sci-chemistry/gromacs: Fixes bug #302048

(Portage version: 2.1.6.13/git/Linux i686)
 (Signed Manifest commit)

7 files changed, 289 insertions, 11 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b2bf6863c..efbe96d0a 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.0.7-r1 (24 Jan 2010)
+
+  24 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -files/gromacs-4.0.4-configure-gfortran.patch, +gromacs-4.0.7-r1.ebuild,
+  gromacs-4.0.9999.ebuild, +files/gromacs-4.0.9999-ccache.patch,
+  +files/gromacs-4.0.9999-configure-gfortran.patch, gromacs-9999.ebuild:
+  Fixes bug #302048
+
   23 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
   gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
   fixed --as-needed confusion
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 88066bcdf..8f8cbe2c8 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,18 +1,21 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479
+AUX gromacs-4.0.9999-ccache.patch 678 RMD160 043d0e207e04a275fe00a3bd2b28f8dc0dfd4b7f SHA1 08bc5ac8bc0b28f68e1ede994d49616dd920af5d SHA256 ca477d54351c418f1d39dda29373a1426c9403ec0d2f21c28fc7568227d47632
+AUX gromacs-4.0.9999-configure-gfortran.patch 760 RMD160 1700579b0c2dfb8cbb743d795aa9f0f9f467c06b SHA1 e6924d3598b20195fcb6809e64f333def5b0f919 SHA256 1a59dfde8a3db8db729bd19691a5945e02be2725fa66ec0b125ab3b931518761
 AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
+DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
-EBUILD gromacs-4.0.9999.ebuild 6864 RMD160 fc8015de95493f42a74652f022edf3e0a4d4910a SHA1 2b4446a5c36bfa00c65997f71306e4577f4d640b SHA256 7da240f14505743ff956fc27416de028b938777bc4788d3b6260f85d080fd25a
-EBUILD gromacs-9999.ebuild 6906 RMD160 04a97312973c80b8a874ebc3c0a49f7ae0bd4333 SHA1 9d2436b152d4c76ffa4fce6c4d413c890c903809 SHA256 69bdc2ac38116b890134dadbb3ad8678005181196b9ff5aae6740665f8ac0d54
-MISC ChangeLog 2457 RMD160 f91f4ed7cb629d7caecaffd04196cdb29461befe SHA1 d29d0947954c6923c8cb8826dd2706ed816a4829 SHA256 e30801541daecc650a0e9622dcd7e43d607e6117e848dc05c060454e53fcea81
+EBUILD gromacs-4.0.7-r1.ebuild 6991 RMD160 cf1550034a70f7f24c72b84c0ef2a40eef161670 SHA1 61115908912949884fe2b4d9551f2fc07a4c56d8 SHA256 56a2cb9ca8f38d2230e9250f755739fb00521084b96e133205cc1375d09b75dc
+EBUILD gromacs-4.0.9999.ebuild 6897 RMD160 970c8bba013ca982a5d0a1984a36c3c5d176df47 SHA1 1a5e3e0a787b2be9a99c75c51aee908a8a4008ec SHA256 72db19297671827ebd0dd1ed0e8ea8b3dd59bc072f267e95b2ea18ed441fd9ff
+EBUILD gromacs-9999.ebuild 6959 RMD160 1421eff1b59a3cc2242d2b0ccb045e0ec94aa780 SHA1 552005d8e7ed51be2c97d7a08b297d1229b0a0bd SHA256 aa4bf2d1f70534912c177e1362eb592ac2e2325c9c3ef1acce5da8ffc7e5b1ea
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diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch
new file mode 100644
index 000000000..68b6a1e66
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch
@@ -0,0 +1,20 @@
+cc is not cache by ccache (bug #302048), work around that
+
+diff --git a/configure.ac b/configure.ac
+index 3100101..db9d0b6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -288,11 +288,11 @@ AC_DEFINE_UNQUOTED([BUILD_MACHINE],["`uname -srm`"],[Hardware and OS version for
+ # normally we use the default compiler, but on alpha/linux we try the compaq ones first
+ case "${host_cpu}-${host_os}" in
+   alpha*-linux*)
+-    cc_names="ccc cc gcc"
++    cc_names="ccc gcc"
+     f77_names="fort f77 g77"
+     ;;
+   *) 
+-    cc_names="cc icc xlc gcc"
++    cc_names="icc xlc gcc"
+     f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90"
+     ;;
+ esac
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
index c330fcaf0..1bf19ddf5 100644
--- a/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
@@ -1,15 +1,17 @@
+enable gfortan as fortan compiler
+
 diff -Naur gromacs-4.0.4-orig/configure.ac gromacs-4.0.4/configure.ac
 --- gromacs-4.0.4-orig/configure.ac	2009-04-09 21:12:31.000000000 +0200
 +++ gromacs-4.0.4/configure.ac	2009-04-09 21:13:38.000000000 +0200
 @@ -320,11 +320,11 @@
  case "${host_cpu}-${host_os}" in
    alpha*-linux*)
-     cc_names="ccc cc gcc"
+     cc_names="ccc gcc"
 -    f77_names="fort f77 g77"
 +    f77_names="fort f77 g77 gfortran"
      ;;
    *) 
-     cc_names="cc icc xlc gcc"
+     cc_names="icc xlc gcc"
