Building Nalu Manually

If you prefer not to build using Spack, below are instructions which describe the process of building Nalu by hand.

Linux

The Linux platform installation instructions follow. Compilers and MPI are expected to be already installed. If they are not, please follow the open-mpi build instructions. Below, we are using openmpi-1.8.8 and gcc-4.8.5

Setup

Prepare the third-party library (TPL) build process by defining some code locations, e.g., gitHubWork/scratch_build and set some paths. One might choose to keep a nalu_module_4.7.2 file.

mkdir <your_base_dir>
cd <your_base_dir>
export nalu_build_dir=$PWD
mkdir $nalu_build_dir/packages
mkdir $nalu_build_dir/install
mkdir $nalu_build_dir/install/lib
export LD_LIBRARY_PATH=/YOUR_PATH_TO_MPI_LIB/1.6.4-gcc-4.7.2-RHEL6/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/YOUR_PATH_TO_GCC/gcc/4.7.2-RHEL6/lib64:$LD_LIBRARY_PATH
PATH=/YOUR_PATH_TO_MPI/bin:$PATH
PATH=$nalu_build_dir/install/bin:$PATH
PATH=$nalu_build_dir/install/trilinos/bin:$PATH

CMake, Version 3.1.0

CMake is provided by the CMake team.

cd $nalu_build_dir/packages
curl -o cmake-3.1.0-rc2.tar.gz http://www.cmake.org/files/v3.1/cmake-3.1.0-rc2.tar.gz
tar -xvf cmake-3.1.0-rc2.tar.gz

Build (we assume the configure command will find the needed compilers):

cd $nalu_build_dir/packages/cmake-3.1.0-rc2
./configure --prefix=$nalu_build_dir/install
gmake
gmake install

SuperLU, Version 4.3

SuperLU is provided by here.

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 -xvf 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/install/SuperLU_4.3 i.e., $nalu_build_dir/install/SuperLU_4.3
BLASLIB       = -L/usr/lib64 -lblas
CC            = mpicc
FORTRAN       = mpif77

On some platforms, the $nalu_build_dir may be mangled. In such cases, you may need to use the entire path to install/SuperLU_4.3.

Next, make some new directories:

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

Libxml2, Version 2.9.2

Libxml2 is found here.

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 (note that python is not required and, hence, the -without-python option to config):

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

Boost, Version 1.55.0

Boost is found here.

Directions for 1.55.0 are as follows:

cd $nalu_build_dir/packages
curl -o boost_1_55_0.tar.gz http://iweb.dl.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz
tar -zxvf boost_1_55_0.tar.gz

Build:

cd $nalu_build_dir/packages/boost_1_55_0

Note: There must be a space before the semicolon at the end of the “using mpi” line in the user-config.jam file.

echo "using mpi : `which mpicxx` ;" >> ./tools/build/v2/user-config.jam
./bootstrap.sh --prefix=$nalu_build_dir/install --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception
./b2 -j 4 2>&1 | tee boost_build_one
./b2 -j 4 install 2>&1 | tee boost_build_intall

For newer versions, e.g., 1.60.0:

./bootstrap.sh --prefix=$nalu_build_dir/install --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception

Next, 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

For versions of Nalu after the v1.1.0-release, Yaml is provided under Github.

cd $nalu_build_dir/packages
git clone https://github.com/jbeder/yaml-cpp

Build Yaml-cpp:

cd $nalu_build_dir/packages/yaml-cpp
mkdir build
cd build
cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_CXX_FLAGS=-std=c++11 -DCMAKE_CC_COMPILER=mpicc -DCMAKE_INSTALL_PREFIX=$nalu_build_dir/install ..
make
make install

Pre-v1.1.0-release; Yaml-cpp, Version 0.3.0

For all versions of Nalu at, or before the v1.1.0-release, the formal version of YAML is 0.3.0. There is no backward compatibility between the versions of YAML.

