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| Original file line number | Diff line number | Diff line change |
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| # SEACAS [[Documentation](http://sandialabs.github.io/seacas-docs/)] [[Wiki](https://github.com/sandialabs/seacas/wiki)] | ||
| [](https://www.codacy.com/gh/gsjaardema/seacas/dashboard?utm_source=github.com&utm_medium=referral&utm_content=gsjaardema/seacas&utm_campaign=Badge_Grade) | ||
| [](https://scan.coverity.com/projects/gsjaardema-seacas) | ||
| [](https://spack.readthedocs.io/en/latest/package_list.html#seacas) | ||
| [](https://ci.appveyor.com/project/gsjaardema/seacas/branch/master) | ||
| [](https://github.com/sandialabs/seacas) | ||
| [](https://github.com/sandialabs/seacas) | ||
| [](https://github.com/sandialabs/seacas) | ||
| [](https://github.com/sandialabs/seacas) | ||
| ## Documentation | ||
| See SEACAS (including Exodus) documentation at http://sandialabs.github.io/seacas-docs/ | ||
|
|
||
| * [Get the sources](#get-the-sources) | ||
| * [Build instructions](#build-instructions) | ||
| * [Configure, Build, and Install SEACAS](#configure-build-and-install-seacas) | ||
| * [Parallel Build](#parallel-build) | ||
| * [Testing](#testing) | ||
| * [Exodus](#exodus) | ||
| * [Trilinos](#trilinos) | ||
| * [SPACK](#spack) | ||
| * [License](#license) | ||
| * [Contact information](#contact-information) | ||
| * NOTE: The old imake-based build has been removed. | ||
| ## Installation | ||
| Installation directions are available at http://github.com/sandialabs/seacas | ||
|
|
||
| ## Get the sources | ||
| ```sh | ||
| 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: | ||
| ## Contact | ||
|
|
||
| ```sh | ||
| cd seacas && export ACCESS=`pwd` | ||
| ``` | ||
| Greg Sjaardema, | ||
| Sandia National Laboratories, | ||
| <[email protected]>, <[email protected]> | ||
|
|
||
| ## Build instructions | ||
| We appreciate feedback from users of this package. Please send | ||
| comments, suggestions, and bug reports to Greg Sjaardema | ||
| <[email protected]>, <[email protected]> | ||
|
|
||
| ### 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](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. Must have C++-14 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](https://github.com/zlib-ng/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. | | ||
| | H5VERSION | V114, V110, V18 | V110 | Use HDF5-1.14.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 | 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 | | ||
| | 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: | ||
| ```sh | ||
| 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: | ||
|
|
||
| ```sh | ||
| 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. | ||
|
|
||
| ```sh | ||
| 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](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](https://opensource.org/licenses/MIT) | | ||
| | getline | `packages/seacas/libraries/suplib_c/getline.c` | [BSD](https://opensource.org/licenses/BSD-3-Clause) | | ||
| | [GetLongOpt](https://searchcode.com/codesearch/view/64130032/) | `packages/seacas/libraries/suplib_cpp/GetLongOpt.C` | public domain | | ||
| | [adler hash](https://en.wikipedia.org/wiki/Adler-32) | `packages/seacas/libraries/suplib_c/adler.c` | [zlib](https://opensource.org/licenses/zlib) | | ||
| | [MurmurHash](https://github.com/aappleby/smhasher) | `packages/seacas/libraries/ioss/src/Ioss_FaceGenerator.C` | public domain | | ||
| | [json include file](http://jsoncpp.sourceforge.net) | `packages/seacas/libraries/ioss/src/visualization/` | [MIT](https://opensource.org/licenses/MIT) | | ||
| | [terminal_color](https://github.com/matovitch/trmclr) | `packages/seacas/libraries/aprepro_lib` | [zlib](https://opensource.org/licenses/zlib) | | ||
| | [Tessil Hash](https://github.com/Tessil/) | `packages/seacas/libraries/ioss/src/hash` | [MIT](https://opensource.org/licenses/MIT) | | ||
| | [doctest](https://github.com/doctest/doctest) | `packages/seacas/libraries/ioss/src/doctest.h` | [MIT](https://opensource.org/licenses/MIT) | | ||
| | [pdqsort](https://github.com/orlp/pdqsort) | `packages/seacas/libraries/ioss/src` | [Zlib License](https://github.com/orlp/pdqsort/blob/master/license.txt) | | ||
| ## Contact information | ||
|
|
||
| Greg Sjaardema (<[email protected]>, <[email protected]>) |
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