commit: 22f5947bb0b1a31ccc37aff042a7a12e8fdc6c33 Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz> AuthorDate: Tue Nov 11 14:06:29 2014 +0000 Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz> CommitDate: Tue Nov 11 14:06:29 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=22f5947b
sci-chemistry/nwchem bumped to 6.5_p26243. IUSE options expanded, including those fore 64 bit integers and CUDA support. CCSDTQ and linear response for CCSDT+ methods selected unconditionally for now. Package-Manager: portage-2.2.14 --- sci-chemistry/nwchem/ChangeLog | 8 + .../nwchem/files/nwchem-6.5-python_makefile.patch | 15 ++ sci-chemistry/nwchem/metadata.xml | 30 ++- sci-chemistry/nwchem/nwchem-6.5_p26243.ebuild | 259 +++++++++++++++++++++ 4 files changed, 311 insertions(+), 1 deletion(-) diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog index d05e285..a9461ce 100644 --- a/sci-chemistry/nwchem/ChangeLog +++ b/sci-chemistry/nwchem/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nwchem-6.5_p26243 (11 Nov 2014) + + 11 Nov 2014; Honza Macháček <[email protected]> + +nwchem-6.5_p26243.ebuild, +files/nwchem-6.5-python_makefile.patch: + Version bump to sci-chemistry/nwchem-6.5_p26243. IUSE options expanded, + including those fore 64 bit integers and CUDA support. CCSDTQ and linear + response for CCSDT+ methods selected unconditionally for now. + 16 Sep 2014; Christoph Junghans <[email protected]> nwchem-6.3_p2-r1.ebuild: clean up diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch new file mode 100644 index 0000000..c37310c --- /dev/null +++ b/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch @@ -0,0 +1,15 @@ +--- src/config/makefile.h 2014-11-03 14:00:59.808794970 +0100 ++++ src/config/makefile.h 2014-11-03 14:29:13.353470102 +0100 +@@ -2521,10 +2521,10 @@ + endif + ifdef USE_PYTHON64 +- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) ++ CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) + else + ifeq ($(GOTMINGW32),1) + CORE_LIBS += $(PYTHONHOME)/libs/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) + else +- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) ++ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) + endif + endif diff --git a/sci-chemistry/nwchem/metadata.xml b/sci-chemistry/nwchem/metadata.xml index 11305d8..95b84c1 100644 --- a/sci-chemistry/nwchem/metadata.xml +++ b/sci-chemistry/nwchem/metadata.xml @@ -7,9 +7,37 @@ <name>Alexey Shvetsov</name> </maintainer> <use> - <flag name="mrcc">Compile the MRCC module</flag> + <flag name="blas"> + Use external BLAS library instead of the internal routines + </flag> + </use> + <use> + <flag name="cuda"> + Enable CUDA GPU support for the Tensor Contraction Engine generated + methods (CI, MBPT, CC) + </flag> + </use> + <use> + <flag name="int64"> + Use 64 bits integers + </flag> + </use> + <use> + <flag name="lapack"> + Use external LAPACK library instead of the internal routines + </flag> + </use> + <use> + <flag name="mrcc"> + Compile the routines for Multi Reference Coupled Clusters theory + </flag> </use> <use> <flag name="nwchem-tests">Install qa tests data</flag> </use> + <use> + <flag name="scalapack"> + Use external SCALAPACK library + </flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243.ebuild new file mode 100644 index 0000000..8013233 --- /dev/null +++ b/sci-chemistry/nwchem/nwchem-6.5_p26243.ebuild @@ -0,0 +1,259 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs + +DATE="2014-09-10" + +DESCRIPTION="Delivering High-Performance Computational Chemistry to Science" +HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"; +SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.gz + http://www.nwchem-sw.org/images/Util_md_sockets.patch.gz + http://www.nwchem-sw.org/images/Hbar.patch.gz + http://www.nwchem-sw.org/images/Tcenxtask.patch.gz + http://www.nwchem-sw.org/images/Hnd_giaxyz_noinline.patch.gz + http://www.nwchem-sw.org/images/Parallelmpi.patch.gz + http://www.nwchem-sw.org/images/Makefile_gcc4x.patch.gz + http://www.nwchem-sw.org/images/Bcast_ccsd.patch.gz + http://www.nwchem-sw.org/images/Elpa_syncs.patch.gz + http://www.nwchem-sw.org/images/Xlmpoles_ifort15.patch.gz"; + +LICENSE="ECL-2.0" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="blas cuda infiniband lapack mpi doc examples int64 nwchem-tests openmp mrcc python scalapack" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} ) + infiniband? ( mpi ) + scalapack? ( !int64 )" + +RDEPEND=" + sys-fs/sysfsutils + blas? ( virtual/blas ) + lapack? ( virtual/lapack ) + scalapack? ( virtual/scalapack ) + cuda? ( dev-util/nvidia-cuda-sdk ) + int64? ( + blas? ( virtual/blas[int64] ) + lapack? ( virtual/lapack[int64] ) + ) + python? ( ${PYTHON_DEPS} )" +DEPEND="${RDEPEND} + app-shells/tcsh + mpi? ( virtual/mpi[fortran] ) + infiniband? ( || ( + sys-cluster/openmpi[fortran,openmpi_fabrics_ofed] + sys-cluster/mvapich2[fortran] + ) ) + doc? ( + dev-texlive/texlive-latex + dev-tex/latex2html )" + +LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}" +S="${WORKDIR}/${PN}" + +pkg_setup() { + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + export CXX="mpic++" + else + tc-export FC F77 CC CXX + fi + + use openmp && FORTRAN_NEED_OPENMP=1 + + fortran-2_pkg_setup + + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local openmp="" + local fcode=ebuild-openmp-flags.f + local _fc=$(tc-getFC) + + pushd "${T}" + cat <<- EOF > "${fcode}" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break + done + + rm -f "${fcode}.*" + popd + + append-flags "${openmp}" + fi + + use python && python-single-r1_pkg_setup +} + +src_unpack() { + unpack ${A} + mv "${LONG_S}" "${S}" +} + +src_prepare() { + pushd "${S}"/src + for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 + do epatch "${WORKDIR}"/"${p}.patch" + done + cd NWints/hondo + epatch "${WORKDIR}"/Hnd_giaxyz_noinline.patch + popd + epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch + use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch + use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch + + sed \ + -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \ + -i src/basis/MakeFile src/basis/GNUmakefile || die + sed \ + -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \ + -i src/nwpw/libraryps/GNUmakefile || die + sed \ + -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \ + -i src/GNUmakefile src/MakeFile || die + + if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then + sed \ + -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \ + -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \ + -i src/config/makefile.h || die + fi +} + +src_compile() { + export NWCHEM_LONG_PATHS=Y + export USE_SUBGROUPS=yes + if use mpi ; then + export MSG_COMMS=MPI + export USE_MPI=y + export USE_MPIF=y + export USE_MPIF4=y + export MPI_LOC="${EPREFIX}"/usr + export MPI_INCLUDE=$MPI_LOC/include + export MPI_LIB=$MPI_LOC/$(get_libdir) + export LIBMPI="$(mpif90 -showme:link)" + if use infiniband; then + export ARMCI_NETWORK=OPENIB + else + export ARMCI_NETWORK=MPI-TS + fi + else + unset USE_MPI + unset USE_MPIF + unset USE_MPIF4 + export MSG_COMMS=TCGMSG + export ARMCI_NETWORK=SOCKETS + fi + if [ "$ARCH" = "amd64" ]; then + export NWCHEM_TARGET=LINUX64 + elif [ "$ARCH" = "ia64" ]; then + export NWCHEM_TARGET=LINUX64 + elif [ "$ARCH" = "x86" ]; then + export NWCHEM_TARGET=LINUX + elif [ "$ARCH" = "ppc" ]; then + export NWCHEM_TARGET=LINUX + else + die "Unknown architecture" + fi + if use python ; then + if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then + export USE_PYTHON64=yes + fi + export PYTHONHOME=/usr + export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }') + export PYTHONPATH="./:${S}/contrib/python/" + export NWCHEM_MODULES="all python" + else + export NWCHEM_MODULES="all" + fi + use mrcc && export MRCC_THEORY="TRUE" + export CCSDTQ="TRUE" + export CCSDTLR="TRUE" + unset BLASOPT + use blas && BLASOPT="$(pkg-config --libs blas)" + use lapack && BLASOPT+="$(pkg-config --libs lapack)" + use scalapack && BLASOPT+="$(pkg-config --libs scalapack)" + export BLASOPT + if use int64; then + BLAS_SIZE=8 + LAPACK_SIZE=8 + SCALAPACK_SIZE=8 + else + BLAS_SIZE=4 + LAPACK_SIZE=4 + SCALAPACK_SIZE=4 + fi + if use cuda; then + export TCE_CUDA=Y + export CUDA_PATH=/opt/cuda + export CUDA=${CUDA_PATH}/bin/nvcc + export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20" + export CUDA_INCLUDE="-I${CUDA_PATH}/include" + export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda" + fi + export LARGE_FILES="TRUE" + + cd src + emake \ + DIAG=PAR \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + NWCHEM_TOP="${S}" \ + NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" + + if use doc; then + cd "${S}"/doc + export VARTEXFONTS="${T}/fonts" + emake \ + DIAG=PAR \ + NWCHEM_TOP="${S}" \ + pdf html + fi +} + +src_install() { + dobin bin/${NWCHEM_TARGET}/nwchem + + insinto /usr/share/NWChem/basis/ + doins -r src/basis/libraries src/data + insinto /usr/share/NWChem/nwpw + doins -r src/nwpw/libraryps + + insinto /etc + doins nwchemrc + + use examples && \ + insinto /usr/share/NWChem/ && \ + doins -r examples + + use nwchem-tests && \ + insinto /usr/share/NWChem && \ + doins -r QA/tests + + use doc && \ + insinto /usr/share/doc/"${P}" && \ + doins -r doc/nwahtml && \ + doins -r web + +} + +pkg_postinst() { + echo + elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc" + elog "or copy it in order to tell NWChem the right position of the" + elog "basis library and other necessary data." + echo +}
