# OLCF Crusher TDS

If this is your first time building MFIX-Exa on Joule2, please review the general notes below and Basics section first.

- To access Summit, you will need an OLCF account and an RSA token.

- The name of the MFIX-Exa account is `cfd122`

- 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 ASCENT_INSTALL_DIR=$HOME/<path/to/my/ascent-install-dir>
      export BOOST_INSTALL_DIR=$HOME/<path/to/my/boost-install-dir>

  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. Boost is only needed for `PrgEnv-cray`; there is a module available for `PrgEnv-gnu`.

- 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

Warning

MFIX-Exa currently experiences a floating point exception when running with ascent support. Make sure all of the fpe traps in your inputs are off.

## Basics

### Source code

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

### Modules

OLCF provides three programming environments on Crusher: `PrgEnv-amd`, `PrgEnv-cray`, and `PrgEnv-gnu`. We’ve had the most success with the latter two and only provide build instructions for them below. Note that in the `PrgEnv-gnu` env you will set different compilers if you are compiling for CPU only (e.g., most of the dependencies) or if you are compiling for the GPU with HIP-support.

    module purge
    module reset
    module load cmake/3.23.2
    module load cpe/22.08
    module load craype-accel-amd-gfx90a
    module load rocm/5.2.0
    module load cray-mpich/8.1.21
    module load cce/15.0.0  # must reload after rocm

    export MPICH_GPU_SUPPORT_ENABLED=1

    export CFLAGS="-I${ROCM_PATH}/include"
    export CXXFLAGS="-I${ROCM_PATH}/include"
    export LDFLAGS="-L${ROCM_PATH}/lib -lamdhip64"

Modules

    module purge
    module reset
    module swap PrgEnv-cray PrgEnv-gnu/8.3.3
    module load cmake/3.23.2
    module load craype-accel-amd-gfx90a
    module load cray-mpich/8.1.21
    module load rocm/5.2.0
    module load cce/14.0.2
    module load boost/1.79.0

CPU compilers

    export CC=$(which cc)
    export CXX=$(which CC)
    export FC=$(which ftn)

GPU compilers

    export CC=$(which hipcc)
    export CXX=$(which hipcc)

    export MPICH_GPU_SUPPORT_ENABLED=1    # GPU-aware MPI

    export CFLAGS="-I${MPICH_DIR}/include -I${ROCM_PATH}/include"
    export CXXFLAGS="-I$OLCF_BOOST_ROOT/include -I${MPICH_DIR}/include -I${ROCM_PATH}/include"
    export LDFLAGS="-L${MPICH_DIR}/lib -L${CRAY_MPICH_ROOTDIR}/gtl/lib -I${ROCM_PATH}/lib -lmpi -lmpi_gtl_hsa"
    export HIPFLAGS="--amdgpu-target=gfx90a"

## 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. These instructions are currently only provided for `cmake`.

    cmake -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

    export AMREX_AMD_ARCH=gfx90a

    cmake -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=no \
          -DMFIX_HYPRE=no \
          -DMFIX_GPU_BACKEND=HIP \
          -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 CSG_DIR=$CSG_INSTALL_DIR
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR

    export BOOST_HOME=$MY_INSTALL_DIR/boost            #PrgEnv-cray ONLY
    export Boost_INCLUDE_DIR="-I$BOOST_HOME/include"   #PrgEnv-cray ONLY

    cmake -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 \
          ../mfix
    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 CSG_DIR=$CSG_INSTALL_DIR
    export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR

    export BOOST_HOME=$MY_INSTALL_DIR/boost            #PrgEnv-cray ONLY
    export Boost_INCLUDE_DIR="-I$BOOST_HOME/include"   #PrgEnv-cray ONLY

    export AMREX_AMD_ARCH=gfx90a

    cmake -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=yes \
          -DMFIX_HYPRE=yes \
          -DAMReX_ASCENT=yes \
          -DAMReX_CONDUIT=yes \
          -DMFIX_GPU_BACKEND=HIP \
          -DGPUS_PER_NODE=8 \
          -DAMReX_TINY_PROFILE=no \
          -DCMAKE_BUILD_TYPE=Release \
          ../mfix
    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. HYPRE

       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
       ./configure --prefix=$HYPRE_INSTALL_DIR \
                   --without-superlu \
                   --disable-bigint \
                   --without-openmp \
                   --enable-shared \
                   --with-hip \
                   --with-gpu-arch=gfx90a \
                   --enable-rocsparse \
                   --enable-rocrand \
                   --enable-unified-memory \
                   --enable-device-memory-pool \
                   --with-MPI-lib-dirs="${MPICH_DIR}/lib ${CRAY_MPICH_ROOTDIR}/gtl/lib ${ROCM_PATH}/lib" \
                   --with-MPI-libs="mpi mpi_gtl_hsa amdhip64" \
                   --with-MPI-include="${MPICH_DIR}/include {ROCM_PATH}/include"
       make -j8 install
       popd

2. 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

3. 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

4. MPFR

       wget https://www.mpfr.org/mpfr-current/mpfr-4.2.0.tar.gz
       tar -zxvf mpfr-4.2.0.tar.gz
       pushd mpfr-4.2.0/
       ./configure --prefix=$CSG_INSTALL_DIR \
                   --with-gmp-lib=${CSG_INSTALL_DIR}/lib \
                   --with-gmp-include=${CSG_INSTALL_DIR}/include
       make -j8 install
       popd

5. 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

6. 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

   Warning

   For some reason, something in PEGTL does not set the experimental filesystem when installing in `PrgEnv-gnu` (but it does in `PrgEnv-cray`). So you you have to force that manually. One hack to do so is shown below.

