Merge branch 'mr/cmake-fetch'

Building MFiX-Exa with CMake

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

There are two options to building MFiX-Exa with cmake:

CMake build is a two-step process. First ``cmake`` is invoked to create

configuration files and makefiles in a chosen directory (``builddir``).

Next, the actual build is performed by invoking ``make`` from within ``builddir``.

The CMake build process is summarized as follows:

o **SUPERBUILD (default):** Utilities download and build AMReX as part

.. highlight:: console

::

    mkdir /path/to/builddir

    cd    /path/to/builddir

    cmake [options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] /path/to/mfix

    make

In the above snippet, ``[options]`` indicates one or more options for the

customization of the build, as described later in this section.

If the option ``CMAKE_BUILD_TYPE`` is omitted,

``CMAKE_BUILD_TYPE=Release`` is assumed.

There are two modes to build MFiX-Exa with cmake:

o **SUPERBUILD (recommended):** AMReX is downloaded and built as part

of the MFiX-Exa build process. This method is strongly encouraged as it

ensures configure options for MFiX-Exa and AMReX are consistent.

ensures that the configuration options for MFiX-Exa and AMReX are consistent.

o **Using an existing AMReX Library:** MFiX-Exa is linked to an existing

o **STANDALONE:** MFiX-Exa source code is built separately and linked to an existing

AMReX installation. This is ideal for continuous integration severs (CI)

and regression testing applications. AMReX library version must meet

MFiX-Exa requirements.

and regression testing applications. AMReX library version and configuration options

must meet MFiX-Exa requirements.

.. note::

   **MFiX-Exa requires CMake 3.14 or higher.**

SUPERBUILD Instructions (recommended)

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

When building in **SUPERBUILD** mode, MFiX-Exa build system will take

care of downloading, configuring and installing AMReX as part of the

MFiX-Exa build. The following commands build MFiX-Exa and AMReX in a

single step.

By default MFiX-Exa CMake looks for an existing AMReX installation on the system. If none is found, it falls back to **SUPERBUILD** mode.

In this mode, MFiX-Exa CMake inherents AMReX CMake targets and configuration options, that is, MFiX-Exa and AMReX are configured and built as a single entity

Assuming no valid AMReX installation is present on the target system, and ``AMReX_ROOT`` is not set (see :ref:`sec:build:standalone`), the following code will build MFiX-Exa in **SUPERBUILD** mode:

.. code:: shell

    > cd mfix

    > mkdir build

    > cd build

    > cmake CONFIG_OPTIONS ..

    > cmake [amrex options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] ..

    > make -j

AMReX is built the first time the ``make`` command is issued. No

external installation of AMReX is needed. However, internet access to

the AMReX github repository is required. The optional string

``CONFIG_OPTIONS`` allows to customize the build of both AMReX and

MFiX-Exa. ``CONFIG_OPTIONS`` is a list of one or more configuration

options given in the form **-D**\ *OPTION=VALUE*\ \`.

``[amrex options]`` in the snippet above is a list of any of the AMReX configuration options listed in the `AMReX user guide <https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html#building-with-cmake>`_

The table below lists configuration options, possible values, and their

effect on the build. Options prefixed by ``AMREX_`` are specific to the

build of AMReX.

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

| Option name     | Description                  | Possible values  | Default     |

|                 |                              |                  | value       |

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

| DEBUG           | Build in debug mode          | ON/OFF           | OFF         |

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

| CMAKE\_Fortran\ | User-defined Fortran flags   | valid F90        | None        |

| _FLAGS          | for MFiX build               | compiler flags   |             |

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

| CMAKE\_CXX\_FLA | User-defined C++ flags for   | valid C++        | None        |

| GS              | MFiX build                   | compiler flags   |             |

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

| AMREX\_Fortran\ | User-defined Fortran flags   | valid F90        | None        |

| _FLAGS          | for AMReX build              | compiler flags   |             |

