- a/scripts/extra/b5D-parallel.sh +++ b/scripts/extra/b5D-parallel.sh @@ -3,7 +3,7 @@ #SBATCH #SBATCH --time=0-00:20 -module load gcc/9.3.0 &> /dev/null +module load StdEnv/2023 gcc/12.3 cd $SLURM_TMPDIR cp $HOME/cq-formation-benchmark5D/solutions/b5D.omp ./ diff --git a/scripts/extra/cuda-matmul.sh b/scripts/extra/cuda-matmul.sh index 747a409..bcf8498 100644 --- a/scripts/extra/cuda-matmul.sh +++ b/scripts/extra/cuda-matmul.sh @@ -3,7 +3,7 @@ #SBATCH --mem-per-cpu=2000M #SBATCH --time=0-00:10 -module load gcc cuda +module load StdEnv/2023 gcc/12.3 cuda/12.4 export Dim=5760 diff --git a/scripts/extra/nbody-openmp.sh b/scripts/extra/nbody-openmp.sh index 9c0b259..b92ccbe 100644 --- a/scripts/extra/nbody-openmp.sh +++ b/scripts/extra/nbody-openmp.sh @@ -2,7 +2,7 @@ #SBATCH --mem-per-cpu=2000M #SBATCH --time=0-00:10 -module load gcc +module load StdEnv/2023 gcc/12.3 cd $SLURM_TMPDIR cp $HOME/cq-formation-nbody/solutions/openmp/{nbody_omp,parameters.txt} ./ diff --git a/scripts/installer/b5D.sh b/scripts/installer/b5D.sh index 9c1d9f0..6279507 100644 --- a/scripts/installer/b5D.sh +++ b/scripts/installer/b5D.sh @@ -7,5 +7,5 @@ if [ ! -d cq-formation-benchmark5D ]; then fi cd cq-formation-benchmark5D/solutions -module load gcc/9.3.0 +module load StdEnv/2023 gcc/12.3 make diff --git a/scripts/installer/cuda-samples.sh b/scripts/installer/cuda-samples.sh index c086248..50e2b21 100644 --- a/scripts/installer/cuda-samples.sh +++ b/scripts/installer/cuda-samples.sh @@ -2,7 +2,7 @@ cd $HOME -VERSION="11.0" +VERSION="12.1" TAR_GZ="v${VERSION}.tar.gz" DOSSIER="cuda-samples-${VERSION}" @@ -21,6 +21,6 @@ fi cd ${DOSSIER} -module load gcc/9.3.0 cuda/11.4 +module load StdEnv/2023 gcc/12.3 cuda/12.2 export PROJECTS=Samples/matrixMul/Makefile make diff --git a/scripts/installer/nbody.sh b/scripts/installer/nbody.sh index ed5db72..fb766cc 100644 --- a/scripts/installer/nbody.sh +++ b/scripts/installer/nbody.sh @@ -7,6 +7,6 @@ if [ ! -d cq-formation-nbody ]; then fi cd cq-formation-nbody/solutions/openmp -module load gcc/9.3.0 +module load StdEnv/2023 gcc/12.3 sed -i 's/ -march=native//g' Makefile make diff --git a/scripts/inv-mat.sh b/scripts/inv-mat.sh index 329b270..072d567 100644 --- a/scripts/inv-mat.sh +++ b/scripts/inv-mat.sh @@ -2,11 +2,11 @@ #SBATCH --mem-per-cpu=2000M #SBATCH --time=0-00:10 -module load gcc/9.3.0 python/3.8.10 +module load StdEnv/2023 gcc/12.3 python/3.11 virtualenv --no-download $SLURM_TMPDIR/venv_numpy source $SLURM_TMPDIR/venv_numpy/bin/activate -pip install --no-index numpy==1.24.2 +pip install --no-index numpy==1.26.4 if [ "$(basename $PWD)" = "scripts" ]; then cd .. diff --git a/scripts/mpi-hello.sh b/scripts/mpi-hello.sh index a7bb9dd..7f50b57 100644 --- a/scripts/mpi-hello.sh +++ b/scripts/mpi-hello.sh @@ -3,6 +3,6 @@ #SBATCH --mem-per-cpu=1000M #SBATCH --time=0-00:10 -module load gcc/9.3.0 &> /dev/null +module load StdEnv/2023 gcc/12.3 mpirun printenv HOSTNAME OMPI_COMM_WORLD_RANK OMPI_COMM_WORLD_SIZE