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The Sandia Engineering Analysis Code Access System (SEACAS) is a suite of preprocessing, postprocessing, translation, and utility applications supporting finite element analysis software using the Exodus database file format.

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SEACAS [Documentation] [Wiki]

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Get the sources

git clone https://github.com/gsjaardema/seacas.git

This will create a directory that will be referred to as seacas in the instructions that follow. You can rename this directory to any other name you desire. Set an environment variable pointing to this location by doing:

cd seacas && export ACCESS=`pwd`

Build instructions

Automatically download and build dependencies (Third-Party Libraries)

There are a few externally developed third-party libraries (TPL) that are required (or optional) to build SEACAS: HDF5, NetCDF, CGNS, MatIO, Kokkos, and (if MPI set) PnetCDF libraries. You can build the libraries using the install-tpl.sh script, or you can install them manually as detailed in TPL-Manual-Install.md.

  • To use the script, simply type ./install-tpl.sh
  • The default behavior can be modified via a few environment variables:
Variable Values Default Description
INSTALL_PATH path to install pwd Root of install path; default is current location
COMPILER clang, gnu, intel, ibm gnu What compiler should be used for non-parallel build
MPI ON, OFF OFF If ON, then build parallel capability
FORCE YES, NO NO Force downloading and building even if lib is already installed.
BUILD YES, NO YES Should TPLs be built and installed.
DOWNLOAD YES, NO YES Should TPLs be downloaded.
USE_PROXY YES, NO NO Sandia specific -- use proxy when downloading tar files
DEBUG YES, NO NO Build debug executable; default is optimized
SHARED YES, NO YES Build shared libraries is YES, archive (.a) if NO
CRAY ON, OFF ON Is this a Cray system (special parallel options)
NEEDS_ZLIB YES, NO NO If system does not have zlib installed, download and install it (HDF5 compression).
NEEDS_SZIP YES, NO NO If system does not have szip installed, download and install it (HDF5 compression).
USE_64BIT_INT YES, NO NO In CGNS, enable 64-bit integers
CGNS ON, OFF ON Should CGNS TPL be built.
MATIO ON, OFF ON Should matio TPL be built.
METIS ON, OFF OFF Should metis TPL be built (parallel decomposition).
PARMETIS ON, OFF OFF Should parmetis TPL be built (parallel decomposition).
ADIOS2 ON, OFF OFF Should adios2 TPL be built.
KOKKOS ON, OFF OFF Should Kokkos TPL be built.
GNU_PARALLEL ON, OFF ON Should GNU parallel script be built.
H5VERSION V12, V110, V18 V110 Use HDF5-1.12.X, HDF5-1.10.X or HDF5-1.8.X
BB YES, NO NO Enable Burst Buffer support in PnetCDF
JOBS {count} 2 Number of "jobs" used for simultaneous compiles
SUDO "" or sudo "" If need to be superuser to install
  • NOTE: The DOWNLOAD and BUILD options can be used to download all TPL source; move to a system with no outside internet access and then build/install the TPLs.
  • The arguments can either be set in the environment as: export COMPILER=gnu, or passed on the script invocation line: COMPILER=gnu ./install-tpl.sh

Configure, Build, and Install SEACAS

At this time, you should have all external TPL libraries built and installed into ${ACCESS}/lib and ${ACCESS}/include. You are now ready to configure the SEACAS CMake build.

  • cd $ACCESS
  • mkdir build
  • cd build
  • edit the ${ACCESS}cmake-config file and adjust compilers and other settings as needed.
  • enter the command ../cmake-config and cmake should configure everything for the build.
  • make && make install
  • If everything works, your applications should be in ${ACCESS}/bin
  • To install in a different location, do INSTALL_PATH={path_to_install} ../cmake-config
  • The default behavior can be modified via a few environment variables:
Variable Values Default Description
INSTALL_PATH path to install pwd Root of install path; default is current location
BUILDDIR {dir} pwd/build Directory to do config and build
COMPILER clang, gnu, intel, ibm gnu What compiler should be used for non-parallel build
SHARED ON, OFF ON Build and use shared libraries is ON
APPLICATIONS ON, OFF ON Should all SEACAS applications be built (see cmake-config)
LEGACY ON, OFF ON Should the legacy SEACAS applications be built (see cmake-config)
FORTRAN ON, OFF ON Should fortran libraries and applications be built (see cmake-config)
ZOLTAN ON, OFF ON Should zoltan library and nem_slice be built
PYTHON_VER 2.7 3.0 3.0 Minimum version of python which should be found
BUILD_TYPE debug, release release what type of build
DEBUG -none- If specified, then do a debug build. Can't be used with BUILD_TYPE
HAVE_X11 ON, OFF ON Does the system have X11 libraries and include files; used for blot, fastq
THREADSAFE ON, OFF OFF Compile a thread-safe IOSS and Exodus library
USE_SRUN ON, OFF OFF If MPI enabled, then use srun instead of mpiexec to run parallel tests
DOXYGEN ON, OFF OFF Run doxygen on several packages during build to generate documentation
OMIT_DEPRECATED YES, NO NO Should the deprecated code be omitted; NO will enable deprecated code
EXTRA_WARNINGS YES, NO NO Build with extra warnings enabled; see list in cmake-config
SANITIZER many NO If not NO, build using specified sanitizer; see list in cmake-config
GENERATOR many "Unix Makefiles" what generator should CMake use; see cmake doc
  • The arguments can either be set in the environment as: export COMPILER=gnu, or passed on the script invocation line: COMPILER=gnu ./install-tpl.sh

