# Perlmutter

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

- The documentation for this system can be found here.

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

      ssh <username>@perlmutter-p1.nersc.gov
      ssh <username>@saul-p1.nersc.gov

  Login with your Iris password + (Google) Authenticator passcode.

- 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 $SCRATCH 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

Warning

Currently, the `cmake GPU build` with hypre support links but does not run. We are still investigating, but recommend using `gmake` on Perlmutter at this time.

## 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 load PrgEnv-gnu/8.3.3
    module load cmake/3.22.0

    export CC=cc
    export CXX=CC
    export FC=ftn

The GPU-enabled builds additionally require

    module load cudatoolkit/11.5

    export CUDACXX=$(which nvcc)
    export CUDAHOSTCXX=CC

    export MPICH_GPU_SUPPORT_ENABLED=1
    export CRAY_ACCEL_TARGET=nvidia80

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 -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 -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=no \
          -DMFIX_HYPRE=no \
          -DMFIX_GPU_BACKEND=CUDA \
          -DAMReX_CUDA_ARCH=8.0 \
          -DGPUS_PER_SOCKET=4 \
          -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 -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 -DMFIX_MPI=yes \
          -DMFIX_OMP=no \
          -DMFIX_CSG=yes \
          -DMFIX_HYPRE=yes \
          -DAMReX_ASCENT=yes \
          -DAMReX_CONDUIT=yes \
          -DMFIX_GPU_BACKEND=CUDA \
          -DAMReX_CUDA_ARCH=8.0 \
          -DGPUS_PER_SOCKET=4 \
          -DGPUS_PER_NODE=4 \
          -DAMReX_TINY_PROFILE=no \
          -DCMAKE_BUILD_TYPE=Release \
          ../
    make -j8

### gmake

    make -C exec -j8 \
         COMP=gnu \
         USE_MPI=TRUE \
         USE_OMP=FALSE \
         USE_CUDA=FALSE \
         USE_TINY_PROFILE=FALSE \
         USE_CSG=FALSE \
         USE_HYPRE=FALSE \
         DEBUG=FALSE

    make -C exec -j8
         COMP=gnu \
         USE_MPI=TRUE \
         USE_OMP=FALSE \
         USE_CUDA=TRUE \
         CUDA_ARCH=8.0 \
         USE_TINY_PROFILE=FALSE \
         USE_CSG=FALSE \
         USE_HYPRE=FALSE \
         DEBUG=FALSE

    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"

    make -C exec -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

    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"

    make -C exec -j8 COMP=gnu \
         USE_MPI=TRUE \
         USE_OMP=FALSE \
         USE_CUDA=TRUE \
         CUDA_ARCH=8.0 \
         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.

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=$HYPRE_INSTALL_DIR \
                   --without-superlu \
                   --disable-bigint \
                   --without-openmp \
                   --enable-shared  \
                   --with-MPI \
                   --with-cuda \
                   --with-gpu-arch='80' \
                   --with-cuda-home=$CUDA_HOME \
                   --enable-cusparse \
                   --enable-curand
       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 --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

5. 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

6. CGAL

       git clone --depth 1 --branch v5.3 https://github.com/CGAL/cgal
       pushd cgal/
       cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR \
                           -DCMAKE_C_COMPILER=$(which cc) \
                           -DCMAKE_CXX_COMPILER=$(which CC)
       cd build/
       make -j8 install
       popd

7. 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

8. CSG EB library (gmake)

   For the gmake install instructions, you need to install libcsgeb to $CSG_LIB_DIR using either cmake or gmake:

       cd subprojects/csg-eb

       export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_INSTALL_DIR

       cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_LIB_DIR \
                           -DCMAKE_BUILD_TYPE=Release

       cd build
       make -j8 install

       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

9. Conduit

       git clone --recursive https://github.com/LLNL/conduit.git
       pushd conduit/
       git checkout v0.8.4
       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:

- 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 –nodes 1 –qos interactive –time 01:00:00 –constraint gpu –gpus 4 –account=<ACCOUNT> grab 1 GPU node (for up to 1 hrs)

Example run scripts:

    #!/bin/bash
    #SBATCH --job-name run-mfix-exa
    #SBATCH -o stdout.%x-%j
    #SBATCH -e stderr.%x-%j
    #SBATCH --account=<ACCOUNT>
    #SBATCH --qos=<QOS>
    #SBATCH --constraint=cpu
    #SBATCH --time=00:02:00
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=16

    # load modules used for build
    module load PrgEnv-gnu/8.3.3
    module load cmake/3.22.0

    srun -n 32 --cpu-bind=cores -c 16 ./mfix inputs > screen.txt

    #!/bin/bash
    #SBATCH --job-name run-mfix-exa
    #SBATCH -o stdout.%x-%j
    #SBATCH -e stderr.%x-%j
    #SBATCH --account=<ACCOUNT>
    #SBATCH --qos=<QOS>
    #SBATCH --constraint=gpu
    #SBATCH --time=00:02:00
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=4  #fixed unless --ntasks/4 is non-int
    #SBATCH --cpus-per-task=32   #fixed
    #SBATCH --gpus-per-task=1    #fixed
    #SBATCH --gpu-bind=single:1  #fixed

    nrs=8

    # load modules used for build
    module load PrgEnv-gnu/8.3.3
    module load cudatoolkit/11.5
    module load cmake/3.22.0

    # GPU-aware MPI
    export MPICH_GPU_SUPPORT_ENABLED=1

    # necessary to use CUDA-Aware MPI and run a job
    export CRAY_ACCEL_TARGET=nvidia80

    srun -n $nrs -G $nrs -c 1 --gpus-per-task 1 --gpu-bind=single:1 ./mfix inputs > screen.txt