Step-by-step SU2 clean parallel Installation (Part 3/3)
Posted July 27, 2014 at 22:15 by pdp.aero
Updated October 4, 2015 at 13:28 by pdp.aero (Updating to recent version)
Updated October 4, 2015 at 13:28 by pdp.aero (Updating to recent version)
For the past
In this section, we are going to install the SU2 2.0.2, pretty old version comparing to current version 3.2.0, and then SU2 2.0.10, after we will finally install the SU2 3.0.0. Again, download the tar file, put the source in a right place, and unpack it. Before building these versions we will need the stands-alone metis.
Metis 4.0.3
Download the tar file from here, put it in your SU2 2.0.2 trunk, then unpack the tar file and direct there. Edit the Makefile.in accordingly.
After editing the makefile, and saving it, enter the make in your terminal to build. After this, we will going to configure the SU2 2.0.2 with Metis 4.0.3 flag.
SU2 2.0.2
This version does not support running in parallel with the CGNS, conversely the 3.2.0 does, so we will configure it without using the CGNS library. Direct to your SU2 2.0.2 directory, and do the following.
You also need to set the environment variables.
You can remove the package by using the make clean and make uninstall.
SU2 2.0.10
This version supports running in parallel with the CGNS, so download the tar file from the github, put it in a appropriate directory, unpack the source. Again, you need to build the stand-alone Metis 4.0.3, so put the unpacked metis folder in your SU2 directory, and follow the aforementioned instruction in the Metis section. Then, do the following.
Again, you also need to set the environment variables.
SU2 3.0.0
This version also supports running in parallel with CGNS, download, unpack, and put it in a right place. Like the previous one, you will need the metis, so copy the unpacked metis folder in your SU2 directory, follow the instruction provided already in the metis section. Then, do the following.
Finally, setting the environment variable according to the following.
SU2 3.2.0
In this version, you don't need to specify the metis flags, it is added to the code as an external library, and it will be built automatically. After downloading the SU2 tar file from its Github link here, unpack the tar file in a proper directory, direct there, and configure it accordingly.
Then, you need to set the environment variables according to your installation directory.
For the future
We build the several versions of the SU2 with parallel support, but in this section we are about to install the CGNS 3.1.14 library with hdf5 in parallel with szip support. The current version, 4.0.1, supports hdf5, SZIP and ZLIB. You can build this version with these options. Still I am not sure about the support of parallel CGNS with hdf5. Therefore, you can follow the below instructions and build the parallel CGNS with hdf5, then add the CGNS flags like previous cases and see what happens.
SZIP 2.1
Download the tar file from here, put it in an appropriate place, and unpack the file. Then, direct there, and build it accordingly.
Then we need to add a link to LD, so follow the provided commands.
Press 'a' for enabling type setting, the type the below line in you terminal. After, press Esc, the enter ':wq' to save and exit.
Enter the below command into the terminal for updating the LD.
HDF5 1.8.13
Download the tar file from here, put it in a right place, unpack the tar file, and direct there. Follow the provided commands.
CGNS 3.1.14 with HDF5
The CGNS 3.1.14 tar file has been downloaded already, if you didn't, download it from the above CGNS 3.1.14 section. You also need cmake, X11, Xmu, OpenGL library before building the CGNS. If you didn't have these, go back to their above sections, and install them. After unpacking the cgns tar file in an appropriate directory, direct there, and follow the provided instructions.
Set the options according to the following, then press c, and then g to generate the configure.
