/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.

Primary LanguageCOtherNOASSERTION

SEACAS [Documentation] [Wiki]

Codacy Badge Analysis Status Spack Version Appveyor Build SEACAS Docker Exodus Docker Github Actions -- CI Serial Github Actions -- CI Variants Github Actions -- CI Intel Github Actions -- CI MSYS2

Get the sources

git clone https://github.com/sandialabs/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.

  • The script requires bash and wget, which you may need to install.
  • To use the script, simply type bash ./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 nvidia gnu What compiler should be used for non-parallel build. Must have C++-17 capability.
MPI YES, NO NO If YES, 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 if YES, archive (.a) if NO
CRAY YES, NO YES 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).
USE_ZLIB_NG YES, NO NO Should the improved zlib-ng library be used to provide ZLIB capability
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 YES, NO YES Should CGNS TPL be built.
MATIO YES, NO YES Should matio TPL be built.
METIS YES, NO NO Should metis TPL be built (parallel decomposition).
PARMETIS YES, NO NO Should parmetis TPL be built (parallel decomposition).
ADIOS2 YES, NO NO Should adios2 TPL be built.
CATALYST2 YES, NO NO Should catalyst 2 TPL be built.
KOKKOS YES, NO NO Should Kokkos TPL be built.
GNU_PARALLEL YES, NO YES Should GNU parallel script be built.
FMT YES, NO YES Should Lib::FMT TPL be built.
CATCH2 YES, NO YES Should Catch2 be built (used for testing).
H5VERSION V114, V110, V18 V114 Use HDF5-1.14.X, HDF5-1.10.X or HDF5-1.8.X
H5CPP YES, NO NO Should the HDF5 C++ library be built/installed
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 YES, NO YES Build and use shared libraries is YES
APPLICATIONS YES, NO YES Should all SEACAS applications be built (see cmake-config)
LEGACY YES, NO YES Should the legacy SEACAS applications be built (see cmake-config)
FORTRAN YES, NO YES Should fortran libraries and applications be built (see cmake-config)
ZOLTAN YES, NO YES Should zoltan library and nem_slice be built
BUILD_TYPE debug, release release what type of build
MODERN YES, NO NO Use "modern" CMake configuration files for netCDF and HDF5
DEBUG -none- If specified, then do a debug build. Can't be used with BUILD_TYPE
HAVE_X11 YES, NO YES Does the system have X11 libraries and include files; used for blot, fastq
THREADSAFE YES, NO NO Compile a thread-safe IOSS and Exodus library
USE_SRUN YES, NO NO If MPI enabled, then use srun instead of mpiexec to run parallel tests
DOXYGEN YES, NO NO 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=YES argument to the install-tpl.sh script invocation when building the TPLs. For example:

   MPI=YES ./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, ioss, and aprepro that can be run via make test or ctest if you configured with -D Seacas_ENABLE_TESTS=YES.

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/sandialabs/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 dependent third-party libraries. 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)

Docker

An Ubuntu-based Docker image, with SEACAS built and installed, is available on Docker Hub.

docker pull mrbuche/seacas

SEACAS is located in /seacas when running the container. There is also a similar image available on Docker Hub with only Exodus built and installed.

docker pull mrbuche/exodus

CMake Example Usage

A simple example of using the SEACAS Exodus library in your external project. Here is the CMakeLists.txt file:

project(ExodusCMakeExample VERSION 1.0 LANGUAGES C Fortran)
cmake_minimum_required(VERSION 3.1...3.26)

#### C ####
find_package(SEACASExodus CONFIG)
add_executable(ExodusWriteC ExodusWrite.c)
target_link_libraries(ExodusWriteC PRIVATE SEACASExodus::all_libs)

#### FORTRAN #####
IF ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
  SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer -fdefault-real-8 -fdefault-integer-8 -fno-range-check")
ELSEIF ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "XL")
  SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qintsize=8 -qrealsize=8")
ELSEIF ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Cray")
  SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -sdefault64")
ELSE()
  SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -r8 -i8")
ENDIF()

find_package(SEACASExodus_for CONFIG)
add_executable(ExodusReadFor ExodusRead.f)
target_link_libraries(ExodusReadFor PRIVATE SEACASExodus_for::all_libs)

A similar CMakeLists.txt file for using the IOSS library would be something like:

cmake_minimum_required(VERSION 3.1...3.26)
project(IossCMakeExample VERSION 1.0 LANGUAGES CXX)

#### C++ IOSS ####
find_package(SEACASIoss CONFIG)
add_executable(IossExample IossExample.C)
target_link_libraries(IossExample PRIVATE SEACASIoss::all_libs)

The cmake-use-example directory contains Exodus example files in the exodus subdirectory and Ioss example files in the ioss subdirectory. These provide short examples of how to build and link a program with the Exodus and/or Ioss libraries.

To use this, copy the contents of the directory to your own filespace and modify the contents as needed.

To configure and build, you would do something like:

  mkdir build; cd build
  CMAKE_PREFIX_PATH={path_to_root_of_seacas_install} cmake ..
  make

And you would then get an executable (ExodusWriteC and ExodusReadFor for Exodus, IossExample for Ioss) compiled and linked against the Exodus and/or Ioss libraries.

Required Software

The SEACAS system requires that there be some libraries and applications already existing on the chosen system prior to building SEACAS and its required Third-Party Liberaries.

These include:

  • The git application is used to access the SEACAS and TPL git repositories

  • CMake is used to generate the build system.

  • C, C++, and (optionally) Fortran compilers. The C compiler must support the C11 standard and C++ must support C+++17. GNU, Clang, Intel, Cray, compilers are supported and tested regularly.

  • For parallel capability, an MPI library is needed. We have used openmpi, mpich, mvapich, intel, and cray MPI libraries. It is recommended to use as current an MPI library as possible.

  • Automake is used to configure some of the TPL builds

  • wget is needed to download some of the TPL library source code.

  • python is required to use the exodus.py and exomerge.py Python interfaces to Exodus databases. Python3 is recommended.

  • To use the blot and fastq applications, an X11 development environment is needed.

  • Flex and Bison are optional if you are developing new capabilities in aprepro.

  • M4 is needed to build the netCDF library.

Mac

On a mac system, I use the brew system which provides all of the applications listed above. The X11 system I use is XQuartz. The Mac also requires Xcode

Linux

On an ubuntu system, the following is used to set up the basic packages needed to compile SEACAS:

apt install -y libaec-dev zlib1g-dev automake autoconf \
libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake \
libzip-dev openmpi-bin libopenmpi-dev \

Windows

On windows, I have used the following packages for MINGW64:

git mingw-w64-x86_64-toolchain make mingw-w64-x86_64-hdf5 \
mingw-w64-x86_64-cgns mingw-w64-x86_64-netcdf mingw-w64-x86_64-zlib \
mingw-w64-x86_64-gcc-fortran mingw-w64-x86_64-gcc-libgfortran \
mingw-w64-x86_64-cmake mingw-w64-x86_64-fmt

There is also a Visual Studio build performed at each commit to the SEACAS git repository. See the file .appveyor.yml for more details.

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
Tessil Hash packages/seacas/libraries/ioss/src/hash MIT
pdqsort packages/seacas/libraries/ioss/src Zlib License

Contact information

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