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Add README and netcdf-mapping file for use in Trilinos
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| # SEACAS [[Documentation](http://gsjaardema.github.io/seacas/)] | ||
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| * [Build instructions](#build-instructions) | ||
| * [Configure, Build, and Install SEACAS](#configure-build-and-install-seacas) | ||
| * [Testing](#testing) | ||
| * [Contact information](#contact-information) | ||
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| ## Build instructions | ||
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| ### Download and build dependencies | ||
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| There are a few externally developed third-party libraries (TPL) that are required to | ||
| build SEACAS | ||
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| * [Zoltan](#zoltan) -- required, part of Trilinos | ||
| * [HDF5](#hdf5) -- optional, but highly recommended | ||
| * [Parallel-NetCDF](#parallel-netcdf) -- optional for parallel | ||
| * [NetCDF](#netcdf) -- required with modifications | ||
| * [MatIO](#matio) -- optional | ||
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| #### Zoltan | ||
| Zoltan is a package in Trilinos and it must be enabled for a SEACAS build. | ||
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| #### HDF5 | ||
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| 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. | ||
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| 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 and do not want compression | ||
| support, you do not have to build hdf5. | ||
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| * Download HDF5 from http://www.hdfgroup.org/HDF5/release/obtain5.html | ||
| * untar it, creating a directory will will refer to as `hdf5-X.X.X` | ||
| * `cd` to that directory and enter the command: | ||
| * Serial: | ||
| ``` | ||
| ./configure --prefix=${WHERE_TO_INSTALL} --enable-shared --enable-production --enable-debug=no --enable-static-exec | ||
| ``` | ||
| * Parallel: | ||
| ``` | ||
| CC=mpicc ./configure --prefix=${WHERE_TO_INSTALL} --enable-shared --enable-production --enable-debug=no --enable-static-exec --enable-parallel | ||
| ``` | ||
| * `make && make install` | ||
| #### Parallel-NetCDF | ||
| For a parallel build of Trilinos, especially to use the | ||
| auto-decomposition support of the Ioss library, you will need the | ||
| parallel-netcdf library, also known as pnetcdf. | ||
| * Download http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz | ||
| * `tar zxvf parallel-netcdf-1.6.1.tar.gz` | ||
| * `cd` to the `parallel-netcdf-1.6.1` directory and enter the command: | ||
| ``` | ||
| CC=mpicc ./configure --disable-fortran --prefix ${WHERE_TO_INSTALL} | ||
| ``` | ||
| * `make && make install` | ||
| #### NetCDF | ||
| The most recent released version is recommended. For use with Exodus, some local modifications to the netcdf.h include file are required. See [NetCDF-Mapping.md](NetCDF-Mapping.md) for an explanation of why these modifications are required (or highly recommended) | ||
| * Download the latest netcdf-c release from http://www.unidata.ucar.edu/downloads/netcdf/index.jsp | ||
| * `tar zxvf netcdf-4.4.0.tar.gz` (or whatever the latest version is) | ||
