From 74c259b36100e1401f3325007d130685ad23e0ac Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:22:26 +0200 Subject: [PATCH 1/9] load foss toolchain instead of intel in mpi examples --- .../Compiling-and-testing-your-software-on-the-HPC/mpihello.pbs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/Compiling-and-testing-your-software-on-the-HPC/mpihello.pbs b/intro-HPC/examples/Compiling-and-testing-your-software-on-the-HPC/mpihello.pbs index 9d4783308e9..47aeea0c757 100644 --- a/intro-HPC/examples/Compiling-and-testing-your-software-on-the-HPC/mpihello.pbs +++ b/intro-HPC/examples/Compiling-and-testing-your-software-on-the-HPC/mpihello.pbs @@ -12,6 +12,6 @@ cd $PBS_O_WORKDIR # load the environment module purge -module load intel +module load foss mpirun ./mpihello From 7c89ab1e42aa3e0391abfba2d6e85b4b7a4e9c23 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:27:56 +0200 Subject: [PATCH 2/9] Update TensorFlow_GPU.sh --- intro-HPC/examples/HPC-UGent-GPU-clusters/TensorFlow_GPU.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/HPC-UGent-GPU-clusters/TensorFlow_GPU.sh b/intro-HPC/examples/HPC-UGent-GPU-clusters/TensorFlow_GPU.sh index ff4e2aa558c..52c8be06ba0 100644 --- a/intro-HPC/examples/HPC-UGent-GPU-clusters/TensorFlow_GPU.sh +++ b/intro-HPC/examples/HPC-UGent-GPU-clusters/TensorFlow_GPU.sh @@ -2,7 +2,7 @@ #PBS -l walltime=5:0:0 #PBS -l nodes=1:ppn=quarter:gpus=1 -module load TensorFlow/2.6.0-foss-2021a-CUDA-11.3.1 +module load TensorFlow/2.11.0-foss-2022a-CUDA-11.7.0 cd $PBS_O_WORKDIR python example.py From b12962f9dd2d89906e25e4c983d68946f9f3a56c Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:28:55 +0200 Subject: [PATCH 3/9] Update multi_core.sh --- intro-HPC/examples/Job-script-examples/multi_core.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/Job-script-examples/multi_core.sh b/intro-HPC/examples/Job-script-examples/multi_core.sh index ce7426bff03..3a38689de0b 100644 --- a/intro-HPC/examples/Job-script-examples/multi_core.sh +++ b/intro-HPC/examples/Job-script-examples/multi_core.sh @@ -2,7 +2,7 @@ #PBS -N mpi_hello ## job name #PBS -l nodes=2:ppn=all ## 2 nodes, all cores per node #PBS -l walltime=2:00:00 ## max. 2h of wall time -module load intel/2017b +module load foss/2023a module load vsc-mympirun ## We don't use a version here, this is on purpose # go to working directory, compile and run MPI hello world cd $PBS_O_WORKDIR From 2ee6a103d7c6288bc632afc41aeb0c42739740f8 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:29:49 +0200 Subject: [PATCH 4/9] Update single_core.sh --- intro-HPC/examples/Job-script-examples/single_core.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/Job-script-examples/single_core.sh b/intro-HPC/examples/Job-script-examples/single_core.sh index f6ed99259e9..a406b09931d 100644 --- a/intro-HPC/examples/Job-script-examples/single_core.sh +++ b/intro-HPC/examples/Job-script-examples/single_core.sh @@ -2,7 +2,7 @@ #PBS -N count_example ## job name #PBS -l nodes=1:ppn=1 ## single-node job, single core #PBS -l walltime=2:00:00 ## max. 2h of wall time -module load Python/3.6.4-intel-2018a +module load Python/3.11.3-GCCcore-12.3.0 # copy input data from location where job was submitted from cp $PBS_O_WORKDIR/input.txt $TMPDIR # go to temporary working directory (on local disk) & run From 9e3df695617a7051305a26c01a95e6f93b163d59 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:34:39 +0200 Subject: [PATCH 5/9] Update jobscript.sh --- intro-HPC/examples/MATLAB/jobscript.