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mac_osx
The Mac platform installation is managed the extensive usage of "HomeBrew". This package provides many Max OS X builds and installations required for Nalu.
Download and Install Homebrew on your local home terminal:
Now you can install homebrew; "brew doctor" will be the first line comamnd 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
brew search libxml2
brew install libxml2
brew install boost
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 HB 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
How to specify install location and compilers with configure and cmake
When building packages that use configure, do a
./configure PREFIX=/usr/local/pachages/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, 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 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 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
In order to support all aspects of Nalu's parallel models, this combination of products is required.
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 I have created an install directory that might look like: $nalu_build_dir/install
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.
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 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.
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.
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.
Proceed to the build section without checking out the Trilinos 12-0-branch.
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 here 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/spdomin/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 is provided by github
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/spdomin/Nalu.git
One may either build the released Nalu version, v1.0.0-release, or the head code base.
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.
Proceed to the build section without checking out the Nalu v1.0.0-release code repository.
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
After the naluX executable is created, please proceed with regression testing to ensure a proper build.
Instructions for the regression testing can be found under the NaluRtest directory.
Please take care to ensure that the NaluRtest branch is consistent with the Trilinos and Nalu version desired. One may also need to checkout the v1.0.0-release code base.