BUILD_CGNSTOOLS ON
BUILD_PCGNS ON
CGNS_BUILD_SHARED ON
CGNS_USE_SHARED ON
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local
ENABLE_64BIT ON
ENABLE_FORTRAN ON
ENABLE_HDF5 ON
ENABLE_SCOPING OFF
ENABLE_TESTS OFF
FORTRAN_NAMING LOWERCASE_
HDF5_INCLUDE_PATH /usr/local/include
HDF5_LIBRARY /usr/local/lib/libhdf5.so
HDF5_NEED_MPI ON
HDF5_NEED_SZIP ON
HDF5_NEED_ZLIB ON
MPI_C_COMPILER /usr/local/bin/mpicc
MPI_C_INCLUDE_PATH /usr/local/include
MPI_C_LIBRARIES /usr/local/lib/libmpich.a;/usr/local/lib/libopa.a;
SZIP_LIBRARY /path/to/your/szip-2.1/szip/lib/libsz.so.2
ZLIB_LIBRARY /usr/lib/x86_64-linux-gnu/libz.so
After generating the configure, do the following.
The final part has been finished here, I hope you found it useful. The backward links to the previous sections are Part 1, Part 2.
Happy high-fidelity optimizing,
PDP
In this section, we are going to install the SU2 2.0.2, pretty old version comparing to current version 3.2.0, and then SU2 2.0.10, after we will finally install the SU2 3.0.0. Again, download the tar file, put the source in a right place, and unpack it. Before building these versions we will need the stands-alone metis.
Metis 4.0.3
Download the tar file from here, put it in your SU2 2.0.2 trunk, then unpack the tar file and direct there. Edit the Makefile.in accordingly.
Code:
# Which compiler to use CC = gcc
SU2 2.0.2
This version does not support running in parallel with the CGNS, conversely the 3.2.0 does, so we will configure it without using the CGNS library. Direct to your SU2 2.0.2 directory, and do the following.
Code:
./configure --prefix=/usr/local/ --with-Metis-lib=/path/to/your/metis-4.0.3/in/SU2/directory/trunk/metis-4.0.3 --with-Metis-include=/path/to/your/metis-4.0.3/in/SU2/directory/trunk/metis-4.0.3/Lib --with-Metis-version=4 --with-MPI=/usr/local/bin/mpicxx make sudo make install
Code:
export SU2_RUN="/usr/local/bin" export SU2_HOME="/path/to/your/SU2/directory/trunk/trunk" export PATH=$PATH:$SU2_RUN
SU2 2.0.10
This version supports running in parallel with the CGNS, so download the tar file from the github, put it in a appropriate directory, unpack the source. Again, you need to build the stand-alone Metis 4.0.3, so put the unpacked metis folder in your SU2 directory, and follow the aforementioned instruction in the Metis section. Then, do the following.
Code:
./configure --prefix=/usr/local/ --with-CGNS-lib=/usr/local/lib --with-CGNS-include=/usr/local/include --with-Metis-lib=/path/to/your/metis-4.0.3/in/SU2/directory/metis-4.0.3 --with-Metis-include=/path/to/your/metis-4.0.3/in/SU2/directory/metis-4.0.3/Lib --with-Metis-version=4 --with-MPI=/usr/local/bin/mpicxx make sudo make install
Code:
export SU2_RUN="/usr/local/bin" export SU2_HOME="/path/to/your/SU2/directory" export PATH=$PATH:$SU2_RUN
SU2 3.0.0
This version also supports running in parallel with CGNS, download, unpack, and put it in a right place. Like the previous one, you will need the metis, so copy the unpacked metis folder in your SU2 directory, follow the instruction provided already in the metis section. Then, do the following.
Code:
./configure --prefix=/usr/local/ --with-CGNS-lib=/usr/local/lib --with-CGNS-include=/usr/local/include --with-Metis-lib=/path/to/your/metis-4.0.3/in/SU2/directory/metis-4.0.3 --with-Metis-include=/path/to/your/metis-4.0.3/in/SU2/directory/metis-4.0.3/Lib --with-Metis-version=4 --with-MPI=/usr/local/bin/mpicxx make sudo make install
Code:
export SU2_RUN="/usr/local/bin" export SU2_HOME="/path/to/your/SU2/directory" export PATH=$PATH:$SU2_RUN
In this version, you don't need to specify the metis flags, it is added to the code as an external library, and it will be built automatically. After downloading the SU2 tar file from its Github link here, unpack the tar file in a proper directory, direct there, and configure it accordingly.
