Link proper openmp lib when using intel compiler

Package-Manager: portage-2.1.9.24/cvs/Linux x86_64

3 files changed, 237 insertions, 6 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index f1de133e998d..f9a32a5912a6 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.24 2010/06/28 21:05:46 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.25 2010/11/16 20:05:49 xarthisius Exp $
+
+*cns-1.2.1-r5 (16 Nov 2010)
+
+  16 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> +cns-1.2.1-r5.ebuild:
+  Link proper openmp lib when using intel compiler
 
   28 Jun 2010; Justin Lecher <jlec@gentoo.org> cns-1.2.1.ebuild,
   cns-1.2.1-r1.ebuild, cns-1.2.1-r2.ebuild, cns-1.2.1-r3.ebuild,
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
index e8d90de25ebd..6ba9f342d1fd 100644
--- a/sci-chemistry/cns/Manifest
+++ b/sci-chemistry/cns/Manifest
@@ -24,14 +24,17 @@ EBUILD cns-1.2.1-r1.ebuild 5585 RMD160 d25d66002ffe133c390912e265f81aae860134c9
 EBUILD cns-1.2.1-r2.ebuild 6132 RMD160 8dd964fed1d90f708689d6e63e9ec0dc6b9f45cf SHA1 7ebbf35a7e8ec2e2f246389a3fdfcf93e8fb5d87 SHA256 853162df3142ce1a46e05d77b2e50672cda0a41efd25daee1261109d91493aaf
 EBUILD cns-1.2.1-r3.ebuild 6258 RMD160 353ad806f567cc71f4137f75f78743ed38d14fed SHA1 9424d69c95fa65418b6c34b2675dc7827f465b59 SHA256 0ee874568facb4e188d4718f034c8cdb60f1517cdc663996468f5b1f6ad46d4e
 EBUILD cns-1.2.1-r4.ebuild 6582 RMD160 544cf18f4dd459c7d2325da7998fef6db0eebaa3 SHA1 e263f40adcd54c724b341e3b49d79286521fe352 SHA256 192c853f998484cd71a7d6bec6a35071c5846dd74cbc67c6bca7ff08c2a029d1
+EBUILD cns-1.2.1-r5.ebuild 6589 RMD160 0faf1a389e72ef6b75a17930ccc814ec6777926c SHA1 bc14809d78f7bcbbea8dbb31ed5a4c57aa25f93c SHA256 fd257513ef87379d509c7f7ed55ab98dbafbc15d297d0c01cc50e5bb02f8686b
 EBUILD cns-1.2.1.ebuild 5620 RMD160 84fae2bc1f0780f77b931ee23a18acdd7353e766 SHA1 4b58160d9a20c103a7f443491ed5e1d5bade2afe SHA256 8504163c5874f0e90582ef37a44800ec2dbf9b112282682c237236e708ed79cf
 EBUILD cns-1.2.ebuild 3497 RMD160 9e097171ebd44f1a7e5dd317beeb6b65aefac2f6 SHA1 3afc4b415d2ef559b717843a05bc6afb8ee651a2 SHA256 1a6094c8bca3797e62c375a2370cc7425e9c1dd1106d20f202681bc5a87da1fc
-MISC ChangeLog 4337 RMD160 022a7c7f918ff9d65e7827a3e56b3b97aac64fdd SHA1 f43a0d2049d1edcdba2f1618c4f8f72da6180923 SHA256 68c4cc815f176428f011d5fc27576e6bdb797b8f180dfab72a512bafde14244a
+MISC ChangeLog 4500 RMD160 4d0cfea2f8c7a9798b000d9bd3ac5a30a8d806e1 SHA1 1aa7a55e53334007978f004beb65140a484b2d20 SHA256 a19abdc674b3431e08e86e9eb3607033c4d3bdf87aa563731bf3709a45c8d062
 MISC metadata.xml 302 RMD160 d60d9cd875115eaba68ad4b504bff76b39a136b0 SHA1 ecdd8feeea2de489927403f1941acfc582c17222 SHA256 a374144760a8ac1f72b1c625c41f98cee3f74511c964133bda119da580664c50
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-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
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diff --git a/sci-chemistry/cns/cns-1.2.1-r5.ebuild b/sci-chemistry/cns/cns-1.2.1-r5.ebuild
new file mode 100644
index 000000000000..ba5850280fcc
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r5.ebuild
@@ -0,0 +1,223 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r5.ebuild,v 1.1 2010/11/16 20:05:49 xarthisius Exp $
+
+EAPI="3"
+
+inherit eutils fortran toolchain-funcs versionator flag-o-matic
+
+MY_PN="${PN}_solve"
+MY_PV="$(delete_version_separator 2)"
+MY_P="${MY_PN}_${MY_PV}"
+
+DESCRIPTION="Crystallography and NMR System"
+HOMEPAGE="http://cns.csb.yale.edu/"
+SRC_URI="${MY_P}_all-mp.tar.gz
+	aria? ( aria2.3.1.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )"
+
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="gfortran ifc"
+
+pkg_nofetch() {
+	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
+	use aria && elog "and http://aria.pasteur.fr/"
+	elog "and place these files:"
+	elog ${A}
+	elog "in ${DISTDIR}."
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	if [[ $(tc-getCC) == *gcc* ]] &&
+		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+		! built_with_use sys-devel/gcc openmp )
