[sci-chemistry/gromacs] Rework using of external blas & lapack. Also fix issues with prefix and mpi build

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

3 files changed, 285 insertions, 6 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c9f385698d2e..a76f422809e9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.66 2011/03/02 17:55:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.67 2011/03/05 12:00:57 alexxy Exp $
+
+*gromacs-4.5.3-r4 (05 Mar 2011)
+
+  05 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.3-r4.ebuild:
+  Rework using of external blas & lapack. Also fix issues with prefix and mpi
+  build
 
   02 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.7-r4.ebuild,
   gromacs-4.0.7-r5.ebuild, gromacs-4.5.3.ebuild, gromacs-4.5.3-r3.ebuild:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index f1da4c744934..0bca62fda762 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
 AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
 DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
@@ -15,13 +15,24 @@ DIST gromacs-manual-4.5.3.pdf 2438528 RMD160 07f5ec0db1a773e77806c79554e5bb4fa85
 EBUILD gromacs-4.0.7-r4.ebuild 9967 RMD160 168b3d2e5273634e710d45e293845ef6e97dd518 SHA1 4fb7f526ed22f2069e955317d8076f0446c3ca53 SHA256 b827418a2513499f9faaddac78450e1fc3245a9b392fd30692db179a1e130748
 EBUILD gromacs-4.0.7-r5.ebuild 9632 RMD160 9793eff619750d001a619bc90eccc977e6c0d12a SHA1 c98731aa5a9b5265839be712e35b1b73864b5ce7 SHA256 4b275be64d364867e4fb25dfc66c5405647f32b66cb2d7c453e0e471ee5d3eb9
 EBUILD gromacs-4.5.3-r3.ebuild 8076 RMD160 d25cab9b9d4c8c1044f7a8f7ea2d60013ee634a8 SHA1 9a57f25a332769c0beae388513e2211c93f65409 SHA256 23b5e142335b35def423d334fcac2ed9def829b47fd3b242a8352bc545bb2bf2
+EBUILD gromacs-4.5.3-r4.ebuild 8148 RMD160 aeb515b8d0a2056bdc6ef6a8e857695102a84c14 SHA1 e0139b6f71c8adc0ebce5f82c9e0aae0c87222e7 SHA256 1bcdc8be87adcbb7b7312d70e5af52f5105153f433d312b17806eee2ade96d08
 EBUILD gromacs-4.5.3.ebuild 7804 RMD160 79ac411bf838927697c419eaaf9d36ed698662e1 SHA1 176a781a35c1a568b106261723cf724a123824f2 SHA256 99174a1320e0b3334722aa1a3dcef7df92ae7a86912cbf027ebab1d8f10e177a
-MISC ChangeLog 12936 RMD160 45357c8bb52e20bdbdc074e179f5a3298ac7d1c3 SHA1 2f22506495b51b552516e336a94111767f153c83 SHA256 3773660a1cbda861c80f78afbc841bc48c2ffa535254bc6a858a7cbed1e49bbe
+MISC ChangeLog 13135 RMD160 8a5562132837242c22ed0847a93ef62957f8b963 SHA1 6a8b4ee0f766f40eceb76854a880d42773929724 SHA256 c254050f41bcc9e4ea21d5608db6182076d335db4abcb74f91706571ce05469c
 MISC metadata.xml 576 RMD160 376a5b9f0b65c82cfe2cb0f3d7fe81b593932fa2 SHA1 5c4da5764221ae19041b8a3665ea2205c71598c6 SHA256 a08022560f16532545db516b50a9f84c112b34e5ae406a778bdaef5046e226fd
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diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r4.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r4.ebuild
new file mode 100644
index 000000000000..1f961b95a841
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.3-r4.ebuild
@@ -0,0 +1,262 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.3-r4.ebuild,v 1.1 2011/03/05 12:00:57 alexxy Exp $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+MANUAL_PV="4.5.3"
+
+inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? (
+		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git
+else
+	PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch )
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+	mirror://gentoo/${P}_upstream20110217.patch.bz2"
+fi
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
+
+DEPEND="
+	app-shells/tcsh
+	dev-util/pkgconfig
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2:2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+#gromacs has gnu exec stacks for speedup
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
+
+src_prepare() {
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	autotools-utils_src_prepare || die
+
+	sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
+		|| die "Failed to change version in configure.ac"
+
+	eautoreconf || die
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+	#if neither single-precision nor double-precision is enabled
+	#build at least default (single)
+	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+
+	for x in ${GMX_DIRS}; do
+		mkdir -p "${WORKDIR}/${P}_${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
+	done
+}
+
+src_configure() {
+	#from gromacs configure
+	if ! use fftw; then
+		ewarn "WARNING: The built-in FFTPACK routines are slow."
+		ewarn "Are you sure you don\'t want to use FFTW?"
+		ewarn "It is free and much faster..."
+	fi
+
+	if [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 5.0 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		use threads && eerror "You cannot compile fortran kernel with threads"
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	# if we need external blas or lapack
+	use blas && export LIBS+=" $(pkg-config blas cblas --libs)"
+	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
+	local sseflag="x86-64-sse"
+	use x86 && sseflag="ia32-sse"
+
+	#a bug in gromacs autotools
+	use sse && append-flags -msse
+	use sse2 && append-flags -msse2
+
+	for x in ${GMX_DIRS}; do
+		local suffix="" sse="sse"
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[ "${x}" = "double" ] && suffix="_d"
+		#double uses sse2, single sse
+		[ "${x}" = "double" ] && sse="sse2"
+		myeconfargs=(
+			--bindir="${EPREFIX}"/usr/bin
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
+			--enable-"${x}"
+			$(use_with dmalloc)
+			$(use_with fftw fft fftw3)
+			$(use_with gsl)
+			$(use_with X x)
+			$(use_with xml)
+			$(use_enable threads)
+			$(use_enable altivec ppc-altivec)
+			$(use_enable ia64 ia64-asm)
+			$(use_with lapack external-lapack)
+			$(use_with blas external-blas)
+			$(use_enable fkernels fortran)
+			--disable-bluegene
+			--disable-la-files
+			--disable-power6
+			--disable-ia32-sse
+			--disable-x86-64-sse
+			$(use_enable $sse $sseflag)
+		)
+		#disable ia32-sse and x86-64-sse and enable what we really need in last line
+
+		einfo "Configuring for ${x} precision"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
+			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
+			CC="$(tc-getCC)" F77="$(tc-getFC)"
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			autotools-utils_src_compile
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			autotools-utils_src_compile mdrun
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${WORKDIR}/${P}_${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			autotools-utils_src_install
+		use mpi || continue
+		#autotools-utils_src_install does not support args
+		#using autotools-utils_src_compile instead
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
+
+		#stolen from autotools-utils_src_install see comment above
+		local args
+		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
+		remove_libtool_files ${args}
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
+
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	elog
+	elog "Please read and cite:"
+	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	elog "http://dx.doi.org/10.1021/ct700301q"
+	elog
+	bash-completion_pkg_postinst
+	elog
+	elog $(g_luck)
+	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
+	elog
+	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	elog
+}