Installation {#installation}

Dependencies

To promote rapid scientific software development and research, FRENSIE is built off of a large number of software libraries. The software that FRENSIE depends on is listed below.

FRENSIE also requires a GNU compiler (4.7.3 or greater) and CMake version 3.0.1 to build correctly. Doxygen version 1.8.8 is recommended but version 1.8.2 and above will also work. All of the above software libraries will be built from source. This process will be described in the next section.

Building Dependent Software Libraries

Before any of the software libraries are built, verify that the system has CMake version 3.0.1 installed. If CMake is not installed or an older version is present, build CMake 3.0.1 using the instructions below.

When building software libraries and executables, the following directory structure should be adopted: software/package/package.xx.xx.xx, software/package/build, software/package/src. "package" will be the name of the particular software package. "package.xx.xx.xx" comes from unpacking the compressed source files (e.g. package.tar.gz). The src directory is created by making a softlink to the package.xx.xx.xx directory. This is done to make the build a bit easier.

Please note that the software libraries should be built in the order that they are described.

Checking out FRENSIE

create a working directory where FRENSIE will be built (e.g. software/frensie)
move to the frensie directory
run git clone [email protected]:aprobinson/FRENSIE.git
run ln -s FRENSIE src

Building CMake

download the CMake 3.0.1 source
move the cmake-3.0.1.tar.gz file to the cmake directory (e.g. software/cmake)
move to the cmake directory
run tar -xvf cmake-3.0.1.tar.gz
run ln -s cmake-3.0.1 src
run mkdir build
move to the build directory (e.g. software/cmake/build)
run ../src/configure --prefix=absolute-path-to_software/cmake
run make -j n, where n is the number of threads to use while building
run make test
run make install
add the following line to the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:$PATH
run exec bash
run cmake --version and verify that the output is 3.0.1

Building HDF5

download the HDF5 1.8.13 source
move the hdf5-1.8.13.tar.gz file to the hdf5 directory (e.g. software/hdf5)
move to the hdf5 directory
run tar -xvf hdf5-1.8.13.tar.gz
run ln -s hdf5-1.8.13 src
run mkdir build
move to the build directory (e.g. software/hdf5/build)
copy FRENSIE/scripts/hdf5.sh into the build directory
change the variables in the script to reflect the desired system paths
run ./hdf5.sh to configure hdf5
run make -j n
run make test
run make install
update the export PATH line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:$PATH
run exec bash

Building Open MPI

download the Open MPI 1.8.2 source
move the openmpi-1.8.2.tar.gz file to the mpi directory (e.g. software/mpi)
move to the mpi directory
run tar -xvf openmpi-1.8.2.tar.gz
run ln -s openmpi-1.8.2 src
run mkdir build
move to the build directory (e.g. software/mpi/build)
run ../src/configure --prefix=absolute-path-to_software/mpi
run make -j n
run make check
run make install
update the export PATH line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:absolute-path-to_software/mpi/bin:$PATH
add the following line to the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:$LD_LIBRARY_PATH
run exec bash

Building Cubit - Optional

Cubit is not open source software so a license must be acquired.
The binary files will be be available for download once a license has been acquired
move the Cubit-14.0-Lin64.tar.gz file to the cubit14.0 directory (e.g. software/cubit14.0)
run tar -xvf Cubit-14.0-Lin64.tar.gz
update the export PATH line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:absolute-path-to_software/mpi/bin:absolute-path-to_software/cubit14.0:$PATH
update the export LD_LIBRARY_PATH line in the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:$LD_LIBRARY_PATH
run exec bash

Building CGM - Only with Cubit

download the CGM 14.1pre source
move the cgm-nightly-trunk.tar.gz file to the cgm directory (e.g. software/cgm)
move to the cgm directory
run tar -xvf cgm-nightly-trunk.tar.gz
run ln -s cgma-14.1pre src
run mkdir build
move to the build directory (e.g. software/cgm/build)
run ../src/configure --enable-optimize --disable-debug --with-cubit=absolute-path-to_software/cubit14.0 --prefix=absolute-path-to_software/cgm
run make -j n
run make check
run make install

Building MOAB

download the MOAB 4.6.3 source
move the moab-4.6.3.tar.gz file to the moab directory (e.g. software/moab)
move to the moab directory
run tar -xvf moab-4.6.3.tar.gz
run ln -s moab-4.6.3 src
run mkdir build
move to the build directory (e.g. software/moab/build)
if DagMC is desired (Cubit 14.0 and CGM must be built):
- run ../src/configure --enable-optimize --disable-debug --with-cgm=absolute-path-to_software/cgm/ --with-hdf5=absolute-path-to_software/hdf5 --prefix=absolute-path-to_software/moab/
- else run ../src/configure --enable-optimize --disable-debug --with-hdf5=absolute-path-to_software/hdf5 --prefix=absolute-path-to_software/moab/
run make -j n
run make check
run make install
update the export PATH line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:absolute-path-to_software/mpi/bin:absolute-path-to_software/cubit14.0:absolute-path-to_software/moab/bin:$PATH
run exec bash

