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linux_rh6
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
Prepare the 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 is provided by 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 is provided by superlu
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 baselien).
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, I have seen the $nalu_build_dir be mangled. In such cases, I needed to use the entire path to install/SuperLU_4.3.
Now, 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 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 otion 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 is found here
Directions for a sample 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 older versions, e.g., 1.60.0, the following is followed:
./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
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
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 is provided by [www.zlib.net] (http://www.zlib.net/)
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 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
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 $nalu_build_dir/packages/
tar -zxvf parallel-netcdf-1.6.1.tar.gz
Configure, build and install:
cd parallel-netcdf-1.6.1
./configure --prefix=$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 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$nalu_install_dir/include -O3" LDFLAGS=-L$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.
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
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:
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 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.
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 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.
Proceed to the build section without checking out the Trilinos 12-0-branch.
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 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/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 \
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/NaluCFD/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.
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
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.