jbakosi / seacas

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.

SEACAS [Documentation]

• Get the sources
• Build instructions
• Configure, Build, and Install SEACAS
• Testing
• Exodus
• Trilinos
• SPACK
• License
• Ubuntu
• Contact information
• For information on building with MPI, see README-PARALLEL.md
• NOTE: The old imake-based build has been removed.

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
JOBS	{count}	2	Number of "jobs" used for simultaneous compiles
FORCE	YES, NO	NO	Force downloading and building even if lib is already installed.
DOWNLOAD	YES, NO	YES	Should TPLs be downloaded.
BUILD	YES, NO	YES	Should TPLs be built and installed.
SHARED	YES, NO	YES	Build shared libraries is YES, archive (.a) if NO
MPI	ON, OFF	OFF	If ON, then build parallel capability
CRAY	YES, NO	NO	Is this a Cray system (special parallel options)
NEEDS_ZLIB	YES, NO	NO	If system does not have zlib installed, download and install it.
CGNS	YES, NO	YES	Should CGNS TPL be built.
USE_64BIT_INT	YES, NO	NO	In CGNS, enable 64-bit integers
MATIO	YES, NO	YES	Should matio TPL be built.
ADIOS2	YES, NO	NO	Should adios2 TPL be built.
KOKKOS	YES, NO	NO	Should Kokkos TPL be built.
GNU_PARALLEL	YES, NO	YES	Should GNU parallel script be built.
H5VERSION	V110, V18	V110	Use HDF5-1.10.X or HDF5-1.8.X
JOBS	#	2	Used in make -j #
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

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:

• You can either clone entire source tree as above, or you can download a zip file containing only the exodus source (and build-related files). The url for the zip file is https://github.com/gsjaardema/seacas/archive/exodus.zip NOTE: Probably out-of-date and better to just clone entire repository.
• 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 Python interface.

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

Ubuntu

There is a PPA available for SEACAS that is updated nightly from SEACAS master. Anyone using Ubuntu can now just add the PPA and do

sudo add-apt-repository ppa:nschloe/seacas-nightly
sudo apt-get update

and then

sudo apt-get install seacas-bin

to get the SEACAS binaries. You can also install 'libseacas-dev' or 'libseacas0'. This is provided by Nico Schlömer.

Contact information

Greg Sjaardema ([e-mail], [e-mail])