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update build docs (#613)
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@spdomin
spdomin committed Feb 15, 2023
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248 changes: 132 additions & 116 deletions docs/source/user/build_manually.rst
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Expand Up @@ -57,116 +57,6 @@ Python v3+
The regression test suite for Nalu uses Python and requires a version greater than 3.


SuperLU v4.3
~~~~~~~~~~~~

Required usage of SuperLU is a deprecated; optional package provided `here <http://crd-legacy.lbl.gov/~xiaoye/SuperLU/>`__. KLU2, as described in the Amesos2 documentation `here <https://trilinos.github.io/amesos2.html>`__, is automatically used in place of SuperLU if not included. If desired, a SuperLU build can instead use KLU2 in place of SuperLU by specifying as such in the MueLu .xml configuration file as follows.

::

<Parameter name="coarse: type" type="string" value="klu2"/>


Prepare:

::

cd $nalu_build_dir/packages
curl -o superlu_4.3.tar.gz http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz
tar xf superlu_4.3.tar.gz

Build:

::

cd $nalu_build_dir/packages/SuperLU_4.3
cp MAKE_INC/make.linux make.inc

To find out what the correct platform extension PLAT is:

::

uname -m

Edit ``make.inc`` as shown below (diffs shown from baseline).

::

PLAT = _x86_64
SuperLUroot = /your_path_to_install/SuperLU_4.3 i.e., $nalu_install_dir/SuperLU/4.3
BLASLIB = -L/usr/lib64 -lblas
CC = mpicc
FORTRAN = mpif77

On some platforms, the ``$nalu_install_dir`` may be mangled and, thus the make will fail. In such cases, you
need to use the entire path to ``your_path_to_install/SuperLU_4.3``.

Next, make some new directories:

::

mkdir $nalu_install_dir/SuperLU/4.3
mkdir $nalu_install_dir/SuperLU/4.3/lib
mkdir $nalu_install_dir/SuperLU/4.3/include
cd $nalu_build_dir/packages/SuperLU_4.3
make
cp SRC/*.h $nalu_install_dir/SuperLU/4.3/include

If you are planning on sharing this install location with other team members, you will likely need to change a
permission on a particular file, ``chmod g+r $nalu_install_dir/SuperLU/4.3/include/superlu_enum_consts.h``.

Libxml2 v2.9.2
~~~~~~~~~~~~~~

Libxml2, which is no longer required for most Nalu builds, is found `here <http://www.xmlsoft.org/sources/>`__.

Prepare:

::

cd $nalu_build_dir/packages
curl -o libxml2-2.9.2.tar.gz http://www.xmlsoft.org/sources/libxml2-2.9.2.tar.gz
tar -xvf libxml2-2.9.2.tar.gz

Build:

::

cd $nalu_build_dir/packages/libxml2-2.9.2
CC=mpicc CXX=mpicxx ./configure -without-python --prefix=$nalu_install_dir/libxml2/2.9.2
make
make install

Boost v1.68.0
~~~~~~~~~~~~~

Required usage of Boost is a deprecated; optional package provide `here <http://www.boost.org>`__.

Prepare:

::

cd $nalu_build_dir/packages
curl -o boost_1_68_0.tar.gz http://iweb.dl.sourceforge.net/project/boost/boost/1.68.0/boost_1_68_0.tar.gz
tar -zxvf boost_1_68_0.tar.gz

Build:

::

cd $nalu_build_dir/packages/boost_1_68_0
./bootstrap.sh --prefix=$nalu_install_dir/boost/1.68.0 --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception

You may or may not need to edit ``project-config.jam`` and add a 'using mpi', e.g,

using mpi: /path/to/mpi/openmpi/bin/mpicc

::

./b2 -j 4 2>&1 | tee boost_build_one
./b2 -j 4 install 2>&1 | tee boost_build_intall

YAML-CPP 0.6.2
~~~~~~~~~~~~~~

Expand Down Expand Up @@ -268,7 +158,7 @@ Build:
Note that we have created an install directory that might look like ``$nalu_build_dir/install``.

NetCDF v4.7.4
***************
*************

NetCDF is provided `here <https://github.com/Unidata/netcdf-c/releases>`__.