+	then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+		ewarn "Switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	epatch "${FILESDIR}"/${PV}-parallel.patch
+
+	if use aria; then
+	pushd "${WORKDIR}"/aria* >& /dev/null
+		# Update the cns sources in aria for version 1.2.1
+		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
+
+		# Update the code with aria specific things
+		cp -rf cns/src/* "${S}"/source/
+	popd >& /dev/null
+	fi
+
+	# the code uses Intel-compiler-specific directives
+	if [[ ${FORTRANC} == gfortran ]]; then
+		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
+		use openmp && \
+			OMPLIB="-lgomp" && append-flags -fopenmp
+		COMP="gfortran"
+		use amd64 && \
+			append-fflags -fdefault-integer-8
+	else
+		epatch "${FILESDIR}"/${PV}-ifort.patch
+		use openmp && OMPLIB="-liomp5" && \
+			append-flags -openmp && append-ldflags -openmp
+		COMP="ifort"
+		use amd64 && append-fflags -i8
+		append-fflags -Vaxlib
+		append-ldflags -Vaxlib
+	fi
+
+	use amd64 && \
+		append-cflags "-DINTEGER='long long int'"
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		"${S}"/cns_solve_env
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
+		"${T}"/cns_solve_env_sh
+
+	einfo "Fixing shebangs..."
+	find "${S}" -type f \
+		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
+}
+
+src_compile() {
+	local GLOBALS
+	local MALIGN
+	if [[ ${FORTRANC} = g77 ]]; then
+		GLOBALS="-fno-globals"
+		MALIGN='\$(CNS_MALIGN_I86)'
+	fi
+
+	# Set up the compiler to use
+	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+	ln -s Makefile.header Makefile.header.${FORTRANC} || die
+	popd 2>/dev/null
+
+	# make install really means build, since it's expected to be used in-place
+	# -j1 doesn't mean we do no respect MAKEOPTS!
+	emake -j1 \
+		CC="$(tc-getCC)" \
+		F77="${FORTRANC}" \
+		LD="${FORTRANC}" \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		compiler="${COMP}" \
+		install \
+		|| die "emake failed"
+
+}
+
+src_test() {
+	# We need to force on g77 manually, because we can't get aliases working
+	# when we source in a -c
+	einfo "Running tests ..."
+	sh -c \
+		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
+		|| die "tests failed"
+	einfo "Displaying test results ..."
+	cat "${S}"/*_g77/test/*.diff-test
+}
+
+src_install() {
+	# Install to locations resembling FHS
+	sed -i \
+		-e "s:${S}:usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
+		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${S}"/cns_solve_env
+	# I don't entirely understand why the sh version requires a leading /
+	# for CNS_SOLVE and CNS_ROOT, but it does
+	sed -i \
+		-e "s:${S}:/usr:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
+		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${T}"/cns_solve_env_sh
+
+	# Get rid of setup stuff we don't need in the installed script
+	sed -i \
+		-e "83,$ d" \
+		-e "37,46 d" \
+		"${S}"/cns_solve_env
+	sed -i \
+		-e "84,$ d" \
+		-e "39,50 d" \
+		"${T}"/cns_solve_env_sh
+
+	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
+		|| die "install cns_solve failed"
+
+	# Can be run by either cns_solve or cns
+	dosym cns_solve /usr/bin/cns
+
+	# Don't want to install this
+	rm -f "${S}"/*linux*/utils/Makefile
+
+	dobin "${S}"/*linux*/utils/* || die "install utils failed"
+
+	sed -i \
+		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+		"${S}"/bin/cns_web || die
+
+	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
+
+	insinto /usr/share/cns
+	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
+	doins "${S}"/bin/cns_info || die
+
+	insinto /etc/profile.d
+	newins "${S}"/cns_solve_env cns_solve_env.csh || die
+	newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
+
+	dohtml \
+		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+		-f all_cns_info_template,omac,def \
+		-r doc/html/* || die
+	# Conflits with app-text/dos2unix
+	rm -f "${D}"/usr/bin/dos2unix
+}
+
+pkg_info() {
+	if use openmp; then
+		elog "Set OMP_NUM_THREADS to the number of threads you want."
+		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
+		elog "variable if using gcc (16384 should be good)."
+	fi
+}
+
+pkg_postinst() {
+	pkg_info
+}