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

| AMREX\_CXX\_FLA | User-defined C++ flags for   | valid C++        | None        |

| GS              | AMReX build                  | compiler flags   |             |

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

| ENABLE\_MPI     | Enable build with MPI        | 0/1              | 1           |

|                 |                              |                  |             |

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

| ENABLE\_OMP     | Enable build with OpenMP     | 0/1              | 0           |

|                 |                              |                  |             |

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

| ENABLE\_FPE     | Build with Floating-Point    | 0/1              | 0           |

|                 | Exceptions checks            |                  |             |

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

| ENABLE\_PTESTS  | Include tests for projection | 0/1              | 0           |

|                 | method in Ctest suite        |                  |             |

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

| ENABLE\_STESTS  | Include tests for SIMPLE     | 0/1              | 1           |

|                 | method in Ctest suite        |                  |             |

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

| AMREX\_ENABLE\_ | Enable build with MPI        | 0/1              | 1           |

| MPI             |                              |                  |             |

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

| AMREX\_ENABLE\_ | Enable build with OpenMP     | 0/1              | 0           |

| OMP             |                              |                  |             |

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

| AMREX\_ENABLE\_ | Enable double precision      | 0/1              | 1           |

| DP              |                              |                  |             |

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

| AMREX\_ENABLE\_ | Enable double precision in   | 0/1              | 1           |

| DP\_PARTICLES   | particles classes            |                  |             |

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

| AMREX\_ENABLE\_ | Include profiling info       | 0/1              | 0           |

| BASE\_PROFILE   |                              |                  |             |

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

| AMREX\_ENABLE\_ | Include tiny profiling info  | 0/1              | 0           |

| TINY\_PROFILE   |                              |                  |             |

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

| AMREX\_ENABLE\_ | Include communicators        | 0/1              | 0           |

| COMM\_PROFILE   | profiling info               |                  |             |

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

| AMREX\_ENABLE\_ | Include trace profiling info | 0/1              | 0           |

| TRACE\_PROFILE  |                              |                  |             |

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

| AMREX\_ENABLE\_ | Include memory profiling     | 0/1              | 0           |

| MEM\_PROFILE    | info                         |                  |             |

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

| AMREX\_ENABLE\_ | Include backtrace info       | 0/1              | 0           |

| BACKTRACE       |                              |                  |             |

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

| AMREX\_ENABLE\_ | Include profile parser       | 0/1              | 0           |

| PROFPARSER      |                              |                  |             |

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

| AMREX\_ENABLE\_ | Build position-independent   | 0/1              | 0           |

| PIC             | code                         |                  |             |

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

| AMREX\_ENABLE\_ | Build position-independent   | 0/1              | 0           |

| ASSERTION       | code                         |                  |             |

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

| AMREX\_GIT\_COM | AMReX commit to be used in   | valid git commit | None        |

| MIT             | the build                    | id/branch        |             |

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

| AMREX\_INSTALL\ | Global path to AMReX install | valid global     | None        |

| _DIR            | directory                    | path             | (superbuild |

|                 |                              |                  | )           |

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

Working with the AMReX submodule

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

``SUPERBUILD mode is enabled automatically when AMREX_INSTALL_DIR is not given.``

**SUPERBUILD** mode relies on a git submodule to checkout the AMReX git repository.

If the AMReX submodule is not initialized, **SUPERBUILD** mode will initialize it and checkout 

the AMReX commit the submodule is pointing to.

Instead, if the AMReX submodule has already been manually initialized and a custom commit has been checked out,

**SUPERBUILD** mode will use that commit. For MFiX-Exa development or testing, you may need to build with a different

branch or release of AMReX.

Example: build mfix with custom fortran flags, AMReX profiling enabled

and single precision particles:

The ``subprojects/amrex`` directory is a Git repo, so use all standard Git

commands. Either ``cd subprojects/amrex`` to run Git commands in the ``amrex``

directory, or use ``git -C subprojects/amrex`` in the MFiX-Exa repo. For

instance, to build with the ``my-amrex-branch`` branch of the AMReX repo:

::

.. code:: shell

    > git -C subprojects/amrex checkout my-amrex-branch

    > git status

    ...

    modified:   subprojects/amrex (new commits)

The branch ``my-amrex-branch`` will then be used when building MFiX-Exa.

