From 5634e36daa6fea6263175b751865286097a73df8 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 24 Nov 2025 10:10:09 -0600 Subject: [PATCH 1/3] add backup files to .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 6cd3533..d463c31 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ docs/source/.mypy_cache docs/build docs/doxygen/html/ +*~ -- GitLab From a2e637520ffcd0a0d1c72b0f1f9b36a89c3017da Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 26 Nov 2025 11:52:18 -0600 Subject: [PATCH 2/3] dos2unix, update version numbers for dependencies --- docs/source_docs/references/hpc/Bridges2.rst | 768 +++++++++---------- 1 file changed, 383 insertions(+), 385 deletions(-) diff --git a/docs/source_docs/references/hpc/Bridges2.rst b/docs/source_docs/references/hpc/Bridges2.rst index d26fbeb..1270c2c 100644 --- a/docs/source_docs/references/hpc/Bridges2.rst +++ b/docs/source_docs/references/hpc/Bridges2.rst @@ -1,385 +1,383 @@ -PSC Bridges-2 -============= - -If this is your first time building MFIX-Exa on Bridges-2, please -review the general notes below and `Basics`_ section first. - -* To access Delta-2, you will need PSC account which can be administered - by the NSF ACCESS allocation management system. -* You can find the name of your account(s) and the current balance with - the ``accounts`` command. -* These instructions build MFIX-Exa on the login nodes using `-j8` CPUs. - You may have to decrease this value if there is high traffic - or you may want to increase this value if you are on a compute - node interactively. -* For the dependencies, it is assumed that you have set the - following environment variables: - - .. code:: bash - - export HYPRE_INSTALL_DIR=$HOME/ - export CSG_INSTALL_DIR=$HOME/ - export CSG_LIB_DIR=$HOME/ - export ASCENT_INSTALL_DIR=$HOME/ - - to a path that you have read/write access to. - You will need to recall these paths later if you want to build - MFIX-Exa with the optional dependencies. - -Basics ------- - -Source code -~~~~~~~~~~~ - -Before building, first obtain a copy of the source code -following the instructions on the -`MFIX-Exa website. `_ - -Modules -~~~~~~~ - -There are (basically) no modules loaded by default on Bridges-2. - -.. code:: bash - - module load gcc/10.2.0 # PrgEnv - module load openmpi/4.0.5-gcc10.2.0 # MPI - module load cuda/11.7.1 # for GPU - module load boost/1.75-gcc10.2.0 # for CSG - - -Building MFIX-Exa ------------------ - -CMake 3.20 or higher is required. You are running version 3.11.4 - - - -The commands below are the superbuild instructions, i.e., -AMReX is built as part of the MFIX-Exa build process. -To build MFIX-Exa with hypre, csg and/or ascent dependencies, -you first need to build and install these libraries and their dependencies. -Instructions on building the necessary dependencies are below -and should be successfully installed first. Only the ``gmake`` method of -building MFIX-Exa is currently recommended. - -.. tabs:: - - .. tab:: CPU - - .. code:: bash - - cp -r exec exec.cpu - make -C exec.cpu -j8 \ - COMP=gnu \ - USE_MPI=TRUE \ - USE_OMP=FALSE \ - USE_CUDA=FALSE \ - USE_TINY_PROFILE=FALSE \ - USE_CSG=FALSE \ - USE_HYPRE=FALSE \ - DEBUG=FALSE - - - .. tab:: GPU - - .. code:: bash - - cp -r exec exec.gpu - make -C exec.gpu -j8 \ - COMP=gnu \ - USE_MPI=TRUE \ - USE_OMP=FALSE \ - USE_CUDA=TRUE \ - CUDA_ARCH=70 \ - USE_TINY_PROFILE=FALSE \ - USE_CSG=FALSE \ - USE_HYPRE=FALSE \ - DEBUG=FALSE - - - .. tab:: CPU-full - - .. code:: bash - - export HYPRE_DIR=$HYPRE_INSTALL_DIR - export HYPRE_HOME=$HYPRE_DIR - - export ASCENT_DIR=$ASCENT_INSTALL_DIR - export CONDUIT_DIR=$ASCENT_DIR - - export CSGEB_HOME=$CSG_LIB_DIR - export LDFLAGS="-lgmp -lmpfr -L$CSG_INSTALL_DIR/lib -Wl,-rpath=$CSG_INSTALL_DIR/lib" - cp -r exec exec.cpu.full - make -C exec.cpu.full -j8 \ - COMP=gnu \ - USE_MPI=TRUE \ - USE_OMP=FALSE \ - USE_CUDA=FALSE \ - USE_TINY_PROFILE=FALSE \ - USE_CSG=TRUE \ - USE_HYPRE=TRUE \ - USE_ASCENT=TRUE \ - USE_CONDUIT=TRUE \ - DEBUG=FALSE - - - .. tab:: GPU-full - - .. code:: bash - - export HYPRE_DIR=$HYPRE_INSTALL_DIR - export HYPRE_HOME=$HYPRE_DIR - - export ASCENT_DIR=$ASCENT_INSTALL_DIR - export CONDUIT_DIR=$ASCENT_DIR - - export CSGEB_HOME=$CSG_LIB_DIR - export LDFLAGS="-lgmp -lmpfr -L$CSG_INSTALL_DIR/lib -Wl,-rpath=$CSG_INSTALL_DIR/lib" - cp -r exec exec.gpu.full - make -C exec.gpu.full -j8 COMP=gnu \ - USE_MPI=TRUE \ - USE_OMP=FALSE \ - USE_CUDA=TRUE \ - CUDA_ARCH=70 \ - USE_TINY_PROFILE=FALSE \ - USE_CSG=TRUE \ - USE_HYPRE=TRUE \ - USE_ASCENT=TRUE \ - USE_CONDUIT=TRUE \ - DEBUG=FALSE - - -Optional build dependencies ---------------------------- - -The following dependencies need to be built and installed -prior to following any of the full build instructions above. - -#. HYPRE - - .. tabs:: - - .. tab:: CPU - - .. code:: bash - - git clone https://github.com/hypre-space/hypre.git - pushd hypre/src/ - git checkout v2.26.0 - ./configure --prefix=$HYPRE_INSTALL_DIR --with-MPI - make -j8 install - popd - - .. tab:: GPU - - .. code:: bash - - git clone https://github.com/hypre-space/hypre.git - pushd hypre/src/ - git checkout v2.26.0 - ./configure --prefix=$HYPRE_INSTALL_DIR \ - --without-superlu \ - --disable-bigint \ - --without-openmp \ - --enable-unified-memory \ - --with-MPI \ - --with-cuda \ - --with-gpu-arch='70' \ - --with-cuda-home=$CUDA_HOME \ - --enable-cusparse \ - --enable-curand - make -j8 install - popd - -#. cmake - - You will need cmake to install some of the dependencies below and the Bridges2 - native version is unsupported at the time of this writing. We'll install a - local one. You will need to set - ``export CMAKE_INSTALL_DIR=$HOME/`` - to a path that you have read/write access to. - - .. code:: bash - - wget https://cmake.org/files/v3.23/cmake-3.23.2.tar.gz - tar -zxvf cmake-3.23.2.tar.gz - pushd cmake-3.23.2 - ./bootstrap --prefix=$CMAKE_INSTALL_DIR - make -j8 install - popd - - After installing cmake, you will need to prepend it to your path - - .. code:: bash - - export PATH=$CMAKE_INSTALL_DIR/bin:$PATH - -#. Catch2 - - .. code:: bash - - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 - pushd Catch2/ - cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR - cd build/ - make -j8 install - popd - -#. GMP - - .. code:: bash - - wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz - tar -xf gmp-6.2.1.tar.xz - pushd gmp-6.2.1 - ./configure --prefix=$CSG_INSTALL_DIR - make -j8 install - popd - -#. MPFR - - .. code:: bash - - wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz - tar -xf mpfr-4.1.0.tar.xz - pushd mpfr-4.1.0/ - ./configure --with-gmp=$CSG_INSTALL_DIR --prefix=$CSG_INSTALL_DIR - make -j8 install - popd - -#. CGAL - - .. code:: bash - - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal - pushd cgal/ - cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR - cd build/ - make -j8 install - popd - - -#. PEGTL - - .. code:: bash - - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL - pushd PEGTL/ - cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR - cd build/ - make -j8 install - popd - -#. CSG EB library - - Make sure you have boost loaded before building. (This is intended to be - executed from inside the mfix repo.) - - .. code:: bash - - make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ - PEGTL_HOME=$CSG_INSTALL_DIR \ - CGAL_HOME=$CSG_INSTALL_DIR \ - CATCH2_HOME=$CSG_INSTALL_DIR \ - ENABLE_CGAL=TRUE - -#. Conduit - - .. code:: bash - - git clone --recursive https://github.com/LLNL/conduit.git - pushd conduit/ - git checkout v0.8.6 - mkdir build && cd build - cmake -S ../src -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ - -DENABLE_OPENMP=OFF \ - -DENABLE_MPI=ON \ - -DENABLE_CUDA=OFF \ - -DCMAKE_BUILD_TYPE=Release - make -j8 install - popd - -#. Vtk-m - - .. code:: bash - - git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git - pushd vtk-m/ - git checkout v1.9.0 - mkdir build && cd build/ - cmake -S ../ -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ - -DVTKm_ENABLE_OPENMP=OFF \ - -DVTKm_ENABLE_MPI=ON \ - -DVTKm_ENABLE_CUDA=OFF \ - -DVTKm_USE_64BIT_IDS=OFF \ - -DVTKm_USE_DOUBLE_PRECISION=ON \ - -DVTKm_USE_DEFAULT_TYPES_FOR_ASCENT=ON \ - -DVTKm_NO_DEPRECATED_VIRTUAL=ON \ - -DCMAKE_BUILD_TYPE=Release - make -j8 install - popd - -#. Ascent - - .. code:: bash - - git clone --recursive https://github.com/Alpine-DAV/ascent.git - pushd ascent - git checkout v0.9.0 - mkdir build && cd build/ - cmake -S ../src -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ - -DCONDUIT_DIR=$ASCENT_INSTALL_DIR \ - -DVTKM_DIR=$ASCENT_INSTALL_DIR \ - -DENABLE_VTKH=ON \ - -DENABLE_FORTRAN=OFF \ - -DENABLE_PYTHON=OFF \ - -DENABLE_DOCS=OFF \ - -DBUILD_SHARED_LIBS=ON \ - -DCMAKE_BUILD_TYPE=Release \ - -DENABLE_GTEST=OFF \ - -DENABLE_TESTS=OFF - make -j8 install - popd - - -Running Jobs ------------- - -Common Slurm commands: - -* ``sinfo`` see available/allocated resources -* ``sbatch runit_cpu.sh`` submit a cpu job to the queue -* ``squeue -u USER`` check job status of user USER -* ``squeue -p PARTITION`` check job status of partition PARTITION -* ``scancel JOBID`` kill a job with id JOBID -* ``salloc -N 1 -p GPU -A peb230001p -t 00:02:00 --exclusive --gpus-per-node=8`` grab an entire GPU node for five minutes -* ``salloc -N 1 -p GPU-shared -A peb230001p -t 00:05:00 --gpus-per-node=2`` grab two GPUs interactively on a shared node for five minutes, you can grab up to four ``--gpus-per-node`` - -Example run script for GPU is below. You can mirror the -interactive commands above to convert this into a shared job script. -CPU-only runs have not been tested on this machine. - -.. code:: bash - - #!/bin/bash - #!/bin/bash - #SBATCH -A peb230001p - #SBATCH -N 1 - #SBATCH -p GPU-shared - #SBATCH -t 00:05:00 - #SBATCH --gpus=v100-32:4 - - # load modules - module load gcc/10.2.0 # PrgEnv - module load openmpi/4.0.5-gcc10.2.0 # MPI - module load cuda/11.7.1 # for GPU - module load boost/1.75-gcc10.2.0 # for CSG - - #echo commands to stdout - set -x - - mpirun -np 4 ./mfix inputs.rt > screen.txt - - +PSC Bridges-2 +============= + +If this is your first time building MFIX-Exa on Bridges-2, please +review the general notes below and `Basics`_ section first. + +* To access Delta-2, you will need PSC account which can be administered + by the NSF ACCESS allocation management system. +* You can find the name of your account(s) and the current balance with + the ``accounts`` command. +* These instructions build MFIX-Exa on the login nodes using `-j8` CPUs. + You may have to decrease this value if there is high traffic + or you may want to increase this value if you are on a compute + node interactively. +* For the dependencies, it is assumed that you have set the + following environment variables: + + .. code:: bash + + export HYPRE_INSTALL_DIR=$HOME/ + export CSG_INSTALL_DIR=$HOME/ + export CSG_LIB_DIR=$HOME/ + export ASCENT_INSTALL_DIR=$HOME/ + + to a path that you have read/write access to. + You will need to recall these paths later if you want to build + MFIX-Exa with the optional dependencies. + +Basics +------ + +Source code +~~~~~~~~~~~ + +Before building, first obtain a copy of the source code +following the instructions on the +`MFIX-Exa website. `_ + +Modules +~~~~~~~ + +There are (basically) no modules loaded by default on Bridges-2. + +.. code:: bash + + module load gcc/10.2.0 # PrgEnv + module load openmpi/4.0.5-gcc10.2.0 # MPI + module load cuda/11.7.1 # for GPU + module load boost/1.75-gcc10.2.0 # for CSG + + +Building MFIX-Exa +----------------- + +CMake 3.20 or higher is required. You are running version 3.11.4 + + + +The commands below are the superbuild instructions, i.e., +AMReX is built as part of the MFIX-Exa build process. +To build MFIX-Exa with hypre, csg and/or ascent dependencies, +you first need to build and install these libraries and their dependencies. +Instructions on building the necessary dependencies are below +and should be successfully installed first. Only the ``gmake`` method of +building MFIX-Exa is currently recommended. + +.. tabs:: + + .. tab:: CPU + + .. code:: bash + + cp -r exec exec.cpu + make -C exec.cpu -j8 \ + COMP=gnu \ + USE_MPI=TRUE \ + USE_OMP=FALSE \ + USE_CUDA=FALSE \ + USE_TINY_PROFILE=FALSE \ + USE_CSG=FALSE \ + USE_HYPRE=FALSE \ + DEBUG=FALSE + + + .. tab:: GPU + + .. code:: bash + + cp -r exec exec.gpu + make -C exec.gpu -j8 \ + COMP=gnu \ + USE_MPI=TRUE \ + USE_OMP=FALSE \ + USE_CUDA=TRUE \ + CUDA_ARCH=70 \ + USE_TINY_PROFILE=FALSE \ + USE_CSG=FALSE \ + USE_HYPRE=FALSE \ + DEBUG=FALSE + + + .. tab:: CPU-full + + .. code:: bash + + export HYPRE_DIR=$HYPRE_INSTALL_DIR + export HYPRE_HOME=$HYPRE_DIR + + export ASCENT_DIR=$ASCENT_INSTALL_DIR + export CONDUIT_DIR=$ASCENT_DIR + + export CSGEB_HOME=$CSG_LIB_DIR + export LDFLAGS="-lgmp -lmpfr -L$CSG_INSTALL_DIR/lib -Wl,-rpath=$CSG_INSTALL_DIR/lib" + cp -r exec exec.cpu.full + make -C exec.cpu.full -j8 \ + COMP=gnu \ + USE_MPI=TRUE \ + USE_OMP=FALSE \ + USE_CUDA=FALSE \ + USE_TINY_PROFILE=FALSE \ + USE_CSG=TRUE \ + USE_HYPRE=TRUE \ + USE_ASCENT=TRUE \ + USE_CONDUIT=TRUE \ + DEBUG=FALSE + + + .. tab:: GPU-full + + .. code:: bash + + export HYPRE_DIR=$HYPRE_INSTALL_DIR + export HYPRE_HOME=$HYPRE_DIR + + export ASCENT_DIR=$ASCENT_INSTALL_DIR + export CONDUIT_DIR=$ASCENT_DIR + + export CSGEB_HOME=$CSG_LIB_DIR + export LDFLAGS="-lgmp -lmpfr -L$CSG_INSTALL_DIR/lib -Wl,-rpath=$CSG_INSTALL_DIR/lib" + cp -r exec exec.gpu.full + make -C exec.gpu.full -j8 COMP=gnu \ + USE_MPI=TRUE \ + USE_OMP=FALSE \ + USE_CUDA=TRUE \ + CUDA_ARCH=70 \ + USE_TINY_PROFILE=FALSE \ + USE_CSG=TRUE \ + USE_HYPRE=TRUE \ + USE_ASCENT=TRUE \ + USE_CONDUIT=TRUE \ + DEBUG=FALSE + + +Optional build dependencies +--------------------------- + +The following dependencies need to be built and installed +prior to following any of the full build instructions above. + +#. HYPRE + + .. tabs:: + + .. tab:: CPU + + .. code:: bash + + git clone https://github.com/hypre-space/hypre.git + pushd hypre/src/ + git checkout v2.26.0 + ./configure --prefix=$HYPRE_INSTALL_DIR --with-MPI + make -j8 install + popd + + .. tab:: GPU + + .. code:: bash + + git clone https://github.com/hypre-space/hypre.git + pushd hypre/src/ + git checkout v2.26.0 + ./configure --prefix=$HYPRE_INSTALL_DIR \ + --without-superlu \ + --disable-bigint \ + --without-openmp \ + --enable-unified-memory \ + --with-MPI \ + --with-cuda \ + --with-gpu-arch='70' \ + --with-cuda-home=$CUDA_HOME \ + --enable-cusparse \ + --enable-curand + make -j8 install + popd + +#. cmake + + You will need cmake to install some of the dependencies below and the Bridges2 + native version is unsupported at the time of this writing. We'll install a + local one. You will need to set + ``export CMAKE_INSTALL_DIR=$HOME/`` + to a path that you have read/write access to. + + .. code:: bash + + wget https://cmake.org/files/v3.23/cmake-3.23.2.tar.gz + tar -zxvf cmake-3.23.2.tar.gz + pushd cmake-3.23.2 + ./bootstrap --prefix=$CMAKE_INSTALL_DIR + make -j8 install + popd + + After installing cmake, you will need to prepend it to your path + + .. code:: bash + + export PATH=$CMAKE_INSTALL_DIR/bin:$PATH + +#. Catch2 + + .. code:: bash + + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 + pushd Catch2/ + cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR + cd build/ + make -j8 install + popd + +#. GMP + + .. code:: bash + + wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz + tar -xf gmp-6.2.1.tar.xz + pushd gmp-6.2.1 + ./configure --prefix=$CSG_INSTALL_DIR + make -j8 install + popd + +#. MPFR + + .. code:: bash + + wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz + tar -xf mpfr-4.1.0.tar.xz + pushd mpfr-4.1.0/ + ./configure --with-gmp=$CSG_INSTALL_DIR --prefix=$CSG_INSTALL_DIR + make -j8 install + popd + +#. CGAL + + .. code:: bash + + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal + pushd cgal/ + cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR + cd build/ + make -j8 install + popd + + +#. PEGTL + + .. code:: bash + + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL + pushd PEGTL/ + cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR + cd build/ + make -j8 install + popd + +#. CSG EB library + + Make sure you have boost loaded before building. (This is intended to be + executed from inside the mfix repo.) + + .. code:: bash + + make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ + PEGTL_HOME=$CSG_INSTALL_DIR \ + CGAL_HOME=$CSG_INSTALL_DIR \ + CATCH2_HOME=$CSG_INSTALL_DIR \ + ENABLE_CGAL=TRUE + +#. Conduit + + .. code:: bash + + git clone --recursive https://github.com/LLNL/conduit.git + pushd conduit/ + git checkout v0.8.6 + mkdir build && cd build + cmake -S ../src -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ + -DENABLE_OPENMP=OFF \ + -DENABLE_MPI=ON \ + -DENABLE_CUDA=OFF \ + -DCMAKE_BUILD_TYPE=Release + make -j8 install + popd + +#. Vtk-m + + .. code:: bash + + git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git + pushd vtk-m/ + git checkout v1.9.0 + mkdir build && cd build/ + cmake -S ../ -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ + -DVTKm_ENABLE_OPENMP=OFF \ + -DVTKm_ENABLE_MPI=ON \ + -DVTKm_ENABLE_CUDA=OFF \ + -DVTKm_USE_64BIT_IDS=OFF \ + -DVTKm_USE_DOUBLE_PRECISION=ON \ + -DVTKm_USE_DEFAULT_TYPES_FOR_ASCENT=ON \ + -DVTKm_NO_DEPRECATED_VIRTUAL=ON \ + -DCMAKE_BUILD_TYPE=Release + make -j8 install + popd + +#. Ascent + + .. code:: bash + + git clone --recursive https://github.com/Alpine-DAV/ascent.git + pushd ascent + git checkout v0.9.0 + mkdir build && cd build/ + cmake -S ../src -DCMAKE_INSTALL_PREFIX=$ASCENT_INSTALL_DIR \ + -DCONDUIT_DIR=$ASCENT_INSTALL_DIR \ + -DVTKM_DIR=$ASCENT_INSTALL_DIR \ + -DENABLE_VTKH=ON \ + -DENABLE_FORTRAN=OFF \ + -DENABLE_PYTHON=OFF \ + -DENABLE_DOCS=OFF \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_GTEST=OFF \ + -DENABLE_TESTS=OFF + make -j8 install + popd + + +Running Jobs +------------ + +Common Slurm commands: + +* ``sinfo`` see available/allocated resources +* ``sbatch runit_cpu.sh`` submit a cpu job to the queue +* ``squeue -u USER`` check job status of user USER +* ``squeue -p PARTITION`` check job status of partition PARTITION +* ``scancel JOBID`` kill a job with id JOBID +* ``salloc -N 1 -p GPU -A peb230001p -t 00:02:00 --exclusive --gpus-per-node=8`` grab an entire GPU node for five minutes +* ``salloc -N 1 -p GPU-shared -A peb230001p -t 00:05:00 --gpus-per-node=2`` grab two GPUs interactively on a shared node for five minutes, you can grab up to four ``--gpus-per-node`` + +Example run script for GPU is below. You can mirror the +interactive commands above to convert this into a shared job script. +CPU-only runs have not been tested on this machine. + +.. code:: bash + + #!/bin/bash + #!