Polaris

If this is your first time building MFIX-Exa on Polaris, please review the general notes below and Basics section first.

  • The documentation for this system can be found here.

  • Polaris can be accessed from a system with ssh client installed. These connections also work from NETL’s SciLAN and Joule:

    ssh <username>@polaris.alcf.anl.gov
    

    Login with your Mobilepass token. No need to prefix or append with anything.

  • 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.

  • The cmake instructions compile to a build directory. The gmake instructions compile to a exec directory.

  • For the dependencies, it is assumed that you have set the following environment variables:

    export HYPRE_INSTALL_DIR=$HOME/<path/to/my/hypre-install-dir>
    export CSG_INSTALL_DIR=$HOME/<path/to/my/csg-dep-install-dir>
    export CSG_LIB_DIR=$HOME/<path/to/my/csg-lib-install-dir>
    export ASCENT_INSTALL_DIR=$HOME/<path/to/my/ascent-install-dir>
    

    to a path that you have read/write access to, such as inside the /lus/grand/projects/<account>/ space corresponding to your account. You will need to recall these paths later if you want to build MFIX-Exa with the optional dependencies.

  • After building the mfix executable (with cmake), you can build the PIC-to-DEM restarter app by executing the following command in the build directory

    cmake --build . --target pic2dem
    

Basics

Source code

Before building, first obtain a copy of the source code following the instructions on the MFIX-Exa website.

Modules

All of the build instructions below have been tested with the following modules and environment helpers

module swap PrgEnv-nvhpc PrgEnv-gnu
module load cmake/3.23.2

The GPU-enabled builds additionally require

module load nvhpc-mixed

export MPICH_GPU_SUPPORT_ENABLED=1
export AMREX_CUDA_ARCH=8.0

Full builds that utilize external dependencies, also require setting certain environment variables as discussed below.

Building MFIX-Exa

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. There are two primary methods of building the code cmake and gmake which are provided separately below.

cmake

cmake -DCMAKE_C_COMPILER=gcc \
      -DCMAKE_CXX_COMPILER=g++ \
      -DCMAKE_Fortran_COMPILER=gfortran \
      -DMFIX_MPI=yes \
      -DMFIX_OMP=no \
      -DMFIX_GPU_BACKEND=NONE \
      -DAMReX_TINY_PROFILE=no \
      -DMFIX_CSG=no \
      -DMFIX_HYPRE=no \
      -DCMAKE_BUILD_TYPE=Release \
      ../
make -j8

Optional build dependencies

The following dependencies need to be built and installed prior to following any of the full build instructions above.

  1. Set environment helpers

    export CC=$(which cc)
    export CXX=$(which CC)
    
    mkdir $HOME/scratch && cd $HOME/scratch
    
  2. HYPRE

    The GPU build for HYPRE seems to only work with cmake.

    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
    
  3. Catch2

    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
    
  4. GMP

    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
    
  5. MPFR

    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
    
  6. Boost

    wget https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.gz
    tar -zxvf boost_1_81_0.tar.gz
    pushd boost_1_81_0/
    ./bootstrap.sh
    ./b2 install --prefix=$CSG_INSTALL_DIR
    popd
    
  7. CGAL

    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
    
  8. PEGTL

    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
    
  9. Conduit

    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
    
  10. Vtk-m

    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
    
  11. Ascent

    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:

  • qsub runit.sh submit a job to the queue

  • qstat -u USER check job status of user USER

  • qdel JOBID kill a job with id JOBID

  • qsub -I -l select=1:system=polaris -l walltime=0:60:00 -l filesystems=home:gran -q debug -A <ACCOUNT> grab 1 GPU node (for up to 1 hrs)

Example run scripts:

Example run script for GPU is below. For CPU-only, remove module load nvhpc-mixed and export MPICH_GPU_SUPPORT_ENABLED=1, and the options ppn and --cpu-bind core from the run line.

#!/bin/bash
#PBS -A <ACCOUNT>
#PBS -q prod
#PBS -l select=64:system=polaris
#PBS -l filesystems=home:eagle
#PBS -l walltime=04:00:00
#PBS -N alcc_tk1
#PBS -k doe
#PBS -o stdout
#PBS -e stderr
#PBS -m be
##PBS -M <email addresses>    # Be default, mail goes to the submitter, use this option to add others (uncomment to use)

NNODES=`wc -l < $PBS_NODEFILE`       # number of nodes requested
RPN=4                                # assume 1 GPU = 1 resource, 4 GPUs / node
RES=$((NNODES*RPN))                  # total number of resources

echo 'procs = '$procs' '
echo '$PBS_O_WORKDIR = '$PBS_O_WORKDIR' '
cd $PBS_O_WORKDIR

module swap PrgEnv-nvhpc PrgEnv-gnu
module load nvhpc-mixed

export MPICH_GPU_SUPPORT_ENABLED=1

set +x                               # report all commands to stderr
env                                  # save the env

mpiexec -n $RES -ppn $RPN --cpu-bind core ./mfix inputs > screen.1
wait 3
mpiexec -n $RES -ppn $RPN --cpu-bind core ./mfix inputs > screen.2
wait 7
mpiexec -n $RES -ppn $RPN --cpu-bind core ./mfix inputs > screen.3

echo 'eof EOF EOR eor'