Yaml is provided by code.google.com.

cd $nalu_build_dir/packages
curl -o yaml-cpp-0.3.0.tar.gz https://yaml-cpp.googlecode.com/files/yaml-cpp-0.3.0.tar.gz
tar -zxvf yaml-cpp-0.3.0.tar.gz
mv yaml-cpp yaml-cpp-0.3.0

Build yaml-cpp:

cd $nalu_build_dir/packages/yaml-cpp-0.3.0
mkdir build
cd build
cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_CC_COMPILER=mpicc -DCMAKE_INSTALL_PREFIX=$nalu_build_dir/install ..
make
make install

Zlib, Version 1.2.8

Zlib is provided here.

cd $nalu_build_dir/packages
curl -o zlib-1.2.8.tar.gz http://zlib.net/zlib-1.2.8.tar.gz
tar -zxvf zlib-1.2.8.tar.gz

Build Zlib:

cd $nalu_build_dir/packages/zlib-1.2.8
CC=gcc CXX=g++ CFLAGS=-O3 CXXFLAGS=-O3 ./configure --prefix=$nalu_build_dir/install/
make
make install

Hdf5, Version 1.8.12

Hdf5 1.8.12 is provided by the HDF group.

cd $nalu_build_dir/packages/
curl -o hdf5-1.8.12.tar.gz http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
tar -zxvf hdf5-1.8.12.tar.gz

Build (parallel enabled):

cd $nalu_build_dir/packages/hdf5-1.8.12
./configure CC=mpicc FC=mpif90 CXX=mpicxx CXXFLAGS="-fPIC -O3" CFLAGS="-fPIC -O3" FCFLAGS="-fPIC -O3" --enable-parallel --with-zlib=$nalu_build_dir/install --prefix=$nalu_build_dir/install
make
make install
make check

Full Parallel-Enabled Nalu using NetCDF (V. 4.3.3.1) and Parallel NetCDF (V. 1.6.1)

In order to support all aspects of Nalu’s parallel models, this combination of products is required.

Parallel NetCDF, Version 1.6.1

Parallel NetCDF is provided on the Argon Trac Page.

cd $nalu_build_dir/packages/
tar -zxvf parallel-netcdf-1.6.1.tar.gz

Configure, build and install:

cd parallel-netcdf-1.6.1
./configure --prefix=$nalu_install_dir CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I$nalu_install_dir/include -O3" LDFLAGS=-L$nalu_install_dir/lib --disable-fortran
make
make install

Note that we have created an install directory that might look like $nalu_build_dir/install.

NetCDF Version 4.3.3.1

NetCDF is provided on Github.

cd $nalu_build_dir/packages/
curl -o netcdf-c-4.3.3.1.tar.gz https://codeload.github.com/Unidata/netcdf-c/tar.gz/v4.3.3.1
tar -zxvf netcdf-c-4.3.3.1.tar.gz

Configure, build and install:

cd netcdf-c-4.3.3.1
./configure --prefix=$nalu_install_dir CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I$nalu_install_dir/include -O3" LDFLAGS=-L$nalu_install_dir/lib --enable-pnetcdf --enable-parallel-tests --enable-netcdf-4 --disable-shared --disable-fsync --disable-cdmremote --disable-dap --disable-doxygen --disable-v2
make -j 4
make install
make check

Note that when using Parallel NetCDF, the proper install directories must be added to the Trilinos configuration file.

Partial Parallel-Enabled Nalu using NetCDF, Version 4.3.1

If Parallel NetCDF is omitted, follow the instructions below. On some platforms, however, autodecompostion may fail.

NetCDF is provided on Github.

Scroll down until you see “NetCDF-C 4.3.1.1 (Bugfix Release)” or similar Click on the “Source (tar.gz)” button to download and then move the tar file to:

cd $nalu_build_dir/packages/
curl -o netcdf-c-4.3.1.1.tar.gz https://codeload.github.com/Unidata/netcdf-c/tar.gz/v4.3.1.1
tar -zxvf netcdf-c-4.3.1.1.tar.gz

Possibly, 4.3.1.1 is hard to get... If so, use the following:

curl -o netcdf-c-4.3.1-rc2.tar.gz https://codeload.github.com/Unidata/netcdf-c/tar.gz/v4.3.1-rc2

Complex Models (expert usage only)

In netcdf/include/netcdf.h, the following defines need to be changed to support complex models.

#define NC_MAX_DIMS     65536    /* max dimensions per file */
#define NC_MAX_VARS     524288   /* max variables per file */

For a definiton of Complex Models, please note the following page:

complexModels

Care should be taken with these settings as sometimes the above setting can exceed platform resources and, therefore, casue fails in the installation test suite.

Build (with parallel I/O):

cd $nalu_build_dir/packages/netcdf-c-4.3.1.1
./configure --prefix=$nalu_build_dir/install CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I$nalu_build_dir/install/include -O3" LDFLAGS=-L$nalu_build_dir/install/lib --disable-fsync --disable-cdmremote --disable-dap --disable-shared --disable-doxygen
make -j 4
make install
make check

Trilinos

Trilinos is managed by the Trilinos project and can be found on Github.

