[gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/

[Honza Macháček]

commit:     94a06710354314bfd07d9a8b124079193ddd1d4a
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Wed Mar 30 14:34:09 2016 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Wed Mar 30 14:34:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=94a06710

sci-chemistry/nwchem version bumped to 6.6 with minor ebuild improvements; Infiniband support should compile, source patched to allow unique names for all atoms

Package-Manager: portage-2.2.27

 .../nwchem/files/nwchem-6.6-unique_tags.patch      |  12 +
 sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild   | 279 +++++++++++++++++++++
 2 files changed, 291 insertions(+)

diff --git a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
new file mode 100644
index 0000000..e129406
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
@@ -0,0 +1,12 @@
+diff -Naurp nwchem-6.6.orig/src/util/nwc_const.fh nwchem-6.6/src/util/nwc_const.fh
+--- nwchem-6.6.orig/src/util/nwc_const.fh	2015-10-01 17:33:14.000000000 +0000
++++ nwchem-6.6/src/util/nwc_const.fh	2015-11-26 10:53:46.386110924 +0000
+@@ -62,7 +62,7 @@
+ * Maximum number of unique tags
+ *
+       integer nw_max_unq_tags
+-      parameter (nw_max_unq_tags = 40)
++      parameter (nw_max_unq_tags = nw_max_atom)
+ *------------------------------------------------------------------------------
+ * Maximum number of general contractions in a shell
+ *

diff --git a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
new file mode 100644
index 0000000..4c10fe8
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
@@ -0,0 +1,279 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
+
+DATE="2015-10-20"
+
+DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+PATCH_REPO="http://www.nwchem-sw.org/images"
+PATCH_LIST="Tddft_mxvec20 Tools_lib64 Config_libs66 Cosmo_meminit Sym_abelian
+Xccvs98 Dplot_tolrho Driver_smalleig Ga_argv Raman_displ Ga_defs Zgesvd Cosmo_dftprint"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.bz2
+	$(for p in ${PATCH_LIST[@]}; do echo ${PATCH_REPO}/${p}.patch.gz; done)"
+
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
+	scalapack? ( !int64 )
+	lapack? ( blas )
+	scalapack? ( blas )"
+
+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}
+	virtual/pkgconfig
+	app-shells/tcsh
+	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}-${PV%_p*}"
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	export FC="mpif90"
+	export F77="mpif77"
+	export CC="mpicc"
+	export CXX="mpic++"
+
+	use openmp && FORTRAN_NEED_OPENMP=1
+
+	fortran-2_pkg_setup
+
+	if use openmp; then
+		# based on _fortran-has-openmp() of fortran-2.eclass
+		local openmp=""
+		local fcode=ebuild-openmp-flags.f
+		local _fc=$(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 "${fcode}.*"
+		popd
+
+		export FC="${FC} ${openmp}"
+		export F77="${F77} ${openmp}"
+		export CC="${CC} ${openmp}"
+		export CXX="${CXX} ${openmp}"
+	fi
+
+	use python && python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	unpack ${A}
+	mv "${LONG_S}" "${S}"
+}
+
+src_prepare() {
+	for p in ${PATCH_LIST[@]}
+		do epatch "${WORKDIR}"/"${p}.patch"
+	done
+	epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
+	epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
+	epatch "${FILESDIR}"/nwchem-6.6-unique_tags.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),$(tc-getFC)):g" \
+			-i src/config/makefile.h || die
+	fi
+}
+
+src_compile() {
+	export NWCHEM_LONG_PATHS=Y
+	use openmp && export USE_OPENMP=1
+	export USE_MPI=y
+	export USE_MPIF=y
+	export USE_MPIF4=y
+	export MPI_LOC="${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
+		export MSG_COMMS=MPI
+		export IB_INCLUDE="-I${MPI_INCLUDE}"
+		export IB_LIB="-L${MPI_LIB}"
+	else
+		unset ARMCI_NETWORK
+	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_METHODS="TRUE" # Multi Reference Coupled Clusters
+	export CCSDTQ="TRUE"                   # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
+	export CCSDTLR="TRUE"                  # CCSDT (and CCSDTQ?) Linear Response
+	export EACCSD="TRUE"                   # Electron Affinities at the CCSD level
+	export IPCCSD="TRUE"                   # Ionisation Potentials at the CCSD level
+	unset BLASOPT
+	local blaspkg="blas"
+	local lapackpkg="lapack"
+	if use int64; then
+		blaspkg="blas-int64"
+		lapackpkg="lapack-int64"
+	fi
+	use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
+	use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
+	use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
+	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 -lstdc++"
+	fi
+	export LARGE_FILES="TRUE"
+
+	cd src
+	if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
+		if use int64; then
+			export BLAS_SIZE=8
+			export LAPACK_SIZE=8
+			export SCALAPACK_SIZE=8
+		else
+			emake \
+				DIAG=PAR \
+				FC="$(tc-getFC)" \
+				CC="$(tc-getCC)" \
+				CXX="$(tc-getCXX)" \
+				NWCHEM_TOP="${S}" \
+				clean
+			emake \
+				DIAG=PAR \
+				FC="$(tc-getFC)" \
+				CC="$(tc-getCC)" \
+				CXX="$(tc-getCXX)" \
+				NWCHEM_TOP="${S}" \
+				64_to_32
+			export BLAS_SIZE=4
+			export LAPACK_SIZE=4
+			export SCALAPACK_SIZE=4
+			export USE_64TO32=y
+		fi
+	fi
+	emake \
+		DIAG=PAR \
+		FC="$(tc-getFC)" \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		NWCHEM_TOP="${S}" \
+		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
+		nwchem_config
+	emake \
+		DIAG=PAR \
+		FC="$(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
+}