| * Modify the following defines in netcdf-4.4.0/include/netcdf.h. | ||
| ``` | ||
| #define NC_MAX_DIMS 65536 /* max dimensions per file */ | ||
| #define NC_MAX_VARS 524288 /* max variables per file */ | ||
| ``` | ||
| * `cd netcdf-4.4.0` and enter the command: | ||
| * serial | ||
| ``` | ||
| CFLAGS="-I${WHERE_TO_INSTALL}/include" \ | ||
| CPPFLAGS="-DNDEBUG" LDFLAGS="-L${WHERE_TO_INSTALL}/lib" \ | ||
| ./configure --enable-netcdf-4 \ | ||
| --disable-fsync --prefix ${WHERE_TO_INSTALL} \ | ||
| --disable-dap --disable-v2 | ||
| ``` | ||
| * parallel | ||
| ``` | ||
| CC='mpicc' CFLAGS="-I${WHERE_TO_INSTALL}/include" \ | ||
| CPPFLAGS="-DNDEBUG" LDFLAGS="-L${WHERE_TO_INSTALL}/lib" \ | ||
| ./configure --enable-netcdf-4 --enable-pnetcdf \ | ||
| --disable-fsync --prefix ${WHERE_TO_INSTALL} \ | ||
| --disable-dap --disable-v2 | ||
| ``` | ||
| * Check the results of the configure and make sure that the listings | ||
| under features are similar to: | ||
| ``` | ||
| # Features | ||
| -------- | ||
| NetCDF-2 API: no | ||
| NetCDF-4 API: yes | ||
| CDF-5 Support: yes | ||
| HDF5 Support: yes | ||
| PNetCDF Support: yes | ||
| NC-4 Parallel Support: yes | ||
| ``` | ||
| There will be other features, but their settings are not important | ||
| for seacas. For a serial build, `PNetCDF` and `NC-4 Parallel Support` | ||
| should be `no` | ||
| * `make && make install` | ||
| #### MatIO | ||
| The MatIO library is used in the `exo2mat` and `mat2exo` programs which convert an exodus file to and from a MATLAB binary file. To use this do: | ||
| * Download matio via git: | ||
| * `git clone https://github.com/tbeu/matio.git` | ||
| * `cd matio` and enter the command: | ||
| ``` | ||
| ./autogen.sh | ||
| # The -L is to find the hdf5 library... | ||
| export LDFLAGS="-L${WHERE_TO_INSTALL}/lib" | ||
| ./configure --with-hdf5=${WHERE_TO_INSTALL} --enable-mat73 --enable-shared --prefix=${WHERE_TO_INSTALL} | ||
| ``` | ||
| * `make && make install` | ||
| ## Configure, Build, and Install Trilinos | ||
| At this time, you should have all external TPL libraries built and | ||
| installed into `${WHERE_TO_INSTALL}/lib` and `${WHERE_TO_INSTALL}/include`. You are now ready | ||
| to configure the SEACAS portion of the Trilinos cmake build. | ||
| The relavant defines for SEACAS are listed below: | ||
| ``` | ||
| -D Trilinos_ENABLE_SEACAS:BOOL=ON | ||
| -D TPL_ENABLE_Netcdf:BOOL=ON | ||
| -D Netcdf_LIBRARY_DIRS:PATH=${WHERE_TO_INSTALL}/lib | ||
| -D TPL_Netcdf_INCLUDE_DIRS:PATH=${WHERE_TO_INSTALL}/include | ||
| -D TPL_Netcdf_Enables_Netcdf4:BOOL=ON (if built with hdf5 libraries which give netcdf-4 capability) | ||
| -D SEACASExodus_ENABLE_MPI:BOOL=OFF|ON (ON if parallel; OFF if serial) | ||
| -D TPL_ENABLE_Matio:BOOL=ON (set to OFF if not available) | ||
| -D Matio_LIBRARY_DIRS:PATH=${WHERE_TO_INSTALL}/lib | ||
| -D TPL_Matio_INCLUDE_DIRS:PATH=${WHERE_TO_INSTALL}/include | ||
| -D TPL_X11_INCLUDE_DIRS:PATH=/usr/X11R6/include (SVDI, blot, fastq require X11 includes and libs) | ||
| -D SEACAS_ENABLE_TESTS=ON | ||
| -D Trilinos_EXTRA_LINK_FLAGS:STRING="-L${WHERE_TO_INSTALL}/lib -lpnetcdf -lhdf5_hl -lhdf5 -lz" | ||
| ``` | ||
| ## Testing | ||
| There are a few unit tests for exodus, and aprepro that can be run via `make test` if you configured with `-D SEACAS_ENABLE_TESTS=ON`. | ||
| ## Contact information | ||
| Greg Sjaardema ([email protected], [email protected]) | ||