Clone the latest version of Trilinos within $nalu_build_dir/packages:

cd $nalu_build_dir/packages/
git clone https://github.com/trilinos/Trilinos.git

In some cases, the master Trilinos code base may have build issues. This is a rare occurance, however, some aspects to Trilinos that Nalu require, e.g., Tpetra, kokkos, STK and Muelu are in active development. If problems arise, one can revert back to a possible successful SHA-1 using bisect. Again, this is hopefully going to be mitigated by the strong SQA efforts at SNL.

Nalu Releases

Unfortunately, Github does not allow for a “live” wiki for each of the existing branches of Nalu.wiki. As such, instructions for the particular releases have been embedded within this head wiki file.

Release v1.0.0-release

For the formal Nalu v1.0.0-release, checkout the following Trilinos Version:

git checkout trilinos-release-12-0-branch

This version is the expected Trilinos code base for the v1.0.0-release Nalu code base. Now proceed to the build section.

Head Code Base

Proceed to the build section without checking out the Trilinos 12-0-branch.

Build

Create new folder in Trilinos called build:

cd $nalu_build_dir/packages/Trilinos
mkdir build

Place into build the script one of the do-configTrilinos_* files.

do-configTrilinos_* will be used to run cmake to build trilinos correctly for Nalu. Note that there are two files: one for ‘release’ and the other ‘debug’. The files can be found on the Nalu GitHub site or copied from $nalu_build_dir/packages/Nalu/build, which is created in the Nalu build step documented below. For example:

Pull latest version of do-configTrilinos_* from Nalu’s GitHub site:

curl -o $nalu_build_dir/packages/Trilinos/build/do-configTrilinos_release https://raw.githubusercontent.com/NaluCFD/Nalu/master/build/do-configTrilinos_release

Or if you create the Nalu directory as directed below, simply copy one of the do-configTrilinos_* files from local copy of Nalu’s git repository:

cp $nalu_build_dir/packages/Nalu/build/do-configTrilinos_release $nalu_build_dir/packages/Trilinos/build

Now edit do-configTrilinos_release to modify the paths so they point to $nalu_build_dir/install.

cd $nalu_build_dir/packages/Trilinos/build
chmod +x do-configTrilinos_release

Make sure all other paths to netcdf, hdf5, etc., are correct (in addition to open-mpi).

./do-configTrilinos_release
make
make install

If after the make, one notes issues with hdf5 and netcdf references not found, add the following:

-DTPL_Netcdf_LIBRARIES:PATH="${netcdf_install_dir}/lib/libnetcdf.a;${hdf_install_dir}/lib/libhdf5_hl.a;${hdf_install_dir}/lib/libhdf5.a;${z_install_dir}/lib/libz.a" \

Just below the netcdf option within the Seacas do-config sections:

-DTPL_ENABLE_Netcdf:STRING=ON \

ParaView Catalyst

Optionally enable ParaView Catalyst for in-situ visualization with Nalu. These instructions can be skipped if you do not require in-situ visualization with Nalu.

Build ParaView SuperBuild v5.3.0

The ParaView SuperBuild builds ParaView along with all dependencies necessary to enable Catalyst with Nalu. Clone the ParaView SuperBuild within $nalu_build_dir/packages:

cd $nalu_build_dir/packages/
git clone --recursive https://gitlab.kitware.com/paraview/paraview-superbuild.git
cd paraview-superbuild
git fetch origin
git checkout v5.3.0
git submodule update

Create a new build folder in $nalu_build_dir/:

cd $nalu_build_dir
mkdir paraview-superbuild-build
cd paraview-superbuild-build

Copy do-configParaViewSuperBuild to paraview-superbuild-build. Edit do-configParaViewSuperBuild to modify the defined paths as follows:

mpi_base_dir=<same MPI base directory used to build Trilinos>
nalu_build_dir=<path to root nalu build dir>

Make sure the MPI library names are correct.

./do-configParaViewSuperBuild
make -j 8

Build Nalu ParaView Catalyst Adapter

Create a new build folder in $nalu_build_dir/:

cd $nalu_build_dir
mkdir nalu-catalyst-adapter-build
cd nalu-catalyst-adapter-build

Copy do-configNaluCatalystAdapter to nalu-catalyst-adapter-build. Edit do-configNaluCatalystAdapter and modify nalu_build_dir at the top of the file to the root build directory path.

./do-configNaluCatalystAdapter
make
make install

Nalu

Nalu is provided here.

