Siesta 5.4.2 | Research Center for Computational Science

Webpage

https://gitlab.com/siesta-project/siesta

Version

5.4.2 (+ hdf5-1.14.6, NetCDF 4.9.3, NetCDF Fortran 4.6.2, libxc 7.0.0)

Build Environment

GCC 15.1.1 (gcc-toolset-15)
Open MPI 4.1.8
MKL 2025.3
Python 3.9
- rumael.yaml (pip3.9 install ruamel.yaml --user)

Files Required

siesta-5.4.2.tar.gz
wannier90-3.1.0.tar.gz
hdf5-1.14.6.tar.gz
netcdf-c-4.9.3.tar.gz
netcdf-fortran-4.6.2.tar.gz
libxc-7.0.0.tar.bz2
(some of additional libraries will be installed during installation)

Build Procedure

#!/bin/sh
SIESTA_VERSION=5.4.2
INSTDIR=/apl/siesta/5.4.2
WORKDIR=/gwork/users/${USER}
BASEDIR=/home/users/${USER}/Software/Siesta/${SIESTA_VERSION}
TARBALL=${BASEDIR}/siesta-${SIESTA_VERSION}.tar.gz
HDF5_VERSION=1.14.6
BASEDIR_HDF5=/home/users/${USER}/Software/HDF5/${HDF5_VERSION}
TARBALL_HDF5=${BASEDIR_HDF5}/hdf5-${HDF5_VERSION}.tar.gz
NETCDF_C_VERSION=4.9.3
NETCDF_F_VERSION=4.6.2
BASEDIR_NETCDF=/home/users/${USER}/Software/NETCDF
TARBALL_NETCDF_C=${BASEDIR_NETCDF}/c${NETCDF_C_VERSION}/netcdf-c-${NETCDF_C_VERSION}.tar.gz
TARBALL_NETCDF_F=${BASEDIR_NETCDF}/f${NETCDF_F_VERSION}/netcdf-fortran-${NETCDF_F_VERSION}.tar.gz
LIBXC_VERSION=7.0.0
BASEDIR_LIBXC=/home/users/${USER}/Software/libxc
TARBALL_LIBXC=${BASEDIR_LIBXC}/${LIBXC_VERSION}/libxc-${LIBXC_VERSION}.tar.bz2
WANNIER90_VERSION=3.1.0
BASEDIR_WANNIER90=/home/users/${USER}/Software/wannier90/${WANNIER90_VERSION}
TARBALL_WANNIER90=${BASEDIR_WANNIER90}/wannier90-${WANNIER90_VERSION}.tar.gz
PARALLEL=12
#---------------------------------------------------------------------------
umask 0022
ulimit -s unlimited
module -s purge
module -s load gcc-toolset/15
module -s load openmpi/4.1.8/gcc15
module -s load mkl/2025.3

export LANG=C
export LC_ALL=C
export OMP_NUM_THREADS=1
#export I_MPI_HYDRA_TOPOLIB=ipl # for intel mpi
# libxc
if [ ! -f ${INSTDIR}/exts/lib/libxc.a ]; then
cd ${WORKDIR}
if [ -d libxc-${LIBXC_VERSION} ]; then
mv libxc-${LIBXC_VERSION} libxc-erase
rm -rf libxc-erase &
fi
tar xf ${TARBALL_LIBXC}
cd libxc-${LIBXC_VERSION}
autoreconf -i
./configure --prefix=${INSTDIR}/exts
make -j${PARALLEL}
make -j${PARALLEL} check
make install
fi

# hdf5
if [ ! -f ${INSTDIR}/exts/lib/libhdf5.a ]; then
cd ${WORKDIR}
if [ -d hdf5-${HDF5_VERSION} ]; then
mv hdf5-${HDF5_VERSION} hdf5-erase
rm -rf hdf5-erase &
fi
tar zxf ${TARBALL_HDF5}
cd hdf5-${HDF5_VERSION}
mkdir build && cd build
cmake .. \
-DCMAKE_INSTALL_PREFIX=${INSTDIR}/exts \
-DHDF5_BUILD_FORTRAN=ON \
-DHDF5_ENABLE_PARALLEL=ON \
-DMPIEXEC_MAX_NUMPROCS=${PARALLEL}
make -j${PARALLEL}
make install
make test # very long...
fi

export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F90=mpif90
export PATH="${INSTDIR}/exts/bin:${PATH}"
export CPATH="${INSTDIR}/exts/include:${CPATH}"
export LD_LIBRARY_PATH="${INSTDIR}/exts/lib:${LD_LIBRARY_PATH}"
export LIBRARY_PATH="${INSTDIR}/exts/lib:${LIBRARY_PATH}"