To revert to the default version of the AMReX submodule, run ``git submodule

update``:

.. code:: shell

    > git submodule update

    > git status

    ...

    nothing to commit, working tree clean

You can edit, commit, pull, and push AMReX changes from ``subprojects/amrex``.

AMReX development is outside the scope of this document. Run ``git status`` in

the top-level MFix-Exa repo to see whether the AMReX submodule has new commits,

modified files, or untracked files.

The CMake variables ``AMREX_GIT_COMMIT_DEVELOP`` and

``AMREX_GIT_COMMIT_DEVELOP`` have been removed. Instead, to update the AMReX

submodule referenced by MFiX-Exa:

.. code:: shell

    cmake -DMFiX_FFLAGS_OVERRIDES="custom flags" -DAMREX_ENABLE_BASE_PROFILE=1 -DAMREX_ENABLE_DP_PARTICLES=0 ..

    > git -C subprojects/amrex checkout UPDATED_AMREX_COMMIT_SHA1

    > git add subprojects/amrex

    > git commit -m 'Updating AMReX version'

Building MFiX-Exa using a separate AMReX installation (no superbuild)

This will only update the AMReX SHA-1 referenced by MFiX-Exa. Uncommitted AMReX

changes and untracked AMReX files under ``subprojects/amrex`` are not added by

``git add subprojects/amrex``. (To commit to the AMReX repo, change directories

to ``subprojects/amrex`` and run Git commands there, before ``git add

subprojects/amrex``.)

.. note::

    Only update the AMReX submodule reference in coordination with the other

    MFiX-Exa developers!

.. _sec:build:standalone:

**STANDALONE** instructions

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

Build AMReX Library

Building AMReX 

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

Clone AMReX from the official Git repository and checkout the

*development* branch.

*development* branch:

.. code:: shell

.. code:: shell

    > cmake . AMREX_CONFIG_OPTIONS \

          -DENABLE_PARTICLES=1 \

          -DENABLE_AMRDATA=1 \

          -DENABLE_EB=1 \

          -DENABLE_3D_NODAL_MLMG=1 \

          -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir

    > mkdir build

    > cd build

    > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] -DENABLE_PARTICLES=yes -DENABLE_AMRDATA=yes -DENABLE_EB=yes [other amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir ..

    > make install

Here,\ ``AMREX_CONFIG_OPTIONS`` are optional configure options for AMReX. Please

refer to the AMReX user guide for a list of all the possible configuration

options. The only options required are **-DENABLE\_PARTICLES=1**,

**-DENABLE\_AMRDATA=1**, **-DENABLE\_EB=1**, and **-DENABLE_3D_NODAL_MLMG=1**.

The options **ENABLE\_PARTICLES=yes**, **ENABLE\_AMRDATA=yes**, and **ENABLE\_EB=yes** are required by MFiX-Exa. ``[other amrex options]`` in the snippet above refers to any other AMReX configuration option in addition to the required ones. Please refer to the `AMReX user guide <https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html#building-with-cmake>`_ for more details on building AMReX with CMake.

Building MFiX-Exa

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

Clone and build MFiX-Exa.

Clone and build MFiX-Exa:

.. code:: shell

    > git clone http://mfix.netl.doe.gov/gitlab/exa/mfix.git

    > mkdir build

    > cd build

    > cmake CONFIG_OPTIONS -DAMREX_INSTALL_DIR=/absolute/path/to/amrex/installdir ..

    > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [mfix options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir ..

    > make -j

Here, ``CONFIG_OPTIONS`` are MFiX-Exa specific configuration options,

that is, any option NOT prefixed by ``AMREX_`` in the table above.

