OLCF Summit

If this is your first time building MFIX-Exa on OLCF’s Summit, 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 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. 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

module load cmake/3.23.2
module load gcc/9.3.0

Do NOT purge your default modules. You do not need to load an MPI module, this is handled by the preloaded spectrum-mpi module. The GPU-enabled builds additionally require

module load cuda/11.5.2

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++ \
      -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

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

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=$(which gcc)
export CXX=$(which g++)
export FC=$(which gfortran)
mkdir $HOME/scratch && cd $HOME/scratch

Note

For whatever reason, building hypre with GPU support does not like this. So if you are building everything all at once, start with hypre with cuda and then set your compilers and build the rest (including hypre without cuda).

  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

  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. 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

  5. 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

  6. 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

module load boost/1.77.0
export Boost_INCLUDE_DIR="-I$OLCF_BOOST_ROOT/include"

export CSG_DIR=$CSG_INSTALL_DIR
export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR

cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_LIB_DIR \
      -DCMAKE_BUILD_TYPE="Release"
cd build
make -j8 install

  7. 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=$ASCENT_INSTALL_DIR \
      -DCMAKE_BUILD_TYPE=Release \
      -DENABLE_OPENMP=OFF \
      -DENABLE_MPI=ON \
      -DENABLE_CUDA=OFF \
      -DCMAKE_C_COMPILER=$(which gcc) \
      -DCMAKE_CXX_COMPILER=$(which g++)
make -j8 install
popd

  8. 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
make -j8 install
popd

  9. 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
make -j8 install
popd

Running Jobs

Common Slurm commands:

  • bsub runit_cpu.sh submit a cpu job to the queue

  • bjobs -u USER check job status of user USER

  • bkill JOBID kill a job with id JOBID

  • bsub -W 0:20 -nnodes 1 -P <ALLOC> grab a node interactively for 20 minutes

Example run scripts for GPU is below. For CPU-only, you remove module load cuda, set --gpu_per_rs 0 and remove --bind packed:1 from the run line.

#!/bin/bash
#BSUB -P CFD122
#BSUB -W 00:20
#BSUB -nnodes 2
#BSUB -J MFIX
#BSUB -o MFIXo.%J
#BSUB -e MFIXe.%J
module load gcc/9.3.0
module load cuda/11.5.2
module load mpfr/4.0.2
module load boost/1.77.0
module list
set -x
omp=1
export OMP_NUM_THREADS=${omp}

jsrun --nrs 12 --tasks_per_rs 1 --cpu_per_rs 1 --gpu_per_rs 1 --launch_distribution packed --bind packed:1 ./mfix inputs > screen.txt