No doubt, you already have cloned Nalu. If not, execute the following command in the location that you want Nalu:

git clone https://github.com/NaluCFD/Nalu.git

Nalu Releases

One may either build the released Nalu version, v1.0.0-release, or the head code base.

Release v1.0.0-release

For the formal Nalu v1.0.0-release, you should have already cloned Trilinos and built the 12.0 release version of Trilinos. To obtain the consistent Nalu version, after the clone, checkout the Nalu release:

git checkout v1.0.0-release

Now proceed to the build section below.

Head Code Base

Proceed to the build section without checking out the Nalu v1.0.0-release code repository.

Build

In Nalu/build, you will find the CMakeLists.txt and do-configNalu.

Copy the do-configNalu_release or debug file to a new, non-tracked file:

cp do-configNalu_release do-configNaluNonTracked

Edit the paths at the top of the files by defining the nalu_build_dir variable. Within Nalu/build, execute the following commands:

./do-configNaluNonTracked
make

This process will create naluX within the Nalu/build location. One may need to create a new yaml-cpp directory (and copy src/include files). You may also build a debug executable by modifying the Nalu config file to use “Debug”. In this case, a naluXd executable is created.

Other useful tools from, e.g., seacas, are under /usr/local/packages/install/trilinos/bin

Build Nalu with ParaView Catalyst Enabled

If you have built ParaView Catalyst and the Nalu ParaView Catalyst Adapter, you can build Nalu with Catalyst enabled.

In Nalu/build, find do-configNaluCatalyst. Copy do-configNaluCatalyst to a new, non-tracked file:

cp do-configNaluCatalyst do-configNaluCatalystNonTracked
./do-configNaluCatalystNonTracked
make

The build will create the same executables as a regular Nalu build, and will also create a bash shell script named naluXCatalyst. Use naluXCatalyst to run Nalu with Catalyst enabled. It is also possible to run naluX with Catalyst enabled by first setting the environment variable:

export CATALYST_ADAPTER_INSTALL_DIR=$nalu_build_dir/install

Nalu will render images to Catalyst in-situ if it encounters the keyword catalyst_file_name in the output section of the Nalu input deck. The catalyst_file_name command specifies the path to a text file containing ParaView Catalyst input deck commands. Consult the catalyst.txt files in the following Nalu regression test directories for examples of the Catalyst input deck command syntax:

ablForcingEdge/
mixedTetPipe/
steadyTaylorVortex/

output:
  output_data_base_name: mixedTetPipe.e
  catalyst_file_name: catalyst.txt

When the above regression tests are run, Catalyst is run as part of the regression test. The regression test checks that the correct number of image output files have been created by the test.

The Nalu Catalyst integration also supports running Catalyst Python script files exported from the ParaView GUI. The procedure for exporting Catalyst Python scripts from ParaView is documented in the Catalyst user guide. To use an exported Catalyst script, insert the paraview_script_name keyword in the output section of the Nalu input deck. The argument for the paraview_script_name command contains a file path to the exported script.

output:
  output_data_base_name: mixedTetPipe.e
  paraview_script_name: paraview_exported_catalyst_script.py

Mac OS X

The Mac platform installation is managed by the extensive usage of “Homebrew”. This package provides many Mac OS X builds and installations required for Nalu.

Homebrew

Download and Install Homebrew on your local home terminal:

Now you can install Homebrew; brew doctor will be the first line command required.

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew doctor

Packages to be obtained from Homebrew

OpenMpi

brew install openmpi

Cmake

brew search cmake  //cmake is there and will pop up on the next line
brew install cmake

Libxml2

brew search libxml2
brew install libxml2

Boost, 1.60.0_2

brew install boost

SuperLU, 4.3

brew tap homebrew/science
brew search superlu
brew install superlu43

The latest version of SuperLU provided by Homebrew is not compatible with head Trilinos due to Trilinos’ usage of some deprecated methods.

Once done with the Homebrew install, make sure everybody can read the files:

sudo chmod -R u+rwX,go+rX,go-w /usr/local/Cellar

Non-Homebrew

Other Nalu required libraries must be managed outside of the Homebrew environment.