Options prefixed by ``AMREX_`` are always ignored when using an external

AMReX installation.

Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search

``/absolute/path/to/amrex/installdir`` before searching system paths

for an available AMReX installation.

``AMReX_ROOT`` can also be set as an environmental variable instead of passing it as a command line option.

``[mfix options]`` indicates any of the configuration option listed in the table below.

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

| Option name     | Description                  | Possible values  | Default     |

|                 |                              |                  | value       |

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

| CMAKE\_Fortran\ | User-defined Fortran flags   | valid Fortran    | None        |

| _FLAGS          |                              | compiler flags   |             |

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

| CMAKE\_CXX\     | User-defined C++ flags       | valid C++        | None        |

| _FLAGS          |                              | compiler flags   |             |

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

| CMAKE\_CUDA\    | User-defined CUDA flags      | valid CUDA       | None        |

| _FLAGS          |                              | compiler flags   |             |

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

| ENABLE\_MPI     | Enable build with MPI        | no/yes           | yes         |

|                 |                              |                  |             |

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

| ENABLE\_OMP     | Enable build with OpenMP     | no/yes           | no          |

|                 |                              |                  |             |

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

| ENABLE\_CUDA    | Enable build with CUDA       | no/yes           | no          |

|                 |                              |                  |             |

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

| ENABLE\_HYPRE   | Enable HYPRE support         | no/yes           | no          |

|                 |                              |                  |             |

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

| ENABLE\_FPE     | Build with Floating-Point    | no/yes           | no          |

|                 | Exceptions checks            |                  |             |

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

Few more notes on building MFiX-Exa

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

.. code:: shell

    > cmake -DCMAKE_CXX_COMPILER=<c++-compiler> -DCMAKE_Fortran_COMPILER=<f90-compiler> CONFIG_OPTIONS  ..

    > cmake -DCMAKE_CXX_COMPILER=<c++-compiler> -DCMAKE_Fortran_COMPILER=<f90-compiler> [options]  ..

When building on a platform that uses the ``module`` utility, use either

the above command (with full path to the compilers) or the following:

.. code:: shell

    > cmake -DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn CONFIG_OPTIONS  ..

    > cmake -DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn [options] ..

MFiX-Exa uses the same compiler flags used to build AMReX, unless

``CMAKE_Fortran_FLAGS``/``CMAKE_CXX_FLAGS`` is explicitly provided, or

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

| avg_int          | Interval, in number of CFD dt's, to write output                      |  Int        | -1        |

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

| avg_file         | Base file name which is appended with the data type (vel_p_, p_g_,    |  String     | avg_region|

|                  | ep_g_ or vel_g_), the number of this type of averaging,  and the .csv |             |           |

| avg_file         | Base file name which is appended with the data type (vel_p, p_g,      |  String     | avg_region|

|                  | ep_g or vel_g), the number of this type of averaging,  and the .csv   |             |           |

|                  | file extension                                                        |             |           |

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

| avg_vel_p        | Average and save particle velocity (if 1)                             |  n*Int      | 0         |

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

| avg_region_z_t   | Upper bound of averaging region in z-direction                        |  n*Real     | None      |

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

The following inputs must be preceded by "mfix."

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

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

|                      | Description                                                             |   Type   | Default   |

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

| geometry             | Which type of EB geometry are we using?                                 |   String |           |

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

| levelset__refinement | Refinement factor of levelset resolution relative to level 0 resolution |   Int    | 1         !

| levelset__refinement | Refinement factor of levelset resolution relative to level 0 resolution |   Int    | 1         |

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

Setting basic EB walls can be specified by inputs preceded by "xlo", "xhi", "ylo", "yhi", "zlo", and "zhi"

  resulting ordering across ranks in a way that balances the load

- Round-robin: sort grids and assign them to ranks in round-robin fashion -- specifically

  FAB *i* is owned by CPU *i*%N where N is the total number of MPI ranks.

  FAB ``i`` is owned by CPU ``i % N`` where N is the total number of MPI ranks.