SEACAS [Documentation]

• Get the sources
• Build instructions
• Configure, Build, and Install SEACAS
• Testing
• Exodus
• 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

Download and build dependencies

There are a few externally developed third-party libraries (TPL) that are required to build SEACAS.

• Zoltan -- required, supplied
• HDF5 -- optional
• NetCDF -- required with modifications
• MatIO -- optional
• GNU Parallel -- optional
• CGNS -- experimental optional

Zoltan

A snapshot of zoltan_distrib_v3.82.tar.gz is provided in seacas/packages/zoltan. This will be built automatically as part of the SEACAS build process.

HDF5

If you are using the netcdf-4 capability in the netcdf library or are using the MatIO library for conversion of exodus to/from matlab format, then you will need the hdf5 library.

The hdf5 library is used for the netcdf4 capability in netcdf which in turn is used by exodus. The netcdf4 capability is typically used for large models (>150 million elements); if you are not planning to create or read models of this size, you do not have to build hdf5.

• Download HDF5 from http://www.hdfgroup.org/HDF5/release/obtain5.html and put it inside seacas/TPL/hdf5
• untar it, creating a directory will will refer to as hdf5-X.X.X
• cd to that directory and enter the command: ./configure --prefix=${ACCESS} --enable-shared --enable-production --enable-debug=no --enable-static-exec
• make && make install

NetCDF

The most recent released version is recommended. For use with Exodus, some local modifications to the netcdf.h include file are required. See NetCDF-Mapping.md for an explanation of why these modifications are required (or highly recommended)

• Download the latest netcdf-c release from http://www.unidata.ucar.edu/downloads/netcdf/index.jsp and put it inside seacas/TPL/netcdf

• cd TPL/netcdf

• tar zxvf netcdf-4.3.3.1.tar.gz

• Modify the following defines in seacas/TPL/netcdf/netcdf-4.3.3.1/include/netcdf.h.

  #define NC_MAX_DIMS     65536    /* max dimensions per file */
  #define NC_MAX_VARS     524288   /* max variables per file */
  

• cd netcdf-4.3.3.1 and enter the command:

  ./configure --enable-netcdf-4  --enable-shared \
    --disable-fsync --prefix ${ACCESS} \
    --disable-dap --disable-cdmremote
  

• If the configure step complains about not being able to find the HDF5 library, you may need to do the following and then redo the configure step

  CFLAGS="-I{HDF5_ROOT}/include"; export CFLAGS
  LDFLAGS="-L{HDF5_ROOT}/lib   "; export LDFLAGS
  

• make && make install

MatIO

The MatIO library is used in the exo2mat and mat2exo programs which convert an exodus file to and from a MATLAB binary file. To use this do:

• Download matio via git:

• cd TPL/matio

• git clone https://github.com/tbeu/matio.git

• cd matio and enter the command:

  ./autogen.sh
  # The -L is to find the hdf5 library...
  export LDFLAGS="-L${ACCESS}/lib"
  ./configure --with-hdf5=${ACCESS} --enable-mat73 --enable-shared --prefix=${ACCESS}
  

• make && make install

GNU Parallel

GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job is typically a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, or a list of tables. In SEACAS, this is only used by epup which runs multiple epu jobs concurrently. To build:

• Download the most recent version of the library from ftp://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2.

```
cd TPL/parallel
tar jxvf /path/to/parallel-latest.tar.bz2
cd parallel-20150522
./configure --prefix ${ACCESS}
```

CGNS

Experimental support for CGNS in the IOSS library is being added. To use this capability, you will need to download and install the CGNS library:

• Download CGNS via git:

```
cd TPL/cgns
git clone https://github.com/CGNS/CGNS.git
```

• Build using CMake.
  • Modify TPL/cgns/runconfigure.sh to meet your environment
  • mkdir build
  • cd build
  • ../../runconfigure.sh
  • make && make install

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

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.
• 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.

License

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

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

to get SEACAS. This is provided by Nico Schlömer.

Contact information

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