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/MATLAB/jobscript.sh b/intro-HPC/examples/MATLAB/jobscript.sh index 3a785317b70..849289c329a 100644 --- a/intro-HPC/examples/MATLAB/jobscript.sh +++ b/intro-HPC/examples/MATLAB/jobscript.sh @@ -7,7 +7,7 @@ # # make sure the MATLAB version matches with the one used to compile the MATLAB program! -module load MATLAB/2018a +module load MATLAB/2022b-r5 # use temporary directory (not $HOME) for (mostly useless) MATLAB log files # subdir in $TMPDIR (if defined, or /tmp otherwise) From d3af0c598eb61d05c52b66552557f43d5bc96e4e Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:35:14 +0200 Subject: [PATCH 6/9] Update mpi_hello.pbs --- .../examples/Multi-core-jobs-Parallel-Computing/mpi_hello.pbs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/Multi-core-jobs-Parallel-Computing/mpi_hello.pbs b/intro-HPC/examples/Multi-core-jobs-Parallel-Computing/mpi_hello.pbs index 7101571d64d..ffb42b14fa7 100644 --- a/intro-HPC/examples/Multi-core-jobs-Parallel-Computing/mpi_hello.pbs +++ b/intro-HPC/examples/Multi-core-jobs-Parallel-Computing/mpi_hello.pbs @@ -11,6 +11,6 @@ cd $PBS_O_WORKDIR # load the environment -module load intel +module load foss mpirun ./mpi_hello From ec5b75a770a577b7bbd0481a097002c8df511a48 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:37:13 +0200 Subject: [PATCH 7/9] Update OpenFOAM_damBreak.sh --- intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh b/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh index dab57a4cd33..021303e6715 100644 --- a/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh +++ b/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh @@ -2,7 +2,7 @@ #PBS -l walltime=1:0:0 #PBS -l nodes=1:ppn=4 # check for more recent OpenFOAM modules with 'module avail OpenFOAM' -module load OpenFOAM/6-intel-2018a +module load OpenFOAM/11-foss-2023a source $FOAM_BASH # purposely not specifying a particular version to use most recent mympirun module load vsc-mympirun From 00e800ba7add40a20432668c8971fba1b7059a33 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:38:04 +0200 Subject: [PATCH 8/9] Update mpihello.pbs --- intro-HPC/examples/Program-examples/04_MPI_C/mpihello.pbs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/Program-examples/04_MPI_C/mpihello.pbs b/intro-HPC/examples/Program-examples/04_MPI_C/mpihello.pbs index c31d6002c5b..86e8e49271c 100644 --- a/intro-HPC/examples/Program-examples/04_MPI_C/mpihello.pbs +++ b/intro-HPC/examples/Program-examples/04_MPI_C/mpihello.pbs @@ -13,6 +13,6 @@ cd $PBS_O_WORKDIR # load the environment module purge -module load intel +module load foss mpirun ./mpihello From e1c0f30de68c76d43e4da0ee8a5d823cff93c0b2 Mon Sep 17 00:00:00 2001 From: lara Date: Mon, 5 Aug 2024 12:50:54 +0200 Subject: [PATCH 9/9] fix link to OpenFOAM example --- intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh b/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh index 021303e6715..ca1991e1a1e 100644 --- a/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh +++ b/intro-HPC/examples/OpenFOAM/OpenFOAM_damBreak.sh @@ -15,7 +15,7 @@ export MYMPIRUN_VARIABLESPREFIX=WM_PROJECT,FOAM,MPI export WORKDIR=$VSC_SCRATCH_NODE/$PBS_JOBID # for single-node jobs mkdir -p $WORKDIR # damBreak tutorial, see also https://cfd.direct/openfoam/user-guide/dambreak -cp -r $FOAM_TUTORIALS/multiphase/interFoam/laminar/damBreak/damBreak $WORKDIR +cp -r $FOAM_TUTORIALS/incompressibleVoF/damBreakLaminar/damBreak $WORKDIR cd $WORKDIR/damBreak echo "working directory: $PWD" # pre-processing: generate mesh