Code:
./configure --prefix=/usr/local/ --with-CGNS-lib=/usr/local/lib --with-CGNS-include=/usr/local/include --with-Jsoncpp-lib=/path/to/your/unpack/jsoncpp-src-0.5.0/libs/linux-gcc-4.8 --with-Jsoncpp-include=/path/to/your/unpack/jsoncpp-src-0.5.0/include --with-MPI=/usr/local/bin/mpicxx make sudo make install sudo make installcheck
Code:
export SU2_RUN="/usr/local/bin" export SU2_HOME="/path/to/your/unpack/SU2-3.2.0" export PATH=$PATH:$SU2_RUN export PYTHONPATH=$PYTHONPATH:$SU2_RUN
We build the several versions of the SU2 with parallel support, but in this section we are about to install the CGNS 3.1.14 library with hdf5 in parallel with szip support. The current version, 4.0.1, supports hdf5, SZIP and ZLIB. You can build this version with these options. Still I am not sure about the support of parallel CGNS with hdf5. Therefore, you can follow the below instructions and build the parallel CGNS with hdf5, then add the CGNS flags like previous cases and see what happens.
SZIP 2.1
Download the tar file from here, put it in an appropriate place, and unpack the file. Then, direct there, and build it accordingly.
Code:
./configure sudo make sudo make check sudo make install
Code:
sudo touch /etc/ld.so.conf.d/szip-2.1.conf sudo chmod 777 /etc/ld.so.conf.d/szip-2.1.conf vi /etc/ld.so.conf.d/szip-2.1.conf
Code:
/path/to/your/szip-2.1/directory/szip/lib
Code:
sudo ldconfig
Download the tar file from here, put it in a right place, unpack the tar file, and direct there. Follow the provided commands.
Code:
CC='/usr/local/bin/mpicc -m64' ./configure --prefix=/usr/local --enable-parallel --with-zlib=/usr/include,/usr/lib --with-szlib=/path/to/your/szip-2.1/szip sudo make sudo make check sudo make install sudo make check-install
The CGNS 3.1.14 tar file has been downloaded already, if you didn't, download it from the above CGNS 3.1.14 section. You also need cmake, X11, Xmu, OpenGL library before building the CGNS. If you didn't have these, go back to their above sections, and install them. After unpacking the cgns tar file in an appropriate directory, direct there, and follow the provided instructions.
Code:
mkdir cgns_Linux cd cgns_Linux cmake /path/to/your/unpack/cgnslib-3.1.4 ccmake .
BUILD_CGNSTOOLS ON
BUILD_PCGNS ON
CGNS_BUILD_SHARED ON
CGNS_USE_SHARED ON
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local
ENABLE_64BIT ON
ENABLE_FORTRAN ON
ENABLE_HDF5 ON
ENABLE_SCOPING OFF
ENABLE_TESTS OFF
FORTRAN_NAMING LOWERCASE_
HDF5_INCLUDE_PATH /usr/local/include
HDF5_LIBRARY /usr/local/lib/libhdf5.so
HDF5_NEED_MPI ON
HDF5_NEED_SZIP ON
HDF5_NEED_ZLIB ON
MPI_C_COMPILER /usr/local/bin/mpicc
MPI_C_INCLUDE_PATH /usr/local/include
MPI_C_LIBRARIES /usr/local/lib/libmpich.a;/usr/local/lib/libopa.a;
SZIP_LIBRARY /path/to/your/szip-2.1/szip/lib/libsz.so.2
ZLIB_LIBRARY /usr/lib/x86_64-linux-gnu/libz.so
After generating the configure, do the following.
Code:
make sudo make install
Happy high-fidelity optimizing,
PDP
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