Building LAPACK

download the LAPACK 3.5.0 source
move the lapack-3.5.0.tgz file to the lapack directory (e.g. software/lapack)
move to the lapack directory
run tar -xvf lapack-3.5.0.tgz
run ln -s lapack-3.5.0 src
run mkdir build
move to the build directory (e.g. software/lapack/build)
copy FRENSIE/scripts/lapack.sh into the build directory
change the variables in the script to reflect the desired system paths
run ./lapack.sh to configure lapack
run make -j n
run make test
run make install
update the export LD_LIBRARY_PATH line in the .bashrc file: ``export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:absolute-path-to_software/lapack/lib:$LD_LIBRARY_PATH`
run exec bash

Building Trilinos

download the Trilinos 11.12.1 source
move the trilinos-11.12.1-Source.tar.gz file to the trilinos directory (e.g. software/trilinos)
move to the trilinos directory
run tar -xvf trilinos-11.12.1-Source.tar.gz
run ln -s trilinos-11.12.1.Source src
run mkdir build
move to the build directory (e.g. software/trilinos/build)
copy FRENSIE/scripts/trilinos.sh into the build directory
change the variables in the script to reflect the desired system paths
run ./trilinos.sh to configure trilinos
run make -j n
run make test
run make install
update the export LD_LIBRARY_PATH line in the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:absolute-path-to_software/lapack/lib:absolute-path-to_software/trilinos/lib:$LD_LIBRARY_PATH
run exec bash

Building ODEPACK

download the ODEPACK source

odkd-sum.txt
opkdmain.f
opkda1.f
opkda2.f
opkddemos.txt

move the above files to the odepack directory (e.g. software/odepack)
copy FRENSIE/scripts/odepack.sh into the odepack directory
run ./odepack.sh to build libodepack.a

Building Boost

download the Boost 1.56.0 source
move the boost_1_56_0.tar.gz file to the boost directory (e.g. software/boost)
move to the boost directory
run tar -xvf boost_1_56_0.tar.gz
move to the boost_1_56_0 directory (e.g. software/boost/boost_1_56_0)
run ./bootstrap.sh --prefix=absolute-path-to_software/boost
run ./b2
run ./b2 install
update the export LD_LIBRARY_PATH line in the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:absolute-path-to_software/lapack/lib:absolute-path-to_software/trilinos/lib:absolute-path-to_software/boost/lib:$LD_LIBRARY_PATH
run exec bash

Building the GNU Scientific Library (GSL)

download the GSL 1.16 source
move the gsl-1.16.tar.gz file to the gsl directory (e.g. software/gsl)
move to the gsl directory
run tar -xvf gsl-1.16.tar.gz
run ln -s gsl-1.16 src
run mkdir build
move to the build directory (e.g. software/gsl/build)
run ../src/configure --prefix=absolute-path-to_software/gsl
run make -j n
run make check
run make install
update the export LD_LIBRARY_PATH line in the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:absolute-path-to_software/lapack/lib:absolute-path-to_software/trilinos/lib:absolute-path-to_software/boost/lib:absolute-path-to_software/gsl/bin:$LD_LIBRARY_PATH
run exec bash

Building Doxygen

download the Doxygen 1.8.8 source
move the doxygen-1.8.8.src.tar.gz file to the doxygen directory (e.g. software/gsl)
move to the doxygen directory
run tar -xvf doxygen-1.8.8.src.tar.gz
move to the doxygen-1.8.8 directory
run ./configure --prefix=absolute-path-to_software/doxygen
run make -j n
run make test
run make install
update the export PATH line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:absolute-path-to_software/mpi/bin:absolute-path-to_software/cubit14.0:absolute-path-to_software/moab/bin:absolute-path-to_software/doxygen/bin:$PATH
run exec bash

Building ROOT

download the appropriate ROOT 6.04/02 Binaries
move the binary file to the root directory (e.g. software/root)
move to the root directory
run 'tar -xvf root_v6.04.02*'
update the 'export PATH' line in the .bashrc file: export PATH=absolute-path-to_software/cmake/bin:absolute-path-to_software/hdf5/bin:absolute-path-to_software/mpi/bin:absolute-path-to_software/cubit14.0:absolute-path-to_software/moab/bin:absolute-path-to_software/doxygen/bin:absolute-path-to_software/root/bin:$PATH
update the export LD_LIBRARY_PATH line in the .bashrc file: export LD_LIBRARY_PATH=absolute-path-to_software/mpi/lib:absolute-path-to_software/cubit14.0/bin:absolute-path-to_software/lapack/lib:absolute-path-to_software/trilinos/lib:absolute-path-to_software/boost/lib:absolute-path-to_software/gsl/bin:absolute-path-to_software/root/lib:$LD_LIBRARY_PATH

