Merge pull request #34 from drangara/perlmutter_instructions

Perlmutter

===========

Coming soon!

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. <https://docs.nersc.gov/systems/perlmutter/>`_

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

  .. code:: bash

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

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

  Login with your Iris password + (Google) Aunthenticator 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:

  .. code:: bash

     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

  .. code:: bash

      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

------

Clone the source code

~~~~~~~~~~~~~~~~~~~~~

Before building, first clone the code, checkout the desired branch, 

(the default is develop), update the submodules and create a build directory 

(for cmake).

.. code:: bash

    git clone https://mfix.netl.doe.gov/gitlab/exa/mfix.git

    cd mfix

    git checkout develop

    git submodule update --init

    mkdir build && cd build/

Modules

~~~~~~~

All of the build instructions below have been tested with the 

following modules and environment helpers

.. code:: bash 

    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

.. code:: bash 

    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 

seperately below.  

cmake

~~~~~

.. tabs::

   .. tab:: CPU

      .. code:: bash

         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

   .. tab:: GPU

      .. code:: bash

         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \

               -DMFIX_MPI=yes \

               -DMFIX_OMP=no \

               -DMFIX_CSG=no \

               -DMFIX_HYPRE=no \

               -DMFIX_GPU_BACKEND=CUDA \

               -DAMReX_CUDA_ARCH=6.0 \

               -DCMAKE_CUDA_ARCHITECTURES="60" \

               -DGPUS_PER_SOCKET=1 \

               -DGPUS_PER_NODE=2 \

               -DAMReX_TINY_PROFILE=no \

               -DCMAKE_BUILD_TYPE=Release \

               ../

         make -j8

   .. tab:: CPU-full

      .. code:: bash

         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/csg-deps

         export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_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 \

               ../mfix

         make -j8

   .. tab:: GPU-full

      .. code:: bash

         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/csg-deps

         export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_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 \

               ../mfix

         make -j8

gmake

~~~~~

.. tabs::

   .. tab:: CPU

      .. code:: bash

         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

   .. tab:: GPU

      .. code:: bash

         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

   .. tab:: CPU-full

      .. code:: bash

         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

   .. tab:: GPU-full

      .. code:: bash

         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. 

#. HYPRE

   .. tabs::

      .. tab:: CPU

         .. code:: bash

            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

      .. tab:: GPU

         .. code:: bash

            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

#. Catch2

   .. code:: bash

      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

#. GMP

   .. code:: bash

      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

#. MPFR

   .. code:: bash

      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

#. Boost

   .. code:: bash

      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

#. CGAL

   .. code:: bash

      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

#. PEGTL

   .. code:: bash

      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

#. CSG EB library  (**gmake**) 

   For the gmake install instructions, you need to install

   `libcsgeb` to `$CSG_LIB_DIR` using either cmake or gmake:

   .. tabs::

      .. tab:: cmake

         .. code:: bash

            cd subprojects/csg-eb

            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

            cd build

            make -j8 install

      .. tab:: gmake

         .. code:: bash

            make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \

            PEGTL_HOME=$CSG_DIR \

            CGAL_HOME=$CSG_DIR \

            CATCH2_HOME=$CSG_DIR \

            ENABLE_CGAL=TRUE

#. Conduit

   .. code:: bash

      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

#. Vtk-m

   .. code:: bash

      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

#. Ascent

   .. code:: bash

      git clone --recursive https://github.com/Alpine-DAV/ascent.git

      pushd ascent

      git checkout v0.8.4

      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 

      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: 

.. tabs::

   .. tab:: CPU

      .. code:: bash

         #!/bin/bash

         #SBATCH --job-name build_mfix-exa

         #SBATCH -o stdout.%x-%j

         #SBATCH -e stderr.%x-%j

         #SBATCH --account=<ACCOUNT>

         ###SBATCH --qos=<QOS>

         #SBATCH --constraint=cpu

         #SBATCH --time=00:20:00

         #SBATCH --nodes=1

         # load needed modules 

         # NOTE: DONT PURGE AND RESET

         module load PrgEnv-gnu/8.3.3

         module load cudatoolkit/11.5

         module load cmake/3.22.0

         # compiler environment hints

         export CC=cc

         export CXX=CC

         export FC=ftn

         ## make

         cmake -DMFIX_MPI=yes \

               -DMFIX_OMP=no \

               -DMFIX_CSG=no \

               -DMFIX_HYPRE=no \

               -DAMReX_TINY_PROFILE=yes \

               -DCMAKE_BUILD_TYPE=Release \

               ../mfix

         make -j 32

   .. tab:: GPU

      .. code:: bash

         #!/bin/bash

         #SBATCH --job-name build_mfix-exa

         #SBATCH -o stdout.%x-%j

         #SBATCH -e stderr.%x-%j

         #SBATCH --account=<ACCOUNT>

         ###SBATCH --qos=<QOS>

         #SBATCH --constraint=gpu

         #SBATCH --time=00:20:00

         #SBATCH --nodes=1

         # load needed modules 

         # NOTE: DONT PURGE AND RESET

         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

         # optimize CUDA compilation for A100

         export AMREX_CUDA_ARCH=8.0

         # compiler environment hints

         export CC=cc

         export CXX=CC

         export FC=ftn

         export CUDACXX=$(which nvcc)

         export CUDAHOSTCXX=CC

         ## make

         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=yes \

               -DCMAKE_BUILD_TYPE=Release \

               ../mfix

         make -j 32