add Summit build instructions, WARNING there is an error in the GPU hypre...

Summit

=======

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 <https://my.olcf.ornl.gov/account-application-new>`_

  and an RSA token. 

* The name of hte 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:

  .. 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. 

  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

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

.. code:: bash 

    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

.. code:: bash 

    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 

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

         module load mpfr/4.0.2

         module load boost/1.77.0

         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

         export BOOST_ROOT=$OLCF_BOOST_ROOT

         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \

               -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

   .. tab:: GPU-full

      .. code:: bash

         module load mpfr/4.0.2

         module load boost/1.77.0

         export HYPRE_DIR=$HYPRE_INSTALL_DIR/hypre

         export HYPRE_ROOT=$HYPRE_DIR

         export HYPRE_LIBRARIES=$HYPRE_DIR/lib

         export HYPRE_INCLUDE_DIRS=$HYPRE_DIR/include

         export ASCENT_DIR=$ASCENT_INSTALL_DIR/ascent

         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

         export BOOST_ROOT=$OLCF_BOOST_ROOT

         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \

               -DBoost_INCLUDE_DIR="$BOOST_ROOT/include" \

               -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=6.0 \

               -DCMAKE_CUDA_ARCHITECTURES="60" \

               -DGPUS_PER_SOCKET=1 \

               -DGPUS_PER_NODE=2 \

               -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=7.0 \

              USE_TINY_PROFILE=FALSE \

              USE_CSG=FALSE \

              USE_HYPRE=FALSE \

              DEBUG=FALSE

   .. tab:: CPU-full

      .. code:: bash

         module load mpfr/4.0.2

         module load boost/1.77.0

         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="-lmpfr -L$CSG_INSTALL_DIR/lib -Wl,-rpath=$CSG_INSTALL_DIR"

         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

         module load mpfr/4.0.2

         module load boost/1.77.0

         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$CSG_INSTALL_DIR -Wl,-rpath=$CSG_INSTALL_DIR"

         make -C exec -j8 COMP=gnu \

              USE_MPI=TRUE \

              USE_OMP=FALSE \

              USE_CUDA=TRUE \

              CUDA_ARCH=6.0 \

              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. 

#. Set environment helpers

   .. code:: bash

      export CC=$(which gcc)

      export CXX=$(which g++)

      export FC=$(which gfortran)

      mkdir $HOME/scratch && cd $HOME/scratch 

#. 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="70" \

                        --with-cuda-home=$OLCF_CUDA_ROOT \

                        --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

#. 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

            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

      .. tab:: gmake

         .. code:: bash

            export CSG_DIR=$CSG_INSTALL_DIR

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

            BOOST_HOME=$OLCF_BOOST_ROOT \

            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 v0.8.6

      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

#. 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 \

            -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

#. Ascent

   .. code:: bash

      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. 

.. code:: bash

   #!/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

Coming soon!