Parallel Build

For some areas of use, a parallel version of SEACAS is required. This will build a "parallel-aware" version of the exodus library and a parallel version of the Ioss library.

The only modification to the serial build described above is to make sure that the mpicc parallel C compiler is in your path and to add the MPI=ON argument to the install-tpl.sh script invokation when building the TPLs. For example:

   MPI=ON ./install-tpl.sh

This will download all requested libraries and build them with parallel capability enabled (if applicable). You can then continue with the steps outlined in the previous section.

Testing

There are a few unit tests for zoltan, exodus, and aprepro that can be run via make test if you configured with -D SEACASProj_ENABLE_TESTS=ON.

There is also a system-level test that just verifies that the applications can read and write exodus files correctly. This test runs off of the installed applications. To run do:

  • make install
  • cd ../SEACAS-Test
  • make clean; make

This will run through several of the SEACAS applications creating a mesh (exodus file) and then performing various manipulations on the mesh. If the test runs successfully, there is some hope that everything has built and is running correctly.

Exodus

If you only want the exodus library, then follow most of the above instructions with the following exceptions:

  • Clone entire source tree as above. (There used to be a zip file, but difficult to keep up-to-date)
  • You only need the netcdf and optionally hdf5 libraries
  • Use the cmake-exodus file instead of cmake-config.
  • This will build, by default, a shared exodus library and also install the exodus.py and exomerge.py Python interfaces.

Trilinos

Although SEACAS is included in Trilinos (https://github.com/trilinos/Trilinos), it is also possible to use the SEACAS code from this repository to override the possibly older SEACAS code in Trilinos. The steps are to directly pull SEACAS from github under Trilinos and then build SEACAS under Trilinos with that version using SEACAS_SOURCE_DIR_OVERRIDE. Here is how you do it:

cd Trilinos/
git clone https://github.com/gsjaardema/seacas.git
cd BUILD/
cmake -DSEACAS_SOURCE_DIR_OVERRIDE:STRING=seacas/packages/seacas -DTrilinos_ENABLE_SEACAS [other options] ..

SPACK

The SPACK package manager (https://spack.io/) can be used to install SEACAS and all depedent third-party libaries. SEACAS is a supported package in SPACK as of December 2018.

git clone https://github.com/spack/spack.git
. spack/share/spack/setup-env.sh
spack install seacas~mpi   # Serial build (most common)

Enter spack info seacas to see information on supported variants and other information about the SEACAS package.

License

SEACAS is licensed under the Modified BSD License. See the LICENSE file for details.

The following externally-developed software routines are used in some of the SEACAS applications and are under a separate license:

Routine Where Used License
getline packages/seacas/libraries/aprepro_lib/apr_getline_int.c MIT
getline packages/seacas/libraries/suplib_c/getline.c BSD
GetLongOpt packages/seacas/libraries/suplib_cpp/GetLongOpt.C public domain
adler hash packages/seacas/libraries/suplib_c/adler.c zlib
MurmurHash packages/seacas/libraries/ioss/src/Ioss_FaceGenerator.C public domain
json include file packages/seacas/libraries/ioss/src/visualization/ MIT
terminal_color packages/seacas/libraries/suplib_cpp zlib
Tessil Hash packages/seacas/libraries/ioss/src/hash MIT
Catch2 packages/seacas/libraries/ioss/src/catch.hpp Boost
{fmt} packages/seacas/libraries/ioss/src/fmt BSD-2-Clause

Contact information

Greg Sjaardema (gsjaardema@gmail.com, gdsjaar@sandia.gov)

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The Sandia Engineering Analysis Code Access System (SEACAS) is a suite of preprocessing, postprocessing, translation, and utility applications supporting finite element analysis software using the Exodus database file format.

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