Update docs

Charles G Waldmanrequested to merge
cgw-docs into main
  • add granular temperature to IC section
  • Joule2 -> Joule3, update build instructions (WIP)

Merge request reports

docs/source_docs/references/hpc/Crusher.rst

+1 −4
Changes for docs/source_docs/references/hpc/Crusher.rst: 1 added line, 4 removed lines.
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OLCF Crusher TDS

================



If this is your first time building MFIX-Exa on Joule2, please 

If this is your first time building MFIX-Exa on Joule3, please

review the general notes below and `Basics`_ section first.



* To access Summit, you will need an
@@ -540,6 +540,3 @@ Example run scripts: 
         srun -N $nodes -n $nrs -c1 --ntasks-per-gpu=1 --gpu-bind=closest ./mfix inputs > screen.txt



         #cpu: srun -N $nodes -n $nrs -c1 ./mfix inputs > screen.txt

docs/source_docs/references/hpc/Frontier.rst

+1 −2
Changes for docs/source_docs/references/hpc/Frontier.rst: 1 added line, 2 removed lines.
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OLCF Frontier

=============



If this is your first time building MFIX-Exa on Joule2, please 

If this is your first time building MFIX-Exa on Joule3, please

review the general notes below and `Basics`_ section first.



* To access Summit, you will need an
@@ -428,4 +428,3 @@ Example run scripts: 
   srun -N $nodes -n $nrs -c1 --ntasks-per-gpu=1 --gpu-bind=closest ./mfix inputs > screen.txt



   #cpu srun -N $nodes -n $nrs -c1 ./mfix inputs > screen.txt

docs/source_docs/references/hpc/Joule2.rst→docs/source_docs/references/hpc/Joule3.rst

+21 −19
Changes for docs/source_docs/references/hpc/Joule3.rst: 21 added lines, 19 removed lines.
Original line number Diff line number Diff line 
Joule 2.0

==========



If this is your first time building MFIX-Exa on Joule2, please

If this is your first time building MFIX-Exa on Joule3, please

review the general notes below and `Basics`_ section first.



* To access Joule2, you will need an NETL HPC account,

* To access Joule3, you will need an NETL HPC account,

  a yubikey (2FA) and the

  `HPC client. <https://hpc.netl.doe.gov/support/hpc-client/index.html>`_

* These instructions build MFIX-Exa on the login nodes using `-j8` CPUs.
@@ -54,15 +54,15 @@ 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

    module load cmake

    module load gnu/13.2.0

    module load openmpi/4.1.5/gnu/13.2.0



The GPU-enabled builds additionally require



.. code:: bash



    module load cuda/11.3

    module load cuda



Full builds that utilize external dependencies, also require setting

certain environment variables as discussed below.
@@ -89,6 +89,8 @@ cmake 


      .. code:: bash



         mkdir build; cd build



         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \

               -DMFIX_MPI=yes \
@@ -105,6 +107,8 @@ cmake 


      .. code:: bash



         mkdir build; cd build



         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \

               -DMFIX_MPI=yes \
@@ -138,8 +142,9 @@ cmake 
         export CSG_DIR=$CSG_INSTALL_DIR

         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"

         export Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/include/"



         mkdir build; cd build



         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \
@@ -159,6 +164,8 @@ cmake 


      .. code:: bash



         mkdir build; cd build



         export HYPRE_DIR=$HYPRE_INSTALL_DIR

         export HYPRE_ROOT=$HYPRE_DIR

         export HYPRE_LIBRARIES=$HYPRE_DIR/lib
@@ -173,7 +180,7 @@ cmake 
         export CMAKE_PREFIX_PATH=$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"

         export BOOST_ROOT="/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5"



         cmake -DCMAKE_C_COMPILER=gcc \

               -DCMAKE_CXX_COMPILER=g++ \
@@ -312,7 +319,6 @@ prior to following any of the full build instructions above. 


            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
@@ -323,7 +329,6 @@ prior to following any of the full build instructions above. 


            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 \
@@ -342,7 +347,7 @@ prior to following any of the full build instructions above. 


   .. code:: bash



      git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2

      git clone --depth 1 https://github.com/catchorg/Catch2

      pushd Catch2/

      cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR

      cd build/
@@ -375,7 +380,7 @@ prior to following any of the full build instructions above. 


   .. code:: bash



      git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal

      git clone --depth 1  https://github.com/CGAL/cgal

      pushd cgal/

      cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR

      cd build/
@@ -387,7 +392,7 @@ prior to following any of the full build instructions above. 


   .. code:: bash



      git clone --branch 3.2.8 https://github.com/taocpp/PEGTL

      git clone  https://github.com/taocpp/PEGTL

      pushd PEGTL/

      cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$CSG_INSTALL_DIR

      cd build/
@@ -409,7 +414,7 @@ prior to following any of the full build instructions above. 