/bin/bash + #SBATCH -A peb230001p + #SBATCH -N 1 + #SBATCH -p GPU-shared + #SBATCH -t 00:05:00 + #SBATCH --gpus=v100-32:4 + + # load modules + module load gcc/10.2.0 # PrgEnv + module load openmpi/4.0.5-gcc10.2.0 # MPI + module load cuda/11.7.1 # for GPU + module load boost/1.75-gcc10.2.0 # for CSG + + #echo commands to stdout + set -x + + mpirun -np 4 ./mfix inputs.rt > screen.txt -- GitLab From 680d548247e14f9fcece05eecb7de6f39d5afe5f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 26 Nov 2025 11:52:37 -0600 Subject: [PATCH 3/3] update version numbers for dependencies --- docs/source_docs/references/hpc/Crusher.rst | 6 +++--- docs/source_docs/references/hpc/Delta.rst | 6 +++--- docs/source_docs/references/hpc/Frontier.rst | 6 +++--- docs/source_docs/references/hpc/Joule2.rst | 6 +++--- docs/source_docs/references/hpc/Perlmutter.rst | 6 +++--- docs/source_docs/references/hpc/Polaris.rst | 6 +++--- docs/source_docs/references/hpc/Summit.rst | 6 +++--- 7 files changed, 21 insertions(+), 21 deletions(-) diff --git a/docs/source_docs/references/hpc/Crusher.rst b/docs/source_docs/references/hpc/Crusher.rst index 965f980..3cf0dde 100644 --- a/docs/source_docs/references/hpc/Crusher.rst +++ b/docs/source_docs/references/hpc/Crusher.rst @@ -286,7 +286,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -324,7 +324,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -336,7 +336,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Delta.rst b/docs/source_docs/references/hpc/Delta.rst index 7af2fd6..7b269a4 100644 --- a/docs/source_docs/references/hpc/Delta.rst +++ b/docs/source_docs/references/hpc/Delta.rst @@ -327,7 +327,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -360,7 +360,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -372,7 +372,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Frontier.rst b/docs/source_docs/references/hpc/Frontier.rst index beadfb7..7aa0cb1 100644 --- a/docs/source_docs/references/hpc/Frontier.rst +++ b/docs/source_docs/references/hpc/Frontier.rst @@ -256,7 +256,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -282,7 +282,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -294,7 +294,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Joule2.rst b/docs/source_docs/references/hpc/Joule2.rst index 1f0dd06..56de8c9 100644 --- a/docs/source_docs/references/hpc/Joule2.rst +++ b/docs/source_docs/references/hpc/Joule2.rst @@ -342,7 +342,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -375,7 +375,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -387,7 +387,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Perlmutter.rst b/docs/source_docs/references/hpc/Perlmutter.rst index 674a0b9..6f455f7 100644 --- a/docs/source_docs/references/hpc/Perlmutter.rst +++ b/docs/source_docs/references/hpc/Perlmutter.rst @@ -332,7 +332,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -376,7 +376,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR \ -DCMAKE_C_COMPILER=$(which cc) \ @@ -389,7 +389,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Polaris.rst b/docs/source_docs/references/hpc/Polaris.rst index 5d07a63..4c4f7be 100644 --- a/docs/source_docs/references/hpc/Polaris.rst +++ b/docs/source_docs/references/hpc/Polaris.rst @@ -254,7 +254,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -298,7 +298,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -309,7 +309,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ diff --git a/docs/source_docs/references/hpc/Summit.rst b/docs/source_docs/references/hpc/Summit.rst index 20b05e9..3e33019 100644 --- a/docs/source_docs/references/hpc/Summit.rst +++ b/docs/source_docs/references/hpc/Summit.rst @@ -358,7 +358,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v2.13.7 https://github.com/catchorg/Catch2 + git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -380,7 +380,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal + git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ @@ -392,7 +392,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch 3.2.2 https://github.com/taocpp/PEGTL + git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR cd build/ -- GitLab