Helpful Notes

How to specify install location and compilers with configure and cmake:

When building packages that use configure, do:

./configure PREFIX=/usr/local/packages/install CC=mpicc CXX=mpicxx

When building packages that use cmake, do a mkdir build; cd build then

cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_CC_COMPILER=mpicc -DCMAKE_INSTALL_PREFIX:PATH=/myPath/install ..`

For all non-Homebrew packages, myPath above will be /usr/local/packages.

mkdir /usr/local/packages
mkdir /usr/local/packages/install

Yaml-cpp

For versions of Nalu after the v1.1.0-release, Yaml is provided under Github

cd $nalu_build_dir/packages
git clone https://github.com/jbeder/yaml-cpp

Build Yaml-cpp:

cd $nalu_build_dir/packages/yaml-cpp
mkdir build
cd build
cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_CXX_FLAGS=-std=c++11 -DCMAKE_CC_COMPILER=mpicc -DCMAKE_INSTALL_PREFIX=$nalu_build_dir/install ..
make
make install

Pre-v1.1.0-release; Yaml-cpp, Version 0.3.0

Yaml is provided by code.google.com.

Follow the yaml installation directions. This process will put the created files in /user/local/include/yaml-cpp. Below are some high level points:

mkdir /usr/local/packages
cd packages/
curl -o yaml-cpp-0.3.0.tar.gz https://yaml-cpp.googlecode.com/files/yaml-cpp-0.3.0.tar.gz
tar -zxvf yaml-cpp-0.3.0.tar.gz
mv yaml-cpp yaml-cpp-0.3.0

This series of commands will create /usr/local/packages/yaml-cpp-0.3.0.

Next, build Yaml-cpp:

cd /usr/local/packages/yaml-cpp-0.3.0
mkdir build
cd build
cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_CC_COMPILER=mpicc -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/packages/install ..
make
make install

Zlib, 1.2.8

Zlib is provided by the zlib project.

cd /usr/local/packages/
curl -o zlib-1.2.8.tar.gz http://zlib.net/zlib-1.2.8.tar.gz
tar -zxvf zlib-1.2.8.tar.gz

Build Zlib:

cd /usr/local/packages/zlib-1.2.8
CC=gcc CXX=g++ CFLAGS=-O3 CXXFLAGS=-O3 ./configure --archs="-arch x86_64" --prefix=/usr/local/packages/install/
make
make install

Hdf5, 1.8.12

Hdf5 1.8.12 is provided by the HDF group.

cd /usr/local/packages/
curl -o hdf5-1.8.12.tar.gz http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
tar -zxvf hdf5-1.8.12.tar.gz

This series of commands will create /usr/local/packages/hdf5-1.8.12.

Build:

cd /usr/local/packages/hdf5-1.8.12
./configure CC=mpicc FC=mpif90 CXX=mpicxx CXXFLAGS="-fPIC -O3" CFLAGS="-fPIC -O3" FCFLAGS="-fPIC -O3" --enable-parallel --with-zlib=/usr/local/packages/install --prefix=/usr/local/packages/install
make
make install
make check

Full Parallel-Enabled Nalu using NetCDF (V. 4.3.3.1) and Parallel NetCDF (V. 1.6.1)

In order to support all aspects of Nalu’s parallel models, this combination of products is required.

Parallel NetCDF, Version 1.6.1

Parallel NetCDF is provided on the Argon Trac Page.

cd $nalu_build_dir/packages/
tar -zxvf parallel-netcdf-1.6.1.tar.gz

Configure, build and install:

cd parallel-netcdf-1.6.1
./configure --prefix=/usr/local/packages/install CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I/usr/local/packages/install/include -O3" LDFLAGS=-L/usr/local/packages/install/lib --disable-fortran
make
make install

Note that we have created an install directory that might look like: $nalu_build_dir/install.

NetCDF Version 4.3.3.1

NetCDF is provided on Github.

cd $nalu_build_dir/packages/
curl -o netcdf-c-4.3.3.1.tar.gz https://codeload.github.com/Unidata/netcdf-c/tar.gz/v4.3.3.1
tar -zxvf netcdf-c-4.3.3.1.tar.gz

Configure, build and install:

cd netcdf-c-4.3.3.1
./configure --prefix=$nalu_install_dir CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I/usr/local/packages/install/include -O3" LDFLAGS=-L/usr/local/packages/install/lib --enable-pnetcdf --enable-parallel-tests --enable-netcdf-4 --disable-shared --disable-fsync --disable-cdmremote --disable-dap --disable-doxygen --disable-v2
make -j 4
make install
make check

Note that when using Parallel NetCDF, the proper install directories must be added to the Trilinos configuration file.

Partial Parallel-Enabled Nalu using NetCDF, Version 4.3.1

If Parallel NetCDF is omitted, follow the instructions below. On some platforms, however, autodecompostion may fail.