Expand Down Expand Up @@ -307,14 +197,140 @@ Prepare:
git checkout develop
mkdir build

Within the build directory, place a configuration file for Trilinos, e.g.,
`do-configTrilinos_release <https://github.com/NaluCFD/Nalu/blob/master/build/do-configTrilinos_release>`__. Ensure that
the proper paths for each required TPL is provided. Follow this customization with a

::

./do-configTrilinos_release
make -j 16
make install


Deprecated TPLS
***********************
The below TPLS are no longer required for Nalu builds. However, instructions for
the particular libraries used in past versions of the code follow.


SuperLU v4.3
~~~~~~~~~~~~

Required usage of SuperLU is a deprecated; optional package provided `here <http://crd-legacy.lbl.gov/~xiaoye/SuperLU/>`__. KLU2, as described in the Amesos2 documentation `here <https://trilinos.github.io/amesos2.html>`__, is automatically used in place of SuperLU if not included. If desired, a SuperLU build can instead use KLU2 in place of SuperLU by specifying as such in the MueLu .xml configuration file as follows.

::

<Parameter name="coarse: type" type="string" value="klu2"/>


Prepare:

::

cd $nalu_build_dir/packages
curl -o superlu_4.3.tar.gz http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz
tar xf superlu_4.3.tar.gz

Build:

::

cd $nalu_build_dir/packages/SuperLU_4.3
cp MAKE_INC/make.linux make.inc

To find out what the correct platform extension PLAT is:

::

uname -m

Edit ``make.inc`` as shown below (diffs shown from baseline).

::

PLAT = _x86_64
SuperLUroot = /your_path_to_install/SuperLU_4.3 i.e., $nalu_install_dir/SuperLU/4.3
BLASLIB = -L/usr/lib64 -lblas
CC = mpicc
FORTRAN = mpif77

On some platforms, the ``$nalu_install_dir`` may be mangled and, thus the make will fail. In such cases, you
need to use the entire path to ``your_path_to_install/SuperLU_4.3``.

Next, make some new directories:

::

mkdir $nalu_install_dir/SuperLU/4.3
mkdir $nalu_install_dir/SuperLU/4.3/lib
mkdir $nalu_install_dir/SuperLU/4.3/include
cd $nalu_build_dir/packages/SuperLU_4.3
make
cp SRC/*.h $nalu_install_dir/SuperLU/4.3/include

If you are planning on sharing this install location with other team members, you will likely need to change a
permission on a particular file, ``chmod g+r $nalu_install_dir/SuperLU/4.3/include/superlu_enum_consts.h``.

Libxml2 v2.9.2
~~~~~~~~~~~~~~

Libxml2, which is no longer required for Nalu builds, is found `here <http://www.xmlsoft.org/sources/>`__.

Prepare:

::

cd $nalu_build_dir/packages
curl -o libxml2-2.9.2.tar.gz http://www.xmlsoft.org/sources/libxml2-2.9.2.tar.gz
tar -xvf libxml2-2.9.2.tar.gz

Build:

::

cd $nalu_build_dir/packages/libxml2-2.9.2
CC=mpicc CXX=mpicxx ./configure -without-python --prefix=$nalu_install_dir/libxml2/2.9.2
make
make install

Boost v1.68.0
~~~~~~~~~~~~~

Required usage of Boost is a deprecated; optional package provide `here <http://www.boost.org>`__.

Prepare:

::

cd $nalu_build_dir/packages
curl -o boost_1_68_0.tar.gz http://iweb.dl.sourceforge.net/project/boost/boost/1.68.0/boost_1_68_0.tar.gz
tar -zxvf boost_1_68_0.tar.gz

Build:

::

cd $nalu_build_dir/packages/boost_1_68_0
./bootstrap.sh --prefix=$nalu_install_dir/boost/1.68.0 --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception

You may or may not need to edit ``project-config.jam`` and add a 'using mpi', e.g,

using mpi: /path/to/mpi/openmpi/bin/mpicc

::

./b2 -j 4 2>&1 | tee boost_build_one
./b2 -j 4 install 2>&1 | tee boost_build_intall


HYPRE
~~~~~

Nalu can use HYPRE solvers and preconditioners, especially for Pressure Poisson
solves. However, this dependency is optional and is not enabled by default.
Users wishing to use HYPRE solver and preconditioner combination must compile
HYPRE library and link to it when building Nalu. This capability is not tested
nightly.
Nalu has deprecated HYPRE solver and preconditioner usage. Users wishing to use HYPRE solver and
preconditioner combination must compile HYPRE library and link to it when building Nalu and also
re-stablish the linear system assembly approach in the code base.

.. code-block:: bash
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