# 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 seperately 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

    cmake -DCMAKE_C_COMPILER=gcc \
          -DCMAKE_CXX_COMPILER=g++ \
          -DCMAKE_Fortran_COMPILER=gfortran \
          -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=no \
          -DMFIX_HYPRE=no \
          -DMFIX_GPU_BACKEND=CUDA \
          -DGPUS_PER_NODE=4 \
          -DAMReX_TINY_PROFILE=no \
          -DCMAKE_BUILD_TYPE=Release \
          ../
    make -j8

    export HYPRE_DIR=$HYPRE_INSTALL_DIR
    export HYPRE_ROOT=$HYPRE_DIR
    export HYPRE_LIBRARIES=$HYPRE_DIR/lib
    export HYPRE_INCLUDE_DIRS=$HYPRE_DIR/include

    export ASCENT_DIR=$ASCENT_INSTALL_DIR
    export CONDUIT_DIR=$ASCENT_DIR
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$ASCENT_DIR/lib/cmake/ascent
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$ASCENT_DIR/lib/cmake/conduit

    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_INSTALL_DIR

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

    export HYPRE_DIR=$HYPRE_INSTALL_DIR
    export HYPRE_ROOT=$HYPRE_DIR
    export HYPRE_LIBRARIES=$HYPRE_DIR/lib
    export HYPRE_INCLUDE_DIRS=$HYPRE_DIR/include

    export ASCENT_DIR=$ASCENT_INSTALL_DIR
    export CONDUIT_DIR=$ASCENT_DIR
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$ASCENT_DIR/lib/cmake/ascent
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$ASCENT_DIR/lib/cmake/conduit

    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_INSTALL_DIR

    cmake -DCMAKE_C_COMPILER=gcc \
          -DCMAKE_CXX_COMPILER=g++ \
          -DCMAKE_Fortran_COMPILER=gfortran \
          -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=yes \
          -DMFIX_HYPRE=yes \
          -DAMReX_ASCENT=yes \
          -DAMReX_CONDUIT=yes \
          -DMFIX_GPU_BACKEND=CUDA \
          -DGPUS_PER_NODE=4 \
          -DAMReX_TINY_PROFILE=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

       git clone https://github.com/hypre-space/hypre.git
       pushd hypre/src/
       git checkout v2.26.0
       cmake -S . -B build \
                  -DCMAKE_INSTALL_PREFIX=$HYPRE_INSTALL_DIR \
                  -DHYPRE_WITH_DSUPERLU=OFF \
                  -DHYPRE_ENABLE_BIGINT=OFF \
                  -DHYPRE_WITH_OPENMP=OFF \
                  -DHYPRE_ENABLE_SHARED=ON \
                  -DHYPRE_WITH_MPI=ON \
                  -DHYPRE_WITH_CUDA=ON \
                  -DCMAKE_CUDA_ARCHITECTURES=80 \
                  -DHYPRE_ENABLE_CUSPARSE=ON \
                  -DHYPRE_ENABLE_CURAND=ON \
                  -DCMAKE_CXX_COMPILER=$(which nvc++) \
                  -DMPI_CXX_COMPILER=$(which CC) \
                  -DCMAKE_C_COMPILER=$(which nvc) \
                  -DMPI_C_COMPILER=$(which cc) \
                  -DHYPRE_INSTALL_PREFIX=$HYPRE_INSTALL_DIR
       cd build/
       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'