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DEPENDENCIES.md

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Installing LaGriT Dependencies

LaGriT requires a number of external dependencies to fully compile.

  • HDF5 -- required
  • NetCDF -- required with modifications
  • zlib -- required
  • ExodusII -- optional but recommended

ExodusII is used for file exportation. If you have no need of this format, you may skip the ExodusII installation after building netCDF and HDF5 and following the Managing Exodus instructions in INSTALL.md.

LaGriT also requires the following compilers:

  • gcc-core
  • gcc-fortran
  • gcc-g++

If you are on Windows, it will be necessary to install Cygwin.

NOTE: This configuration also depends on what you use as your fortran, c++, and gcc compilers. You can add these variables to the ./configure commands without adding the word 'export', or you can set these as global variables in your .bashrc file (recommended).

  export FC="/bin/gfortran"
  export CC="/bin/gcc"
  export CXX="/bin/c++"
  export FC90="/bin/gfortran"
  export RANLIB="/bin/gcc-ranlib"
  export AR="/bin/gcc-ar"

1. Compiling zlib

1.1. Unpack zlib and navigate to the directory

1.2. Compile for Cygwin:

./configure --static --prefix=$HOME --64

1.3. Type in make and then make sure there is no errors with make check

1.4. Use make install to finish installing zlib

1.5. Use make clean to clean up the library directory of build files.

2. Compiling HDF5

2.1. Unpack the tar source file, in it you should find a folder named release_docs, which contains installation instructions in file called INSTALL_Cygwin.txt. I will follow these, while giving the actual commands I used.

CYGWIN NOTE: On Windows, when you run the configure script, it might complain about new line characters. If this happens stop the script with Ctrl+C, and run dos2unix -f targetfile on the file where it throws an error. Use make clean afterwards to clean up your build.

2.2. In Hdf5 directory use the following command to configure the build script:

CFLAGS="-m64 -g" FCFLAGS="-m64 -g" CXXFLAGS="-m64 -g" ./configure --disable-shared --with-zlib=/cygdrive/c/Users/304285/dev/cygwin/home/304285/include,/cygdrive/c/Users/304285/dev/cygwin/home/304285/lib --prefix=$HOME --enable-fortran --enable-cxx --enable-static-exec

CFLAGS="-m64 -g" FCFLAGS="-m64 -g" CXXFLAGS="-m64 -g" ./configure --disable-shared --with-zlib=/lib/libz.a --prefix=$HOME --enable-fortran --enable-cxx --enable-static-exec 

--host=x86_64-w64-mingw32
--build=x86_64-w64-mingw32
--with-gnu-ld

2.3. Once configuration is complete, type in make to build the library, and make check to test it.

2.4. Run make install and make check-install to test it.

2.5. Run make clean to clean up your library of build files.

3. Compiling netCDF

NOTE: After version 4.1.3, NetCDF-fortran became a different distribution so the use of environment variables set for fortran is unnecessary.

3.1. Unpack NetCDF and navigate to the directory, the installation instructions can be traced here: http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/

3.2. Configure the build script

CPPFLAGS="-I$HOME/include -m64 -g" LDFLAGS="-L$HOME/lib -m64 -g" LIBS="-L$HOME/lib -lhdf5_hl -lhdf5 -lz" ./configure --disable-shared --disable-dap --enable-netcdf-4 --prefix=$HOME CFLAGS="-m64 -g"

NOTE: Possibly helpful options: --build, --host

3.3. Build the library with make, and test it with make check

3.4. Finish the install with make install and make clean

4. Compiling Exodus

For Exodus II bug reports, documentation errors, and enhancement suggestions, contact:

Gregory D. Sjaardema

(505) 844-2701

gdsjaar@sandia.gov

4.1. Now before we start installing ExodusII, we need to make some slight modifications to NetCDF in $NETCDF_HOME/include/netcdf.h by changing the following variables as stated in exodus README file:

#define NC_MAX_DIMS  65536 
#define NC_MAX_VARS 524288 
#define NC_MAX_VAR_DIMS 8

4.2. Unpack Exodus and navigate to the exodus directory

4.3. Here we have two options for compiling ExodusII as described in the README, 1st is with Makefile.standalone, and 2nd is with cmake

4.3.1. Using Makefile.standalone (INCOMPLETE: Might need to add additional arguments):

a) Use the following make command:

make -f Makefile.standalone NETCDF=$HOME ARFLAGS=-rcv CFLAGS="-m64" FCFLAGS="-m64" CXXFLAGS="-m64"

b) Copy the Exodus libararies to our local libraries

cp libexodus.a libexoIIv2for.a $HOME/lib

4.3.2. Using cmake (Harder difficulty since requires manipulation of additional libs but completed):

CYGWIN NOTE: To be able to use cmake on my Cygwin installation I had to copy over my cmake executable from /bin/cmake to /home/304285/bin/cmake, and my cmake root files from /usr/share/cmake-3.1.2 to /home/304285/share/cmake-3.1.2. My PATH variable was set up to read my /home/304285/bin directory last and it overwrote the cmake I had in /bin/cmake. (Otherwise it throws could not find CMAKE_ROOT/Module directory not found/Error executing cmake::LoadCache())

a) Run sh cmake-script once you make appropriate changes to your cmake-script file, this was mine:

    EXTRA_ARGS=$@

    # Fortran compiler
    FC="/bin/gfortran"

    # Root to where netcdf and hdf5 libraries and includes 
    # are installed. Libraries will be in LIB_ROOT/lib and 
    # includes will be in LIB_ROOT/include
    LIB_ROOT=/usr/local/lib

    # Root of where to install the exodus libraries and
    # include files.  Library will be in INSTALL_ROOT/lib
    # and include file in INSTALL_ROOT/include
    INSTALL_ROOT=$HOME

    # Complete path to where the exodus.py file should be installed
    PYTHON_INSTALL=${INSTALL_ROOT}/python

    # Add the following for a static build, mine kept throwing me memory truncation error
    # -DCMAKE_EXE_LINKER_FLAGS:STRING="-static" \

    rm -f CMakeCache.txt

    cmake  \
    -DBUILD_SHARED:BOOL=OFF \
    -DBUILD_SHARED_LIBS:BOOL=OFF \
    -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_ROOT} \
    -DCMAKE_Fortran_COMPILER:FILEPATH=${FC} \
    -DNETCDF_NCDUMP:PATH='which ncdump' \
    -DNETCDF_INCLUDE_DIR:PATH=/usr/include \
    -DNETCDF_LIBRARY:PATH=/lib/libnetcdf.dll.a \
    -DHDF5HL_LIBRARY:PATH=/lib/libhdf5_hl.dll.a \
    -DHDF5_LIBRARY:PATH=/lib/libhdf5.dll.a \
    -DZLIB_LIBRARY:PATH=/lib/libz.dll.a \
    -DCURL_LIBRARY:PATH=/lib/libcurl.dll.a \
    -DPYTHON_INSTALL:PATH=${PYTHON_INSTALL} \
    -DCMAKE_C_FLAGS:STRING="-g -m64 -Dwin64 -mwindows" \
    -DCMAKE_CXX_FLAGS:STRING="-g -m64" \
    -DCMAKE_Fortran_FLAGS:STRING="-g -m64 -fcray-pointer -fdefault-integer-8 -Dwin64 -w -mwindows -fno-exceptions" \
    -DCMAKE_RANLIB:FILEPATH=/bin/gcc-ranlib \
    -DCMAKE_AR:FILEPATH=/bin/gcc-ar \
    -DCYGWIN:BOOL=TRUE \
    -DCMAKE_LEGACY_CYGWIN_WIN32=1 \
    -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
    $EXTRA_ARGS

b) There is a bug when it makes tests with static libraries, the following 2 files need to be changed for 'make' to work:

i) ../exodus-6.09/exodus/forbind/CMakeLists: change line 56 and have ${HDF5HL_LIBRARY} come before ${HDF5_LIBRARY}

ii) ../exodus-6.09/exodus/cbind/CMakeLists: change line 284 with the same library ordering

c) Now run make

NOTE: When compiling with static linker flags, make throws a truncating error, to fix this I have attempted many options in the cmake-script that are listed here, however in the end I just ended up not using -static as a linker flag:

      # -DCMAKE_GENERATOR:STRING="Unix Makefiles" \
      # -DCMAKE_LEGACY_CYGWIN_WIN32=1 \
      # -DCMAKE_Fortran_FLAGS:STRING="-g -fcray-pointer -fno-exceptions -fdefault-integer-8 -m64" \
      # -DCMAKE_STATIC_LINKER_FLAGS:STRING="-ncmodel=medium" \
      # --large-address-aware --relax --high-entropy-va
      # -DCMAKE_EXE_LINKER_FLAGS:STRING="-static" \
      # -DCYGWIN:BOOL=TRUE \
      # -DCMAKE_LEGACY_CYGWIN_WIN32=1 \

d) To test your build use make check

CYGWIN NOTE: After testing the build it throws a message about truncating to 32 bit. What causes this is probably the fact that floats on Windows 64 bit are 4 bit, while on Cygwin they are 8 bit since Cygwin emulated a Linux system.

e) Run make install

If you run into errors building LaGriT or have suggestions on how to improve this documentation, please email Terry Miller (tamiller@lanl.gov), Dylan Harp (dharp@lanl.gov), or Daniel Livingston (livingston@lanl.gov).