Netcdf is provided on Github.

Scroll down until you see “NetCDF-C 4.3.1.1 (Bugfix Release)” or similar Click on the “Source (tar.gz)” button to download and then move the tar file to: /usr/local/packages

cd /usr/local/packages
tar -xvf netcdf-c-4.3.1.1.tar

This process will create /usr/local/packages/netcdf-c-4.3.1.1.

Build:

cd /usr/local/packages/netcdf-c-4.3.1.1
./configure --prefix=/usr/local/packages/install CC=mpicc FC=mpif90 CXX=mpicxx CFLAGS="-I/usr/local/packages/install/include -O3" LDFLAGS="-L/usr/local/packages/install/lib" --disable-fsync --disable-cdmremote --disable-dap --disable-shared --disable-doxygen
make
make install
make check

Trilinos

Trilinos is managed by the Trilinos project and can be found on github.

Clone the latest version of Trilinos within /packages:

cd /usr/local/packages/
git clone https://github.com/trilinos/Trilinos.git

In some cases, the master Trilinos code base may have build issues. This is a rare occurance, however, some aspects to Trilinos that Nalu require, e.g., Tpetra, kokkos, STK and Muelu are in active development. If problems arise, one can revert back to a possible successful SHA-1 using bisect. Again, this is hopefully going to be mitigated by the strong SQA efforts at SNL.

Nalu Releases

Nalu has two main release so far.

Release v1.0.0-release

For the formal v1.0.0-release, check-out the following Trilinos Version:

git checkout trilinos-release-12-0-branch

This version is the expected Trilinos code base for the v1.0.0-release Nalu code base. Now proceed to the build section.

Head Code Base

Proceed to the build section without checking out the Trilinos 12-0-branch.

Build

Create new folder in Trilinos called build:

cd /usr/local/packages/Trilinos
mkdir build

Place into build the script one of the do-configTrilinos_* files.

do-configTrilinos_* will be used to run cmake to build trilinos correctly for Nalu. Note that there are two files: one for ‘release’ and the other ‘debug’. The files can be found on the Nalu GitHub site or copied from $nalu_build_dir/packages/Nalu/build, which is created in the Nalu build step documented below. For example:

Pull latest version of do-configTrilinos_* from Nalu’s GitHub site:

curl -o $nalu_build_dir/packages/Trilinos/build/do-configTrilinos_release https://raw.githubusercontent.com/NaluCFD/Nalu/master/build/do-configTrilinos_release

Or if you create the Nalu directory as directed below, simply copy one of the do-configTrilinos_* files from local copy of Nalu’s git repository:

cp $nalu_build_dir/packages/Nalu/build/do-configTrilinos_release $nalu_build_dir/packages/Trilinos/build

Now edit the do-configTrilinos_release to modify the defined paths as follows:

mpi_base_dir=/usr/local/Cellar/open-mpi/1.8.3
nalu_build_dir=/usr/local/packages

Next, note that some packages, i.e., boost and superLu were provided by Homebrew. As such, make sure that boost_dir and super_lu point to /usr/local/Cellar.

Build:

cd /usr/local/packages/Trilinos/build
./do-configTrilinos_release
make
make install

Nalu

Nalu is provided here.

No doubt, you already have cloned Nalu. If not, execute the following command in the location that you want Nalu:

git clone https://github.com/NaluCFD/Nalu.git

Nalu Releases

One may either build the released Nalu version, v1.0.0-release, or the head code base.

Release v1.0.0-release

For the formal Nalu v1.0.0-release, you should have already cloned Trilinos and built the 12.0 release version of Trilinos. To obtain the consistent Nalu version, after the clone, checkout the Nalu release,

git checkout v1.0.0-release

Now proceed to the build section below.

Head Code Base

Proceed to the build section without checking out the Nalu v1.0.0-release code repository.

Build

In Nalu/build, you will find the CMakeLists.txt and do-configNalu_release.

Again, note that there is a debug version as well. Copy the do-configNalu_release to a new, non-tracked file,

cp do-configNalu_release do-configNaluNonTracked

Edit the paths at the top of the files by defining the nalu_build_dir variable as:

nalu_build_dir=/usr/local/packages

Within Nalu/build, execute the following commands:

./do-configNaluNonTracked
make

This process will create naluX within the Nalu/build location. Setting the DEBUG CMake option will create a naluXd executable.

Other useful tools from, e.g., seacas, are under /usr/local/packages/install/trilinos/bin.