# netcdf-c
if [ ! -f ${INSTDIR}/exts/lib/libnetcdf.a ]; then
cd ${WORKDIR}
if [ -d netcdf-c-${NETCDF_C_VERSION} ]; then
mv netcdf-c-${NETCDF_C_VERSION} netcdf-c-erase
rm -rf netcdf-c-erase &
fi
tar zxf ${TARBALL_NETCDF_C}
cd netcdf-c-${NETCDF_C_VERSION}
LDFLAGS="-L${INSTDIR}/exts/lib" \
./configure --prefix=${INSTDIR}/exts \
--enable-parallel-tests
make -j${PARALLEL}
make -j${PARALLEL} check
make install
fi

# netcdf-f
if [ ! -f ${INSTDIR}/exts/lib/libnetcdff.a ]; then
cd ${WORKDIR}
if [ -d netcdf-fortran-${NETCDF_F_VERSION} ]; then
mv netcdf-fortran-${NETCDF_F_VERSION} netcdf-fortran-erase
rm -rf netcdf-fortran-erase &
fi
tar zxf ${TARBALL_NETCDF_F}
cd netcdf-fortran-${NETCDF_F_VERSION}
LDFLAGS="-L${INSTDIR}/exts/lib" \
./configure --prefix=${INSTDIR}/exts \
--enable-parallel-tests
make -j${PARALLEL}
make -j${PARALLEL} check
make install
fi

# siesta
cd ${WORKDIR}
if [ -d siesta-${SIESTA_VERSION} ]; then
mv siesta-${SIESTA_VERSION} siesta-erase
rm -rf siesta-erase
fi
tar zxf ${TARBALL}
cd siesta-${SIESTA_VERSION}

unset CC
unset CXX
unset FC
unset F90
export WANNIER90_PACKAGE=${TARBALL_WANNIER90}
mkdir build && cd build
cmake .. \
-DCMAKE_INSTALL_PREFIX="${INSTDIR}" \
-DCMAKE_PREFIX_PATH="${INSTDIR}/exts" \
-DCMAKE_C_COMPILER=mpicc \
-DCMAKE_CXX_COMPILER=mpicxx \
-DCMAKE_Fortran_COMPILER=mpif90 \
-DPython3_EXECUTABLE=/usr/bin/python3.9 \
-DSIESTA_WITH_MPI=ON \
-DBLAS_LIBRARY="-m64 -L${MKLROOT}/lib -Wl,--no-as-needed -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -lpthread -lm -ldl" \
-DLAPACK_LIBRARY=NONE \
-DSCALAPACK_LIBRARY=NONE \
-DNetCDF_PARALLEL=ON \
-DNetCDF_ROOT="${INSTDIR}/exts" \
-DSIESTA_WITH_OPENMP=OFF \
-DSIESTA_WITH_DFTD3=ON \
-DSIESTA_WITH_LIBXC=ON \
-DSIESTA_WITH_ELSI=ON \
-DSIESTA_WITH_WANNIER90=ON

make -j ${PARALLEL}
SIESTA_TESTS_VERIFY=1 ctest
make install
cp -r Testing/Temporary ${INSTDIR}/testlog
cd ../
cp -r Examples ${INSTDIR}

Test Results

The same test errors occurred as in version 5.4.1.

Notes

The same build procedure is almost the same as the case of version 5.4.1. (newer GCC is employed)
GCC15 version is slightly more efficient than GCC14 version. We thus employ GCC15 for this version.
GCC+Intel MPI version failed with compilation error on MPI_IN_PLACE.
- -DSIESTA_WITH_MPI_INTERFACES=legacy doesn't help.
Although Intel (llvm)+Intel MPI can build the executable, numerous errors occurred during the test.