            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 Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/include"

            export CSG_DIR=$CSG_INSTALL_DIR

            export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR
@@ -424,7 +429,7 @@ prior to following any of the full build instructions above. 
         .. 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 \

            BOOST_HOME=/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.4 \

            PEGTL_HOME=$CSG_DIR \

            CGAL_HOME=$CSG_DIR \

            CATCH2_HOME=$CSG_DIR \
@@ -436,7 +441,6 @@ prior to following any of the full build instructions above. 


      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 \

            -DENABLE_OPENMP=OFF \
@@ -452,7 +456,6 @@ prior to following any of the full build instructions above. 


      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 \
@@ -472,7 +475,6 @@ prior to following any of the full build instructions above. 


      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 \

docs/source_docs/references/hpc.rst

+1 −2
Changes for docs/source_docs/references/hpc.rst: 1 added line, 2 removed lines.
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@@ -29,5 +29,4 @@ Follow the guide here instead of the generic instructions. 
   :caption: NETL Systems

   :maxdepth: 0



   hpc/Joule2

   hpc/Joule3

docs/source_docs/references/units.rst

+20 −17
Changes for docs/source_docs/references/units.rst: 20 added lines, 17 removed lines.
Original line number Diff line number Diff line
@@ -9,43 +9,46 @@ units. 
+--------------------------------+-----------------------------------------+

| Physical quantity              | MFIX-Exa SI unit                        |

+================================+=========================================+

+--------------------------------+-----------------------------------------+

| amount of substance            | mole [:math:`mol`]                      |

+--------------------------------+-----------------------------------------+

| length                         | meter [:math:`m`]                       |

| density                        | [:math:`kg \cdot m^{-3}`]               |

+--------------------------------+-----------------------------------------+

| mass                           | kilogram [:math:`kg`]                   |

| diffusivity                    | [:math:`m^2 \cdot s^{-1}`]              |

+--------------------------------+-----------------------------------------+

| time                           | second [:math:`s`]                      |

| dynamic viscosity              | [:math:`Pa \cdot s`]                    |

+--------------------------------+-----------------------------------------+

| energy                         | Joule [:math:`J`]                       |

+--------------------------------+-----------------------------------------+

| force                          | Newton [:math:`N`]                      |

+--------------------------------+-----------------------------------------+

| temperature                    | Kelvin [:math:`K`]                      |

| granular temperature           | [:math m^{2} \cdot s{-2}                |

+--------------------------------+-----------------------------------------+

| pressure                       | Pascal [:math:`Pa`]                     |

| heat of formation              | [:math:`J \cdot kg^{-1}`]               |

+--------------------------------+-----------------------------------------+

| energy                         | Joule [:math:`J`]                       |

| length                         | meter [:math:`m`]                       |

+--------------------------------+-----------------------------------------+

| power                          | Watt [:math:`W`]                        |

| mass                           | kilogram [:math:`kg`]                   |

+--------------------------------+-----------------------------------------+

| density                        | [:math:`kg \cdot m^{-3}`]               |

| molecular weight               | [:math:`kg \cdot mol^{-1}`]             |

+--------------------------------+-----------------------------------------+

| velocity                       | [:math:`m \cdot s^{-1}`]                |

| power                          | Watt [:math:`W`]                        |

+--------------------------------+-----------------------------------------+

| dynamic viscosity              | [:math:`Pa \cdot s`]                    |

| pressure                       | Pascal [:math:`Pa`]                     |

+--------------------------------+-----------------------------------------+

| diffusivity                    | [:math:`m^2 \cdot s^{-1}`]              |

| reaction rate (Euler-Euler)    | [:math:`mol \cdot m^{-3} \cdot s^{-1}`] |

+--------------------------------+-----------------------------------------+

| specific heat capacity         | [:math:`J \cdot kg^{-1} \cdot K^{-1}`]  |

| reaction rate (Euler-Lagrange) | [:math:`mol \cdot s^{-1}`]              |

+--------------------------------+-----------------------------------------+

| thermal conductivity           | [:math:`W \cdot m^{-1} \cdot K^{-1}`]   |

| specific heat capacity         | [:math:`J \cdot kg^{-1} \cdot K^{-1}`]  |

+--------------------------------+-----------------------------------------+

| spring coefficient             | [:math:`N \cdot m^{-1}`]                |

+--------------------------------+-----------------------------------------+

| molecular weight               | [:math:`kg \cdot mol^{-1}`]             |

| temperature                    | Kelvin [:math:`K`]                      |

+--------------------------------+-----------------------------------------+

| heat of formation              | [:math:`J \cdot kg^{-1}`]               |

| thermal conductivity           | [:math:`W \cdot m^{-1} \cdot K^{-1}`]   |

+--------------------------------+-----------------------------------------+

| reaction rate (Euler-Euler)    | [:math:`mol \cdot m^{-3} \cdot s^{-1}`] |

| time                           | second [:math:`s`]                      |

+--------------------------------+-----------------------------------------+

| reaction rate (Euler-Lagrange) | [:math:`mol \cdot s^{-1}`]              |

| velocity                       | [:math:`m \cdot s^{-1}`]                |

+--------------------------------+-----------------------------------------+