Commit fb2f2643 authored by William D. Fullmer's avatar William D. Fullmer
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clean up Joule HPC page

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docs/source_docs/getting_started/Hpc.rst

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.. toctree::

   :caption: NETL Systems

   :caption: DOE Systems

   :maxdepth: 1



   hpc/Joule2

   hpc/Joule2v2



.. toctree::

   :caption: LCF Systems

   :maxdepth: 1



   hpc/Cori

   hpc/Crusher

   hpc/Perlmutter

   hpc/Polaris

   hpc/Spock

   hpc/Summit





.. toctree::

   :caption: NETL Systems

   :maxdepth: 1



   hpc/Joule2

docs/source_docs/getting_started/hpc/Cori.rst

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Summit

=======



Coming soon!

docs/source_docs/getting_started/hpc/Joule2.rst

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docs/source_docs/getting_started/hpc/Joule2v2.rst

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Joule 2.0

==========



Notes

-----



* These instructions build 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, we assume you will set the environment 

  path variables `HYPRE_INSTALL_DIR`, `CSG_INSTALL_DIR`,  

  `ASCENT_INSTALL_DIR` and `$CSG_LIB_DIR` to a descriptive 

  path that the user has read/write access to. 

* After building the `mfix` executable (with cmake), you can 

  build the PIC-to-DEM restarter app by: `cmake --build . --target pic2dem`





Basics

------



Access

>>>>>>>



You need an NETL HPC account, yubikey and the `HPC client <https://hpc.netl.doe.gov/support/hpc-client/index.html>`_





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 -p gpu` grab a GPU node interactively (for up to 48 hrs) 

* `salloc -N 2 -p dev -q dev` grab two development nodes (for up to 2 hrs)





Clone the source code

>>>>>>>>>>>>>>>>>>>>>

   

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

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



.. 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 purge

    module load cmake/3.23.1

    module load gnu/9.3.0

    module load openmpi/4.0.4_gnu9.3



The GPU-enabled builds additionally require



.. code:: bash 



    module load cuda/11.3



Full builds, i.e., with external dependencies, also require setting 

certain environment variables as discussed below. 





Building MFIX-Exa

-----------------



cmake

>>>>>



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.  



.. 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



         module load boost/1.77.0_gnu9.3

         export Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.77.0/gnu/9.3.0/openmpi/4.0.4/include"



         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 \

               ../mfix

         make -j8



   .. tab:: GPU-full



      .. code:: bash



         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



         module load boost/1.77.0_gnu9.3

         export BOOST_ROOT="/nfs/apps/Libraries/Boost/1.77.0/gnu/9.3.0/openmpi/4.0.4"



         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=6.0 \

              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



         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



         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









Full-build dependencies

-----------------------



The following dependencies will need to be installed prior to following any of the full build instructions above. 



#. Set environment helpers



   .. code:: bash



      export CC=$(which mpicc)

      export CXX=$(which mpic++)

      export F77=$(which mpif77)

      export FC=$(which mpifort)

      export F90=$(which mpif90)

      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='60' \

                        --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



#. 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 instaill instructions you will 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_gnu9.3



            export Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.77.0/gnu/9.3.0/openmpi/4.0.4/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

            cd build

            make -j8 install



      .. tab:: gmake



         .. code:: bash



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

            BOOST_HOME=/nfs/apps/Libraries/Boost/1.77.0/gnu/9.3.0/openmpi/4.0.4 \

            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

      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

docs/source_docs/getting_started/hpc/Spock.rst

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Spock

======



Coming soon!