   Make sure that “experimental” precedes filesystem on or near lines 47 and 51 in `CSG_INSTALL_DIR/include/tao/pegtl/internal/filesystem.hpp`

       ...
       #include <experimental/filesystem>

       namespace TAO_PEGTL_NAMESPACE::internal
       {
       namespace filesystem = ::std::experimental::filesystem;
       ...

7. 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=$BOOST_INSTALL_DIR
       popd

   Warning

   Only needed for PrgEnv-cray. This appears to build with the native gcc/g++ compilers, not the cray wrapped cc/CC compilers, but “it works.”

8. 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 \
             -DCMAKE_BUILD_TYPE=Release \
             -DENABLE_OPENMP=OFF \
             -DENABLE_MPI=ON \
             -DENABLE_CUDA=OFF \
             -DENABLE_PYTHON=OFF \
             -DENABLE_GTEST=OFF \
             -DENABLE_TESTS=OFF
       make -j8 install
       popd

9. 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 \
             -DCMAKE_BUILD_TYPE=Release \
             -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 \
             -DVTKm_ENABLE_TESTING=OFF
       make -j8 install
       popd

10. 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=$ASCENT_INSTALL_DIR \
              -DCMAKE_BUILD_TYPE=Release \
              -DCONDUIT_DIR=$ASCENT_INSTALL_DIR \
              -DVTKM_DIR=$ASCENT_INSTALL_DIR \
              -DENABLE_VTKH=ON \
              -DENABLE_FORTRAN=OFF \
              -DENABLE_PYTHON=OFF \
              -DENABLE_DOCS=OFF \
              -DBUILD_SHARED_LIBS=ON \
              -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 -A CFD122_crusher -J build -t 01:00:00` grab an interactive node for an hour

Example run scripts:

    #!/bin/bash -l

    #SBATCH -A CFD122_crusher
    #SBATCH -J mfix-timing
    #SBATCH -o job_%x-%j.out
    #SBATCH -e job_%x-%j.err
    #SBATCH --threads-per-core=1
    #SBATCH --exclude=crusher[026,027,028,081,126,114,115]
    #SBATCH -t 00:05:00
    #SBATCH -N 2

    nodes=2
    nrs=12
    omp=1

    module purge
    module reset
    module load cpe/22.08
    module load craype-accel-amd-gfx90a
    module load rocm/5.2.0
    module load cray-mpich/8.1.21
    module load cce/15.0.0  # must be loaded after rocm

    export OMP_NUM_THREADS=$omp
    export MPICH_GPU_SUPPORT_ENABLED=1    # remove for cpu only
    #export FI_MR_CACHE_MAX_COUNT=0       # libfabric disable caching
    export FI_MR_CACHE_MONITOR=memhooks   # alt cache monitor
    export FI_CXI_RX_MATCH_MODE=software
    export FI_CXI_REQ_BUF_SIZE=12582912
    export FI_CXI_REQ_BUF_MIN_POSTED=6
    export FI_CXI_DEFAULT_CQ_SIZE=131072

    srun -N $nodes -n $nrs -c1 --ntasks-per-gpu=1 --gpu-bind=closest ./mfix inputs > screen.txt

    #cpu: srun -N $nodes -n $nrs -c1 ./mfix inputs > screen.txt

    #!/bin/bash -l

    #SBATCH -A CFD122_crusher
    #SBATCH -J mfix-timing
    #SBATCH -o job_%x-%j.out
    #SBATCH -e job_%x-%j.err
    #SBATCH --threads-per-core=1
    #SBATCH --exclude=crusher[026,027,028,081,126,114,115]
    #SBATCH -t 00:05:00
    #SBATCH -N 2

    nodes=2
    nrs=12
    omp=1

    module purge
    module reset
    module load cpe/22.08
    module load craype-accel-amd-gfx90a
    module load rocm/5.2.0
    module load cray-mpich/8.1.21
    module load cce/15.0.0  # must be loaded after rocm

    export OMP_NUM_THREADS=$omp
    export MPICH_GPU_SUPPORT_ENABLED=1    # remove for cpu only
    #export FI_MR_CACHE_MAX_COUNT=0       # libfabric disable caching
    export FI_MR_CACHE_MONITOR=memhooks   # alt cache monitor
    export FI_CXI_RX_MATCH_MODE=software
    export FI_CXI_REQ_BUF_SIZE=12582912
    export FI_CXI_REQ_BUF_MIN_POSTED=6
    export FI_CXI_DEFAULT_CQ_SIZE=131072

    srun -N $nodes -n $nrs -c1 --ntasks-per-gpu=1 --gpu-bind=closest ./mfix inputs > screen.txt

    #cpu: srun -N $nodes -n $nrs -c1 ./mfix inputs > screen.txt