Building FRENSIE

At this point all of the dependent software libraries should have been built. If any errors were encountered do not try to proceed to building FRENSIE. If no errors were encountered, follow the instructions below.

move to the frensie working directory - not the repo itself (e.g. software/frensie)
run mkdir build
move to the build directory (e.g. software/frensie/build)
copy the FRENSIE/scripts/frensie.sh into the build directory
change the variables in the script to reflect the desired system paths
run ./frensie.sh to configure FRENSIE
run make -j n
run make test
run make manual
run make install

Note: The FRENSIE build system needs to know where the Trilinos source files and Moab source files are. Therefore, there are two optional CMake variables called TRILINOS_SOURCE and MOAB_SOURCE that can be set if the source files are in a non-standard location (not in TRILINOS_PREFIX/src or MOAB_PREFIX/src ). This variable is shown in the frensie.sh script.

There are two reasons why the Trilinos source file location is needed. The first is that Trilinos provides a standard unit test main file that can be used to compile basic unit test suites. The second reason is because of a bug that has been found in the Teuchos_TwoDArray.hpp file. A patch file has been created and will be applied by the build system.

The reason why the moab source file location is needed is because of a race condition that was found in the DagMC.cpp file. Without patching this file the only safe way to run DagMC with threads is by placing omp critical blocks around each DagMC call, which results in very poor thread scaling. A patch file has been create which will be applied by the build system. The first time the patch is applied, the build system will report an error and indicate that moab must be rebuilt before it can proceed. After rebuilding moab (using the same steps outlined above), frensie can be reconfigured and the build system should report no errors. After applying the patch to fix the race condition, close to linear thread scaling should be observed.

Because this will eventually be an open source project, the goal is to be able to build FRENSIE without having to acquire commercial software licenses. Currently, the geometry capabilities within FRENSIE are only activated when the DagMC configure option is set to ON (e.g. -D FRENSIE_ENABLE_DAGMC:BOOL=ON), which requires a CUBIT license. In the future, more software libraries will be incorporated into FRENSIE which will allow for geometry capabilities to be built without building DagMC.

Note: There are several other configure options that can be changed in the frensie.sh script.

-D FRENSIE_ENABLE_DBC:BOOL=ON turns on very thorough Design-by-Contract checks that can be a very useful debugging tool.
-D FRENSIE_ENABLE_OPENMP:BOOL=ON enables OpenMP thread support.
-D FRENSIE_ENABLE_MPI:BOOL=ON enables MPI support.
-D DOXYGEN_PREFIX:PATH=path-to-doxygen-install-dir indicates where the doxygen install directory is located. If your system already has Doxygen 1.8.2 or above, there is no need to install version 1.8.8 and this option can be deleted from the frensie.sh script.
-D MCNP_DATA_DIR:PATH=path-to-mcnp-data indicates where the nuclear data used by MCNP6 is located on the system. When this configure option is used, the FACEMC executable can be tested using the nuclear data used by MCNP6 by running make test or make test-slow. To disable these tests delete this configure option from the frensie.sh script.
-D SETUP_DASHBOARD_CLIENT:BOOL=ON allows the machine to be used as a dashboard client (see the next section).

Dashboard

A private dashboard has been set up for developers. Please register with the dashboard and send an email to Alex Robinson indicating that you would like to have access to the dashboard.

To set up a dashboard client, simply set the dashboard client setup configure option to on (e.g. -D SETUP_DASHBOARD_CLIENT:BOOL=ON). This will add three new make targets: make Experimental, make Nightly and make Continuous. The experimental target should be used to test that the client has been set up correctly. The nightly and continuous targets can be executed on the client machine at regular intervals using cron and crontab (if on a Linux system). However, it is recommended that these targets are never used and instead the shell scripts frensie-run-nightly.sh and frensie-run-ci.sh (found in the scripts directory) are used. Because cron only loads a few environment variables when it executes commands, it is necessary to write shell scripts that load the necessary environment variables, which is what the two scripts do.

Before setting up the crontab entries, a separate frensie build should be created (following the steps above) for nightly builds (e.g. software/frensie-nightly) and for continuous builds (e.g. software/frensie-ci, if a continuous integration system is desired). Once those builds have been completed, the crontab entries can be created by executing crontab -e. This will open up the table with the default text editor. At the bottom of this file, add the following lines:

0 1 * * * abs-path-to-nightly-build-dir/frensie-run-nightly.sh
*/5 * * * * abs-path-to-ci-build-dir/frensie-run-ci.sh

The second line can be omitted if the client will only do nightly builds. Note that the first line tells cron to run the nightly script every day at 1:00 AM. The second line tells cron to run the ci script every 5 minutes (if no changes to the master branch have occured nothing happens).

Feedback

If any issues are encountered during the build process please direct your questions to Alex Robinson

sandialabs / frensie-0.3.0 Goto Github PK

frensie-0.3.0's Introduction