3. Dependencies¶

3.1. NetCDF¶

NetCDF (Network Common Data Form) is a common format for scientific data (Unidata [62]) that is also used by SICOPOLIS. The NetCDF C and Fortran libraries are required.

For GCC, installation from a package manager is recommended. Under openSUSE Leap 15.3, install netcdf, netcdf-devel, netcdf-devel-static, netcdf-fortran, netcdf-fortran-devel, netcdf-fortran-static, ncview. This requires the repositories “Software for Scientists and Engineers” and “sebschub’s Home Project”. Details (especially the required repositories) will differ for other systems.

For the Intel compiler, building from the source code is required. The C and Fortran sources are available for download on the NetCDF website as zip or tar archives. Unzip the archives into temporary directories.

Prior to version 4.2, a single archive contained both the C and Fortran libraries. A minimal installation for version 4.1.3 (without NetCDF-4 support) can be done by changing to the source directory, then:

export NCDIR=/opt/netcdf
export CC=icc
export FC=ifort
export CFLAGS="-O2"
export CPPFLAGS=
export FCFLAGS="-O2"
export FFLAGS=${FCFLAGS}
./configure --prefix=${NCDIR} --libdir=${NCDIR}/lib \
            --disable-netcdf-4
make install

Since version 4.2, the C and Fortran libraries must be installed separately. If NetCDF-4 support is dispensable, the following installation should work (tested under openSUSE Leap 15.2 and icc/ifort 19.1 with versions netcdf-c-4.8.0 and netcdf-fortran-4.5.3).

Change to the source directory of the C library, then:

export NCDIR=/opt/netcdf
export CC=icc
export FC=ifort
export CFLAGS="-O2"
export CPPFLAGS=
export FCFLAGS="-O2"
export FFLAGS=${FCFLAGS}
./configure --prefix=${NCDIR} --libdir=${NCDIR}/lib \
            --disable-netcdf-4 --enable-logging
make install

Change to the source directory of the Fortran library, then:

export NFDIR=/opt/netcdf
export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}
export CPPFLAGS=-I${NCDIR}/include
export LDFLAGS=-L${NCDIR}/lib
./configure --prefix=${NFDIR} --libdir=${NFDIR}/lib \
            --disable-netcdf-4 --enable-logging
make install

The recommended, complete build with NetCDF-4 support requires additional libraries. Download the sources of the data-compression library zlib (https://www.zlib.net/), the Hierarchical Data Format HDF5 (https://www.hdfgroup.org/) and the NetCDF-4 C and Fortran libraries (https://doi.org/10.5065/D6H70CW6). Unpack all archives.

Step 1: Installation of zlib. Change to the source directory, then:

export ZDIR=/opt/zlib
export CC=icc
export FC=ifort
export CFLAGS="-O2"
export CPPFLAGS=
export FCFLAGS="-O2"
export FFLAGS=${FCFLAGS}
./configure --prefix=${ZDIR} --libdir=${ZDIR}/lib
make check
make install

Step 2: Installation of HDF5. Change to the source directory, then:

export ZDIR=/opt/zlib
export H5DIR=/opt/hdf5
export LD_LIBRARY_PATH=${ZDIR}/lib:${LD_LIBRARY_PATH}
export CC=icc
export FC=ifort
export CFLAGS="-O2"
export CPPFLAGS=
export FCFLAGS="-O2"
export FFLAGS=${FCFLAGS}
./configure --with-zlib=${ZDIR} \
            --prefix=${H5DIR} --libdir=${H5DIR}/lib \
            --enable-hl \
            --with-default-api-version=v18
make check
make install

Step 3: Installation of NetCDF-4. Change to the source directory of the C library, then:

export ZDIR=/opt/zlib
export H5DIR=/opt/hdf5
export NCDIR=/opt/netcdf
export LD_LIBRARY_PATH=${H5DIR}/lib:${LD_LIBRARY_PATH}
export CC=icc
export FC=ifort
export CFLAGS="-O2"
export CPPFLAGS="-I${H5DIR}/include -I${ZDIR}/include"
export LDFLAGS="-L${H5DIR}/lib -L${ZDIR}/lib"
export FCFLAGS="-O2"
export FFLAGS=${FCFLAGS}
./configure --prefix=${NCDIR} --libdir=${NCDIR}/lib \
            --enable-logging --disable-dap-remote-tests
make install
make check

Change to the source directory of the Fortran library, then:

export NFDIR=/opt/netcdf
export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}
export CPPFLAGS=-I${NCDIR}/include
export LDFLAGS=-L${NCDIR}/lib
./configure --prefix=${NFDIR} --libdir=${NFDIR}/lib \
            --enable-logging --disable-dap-remote-tests
make install
make check

This was tested under openSUSE Leap 15.3 and icc/ifort 19.1 with versions zlib-1.2.11, hdf5-1.12.1, netcdf-c-4.8.1 and netcdf-fortran-4.5.4.

If installation from a package manager does not work out for GCC, try the above procedure, replacing everywhere icc and ifort by gcc and gfortran, respectively.

If needed, further instructions can be found on the NetCDF website.

Installation under /opt usually requires admin rights. The same holds for the common alternative /usr/local. For a local installation, replace it by /home/<my_user_name>/local.

3.2. Lis¶

Lis (Library of Iterative Solvers for linear systems) is a software library for solving discretized linear equations (Nishida [48]).

Download the source of Lis as a zip archive from https://www.ssisc.org/lis/. Unzip the archive and change to the source directory.

For GCC, install lis by executing:

export LISDIR=/opt/lis
./configure --prefix=${LISDIR} --libdir=${LISDIR}/lib \
            --enable-fortran --enable-f90 \
            --enable-omp --enable-saamg --enable-fma \
            CC=gcc FC=gfortran F77=gfortran \
            CFLAGS="-mcmodel=medium" CPPFLAGS="-mcmodel=medium" \
            FCFLAGS="-mcmodel=medium" FFLAGS="-mcmodel=medium"
make install

This was tested under openSUSE Leap 15.2 and Linux Mint 20.1 with lis-2.0.30. Some modifications might be needed under different systems.

For the Intel compiler, replace gcc and gfortran by icc and ifort, respectively.

Installation under /opt usually requires admin rights. The same holds for the common alternative /usr/local. For a local installation, replace it by /home/<my_user_name>/local.