 -    f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90"
 +    f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90 gfortran"
      ;;
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild
new file mode 100644
index 000000000..4d2cd2607
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild
@@ -0,0 +1,243 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7.ebuild,v 1.2 2009/12/08 15:08:23 alexxy Exp $
+
+EAPI="2"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+inherit autotools bash-completion eutils fortran multilib
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+src_prepare() {
+
+	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
+	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.patch"
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	use fkernels && epatch "${FILESDIR}/${PN}-4.0.9999-configure-gfortran.patch"
+
+	eautoreconf
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" single"
+	use double-precision && GMX_DIRS+=" double"
+	for x in ${GMX_DIRS}; do
+		mkdir "${S}-${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
+		use mpi || continue
+		mkdir "${S}-${x}_mpi" || die
+	done
+}
+
+src_configure() {
+	local myconf
+	local myconfsingle
+	local myconfdouble
+	local suffixdouble
+
+	#leave all assembly options enabled mdrun is smart enough to deside itself
+	#there so no gentoo on bluegene!
+	myconf="${myconf} --disable-bluegene"
+
+	#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 [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		FORTRAN="g77 gfortran ifc"
+		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+	else
+		myconf="${myconf} --disable-fortran"
+	fi
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		myconf="${myconf} $(use_enable static all-static)"
+	else
+		myconf="${myconf} --enable-shared"
+	fi
+
+	myconf="--datadir=/usr/share \
+			--bindir=/usr/bin \
+			--libdir=/usr/$(get_libdir) \
+			--docdir=/usr/share/doc/"${PF}" \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_with X x) \
+			$(use_with xml) \
+			${myconf}"
+
+	#if we build single and double - double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffixdouble="_d"
+	else
+		suffixdouble=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
+	myconfsingle="${myconf} --enable-float --program-suffix=''"
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		cd "${S}-${x}"
+		local p=myconf${x}
+		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		einfo "Compiling for ${x} precision"
+		emake || die "emake for ${x} precision failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake mdrun || die "emake mdrun for ${x} precision failed"
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${S}-${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${D}"/usr/bin/GMXRC*
+
+	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${D}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -r "${D}"/usr/bin/completion.*
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL README
+	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
+}
+
+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 $(luck)
+	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
+	elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
index 7d8e4ff37..03585ac67 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
@@ -41,6 +41,7 @@ RESTRICT="test"
 src_prepare() {
 
 	epatch "${FILESDIR}/${P}-docdir.patch"
+	epatch "${FILESDIR}/${P}-ccache.patch"
 	# Fix typos in a couple of files.
 	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
 		|| die "Failed to fixup demo script."
@@ -62,7 +63,7 @@ src_prepare() {
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
+	use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"
 
 	eautoreconf
 
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 2f85ba2d2..dad31f359 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -41,6 +41,7 @@ RESTRICT="test"
 src_prepare() {
 
 	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
+	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.patch"
 	# Fix typos in a couple of files.
 	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
 		|| die "Failed to fixup demo script."
@@ -62,7 +63,7 @@ src_prepare() {
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
+	use fkernels && epatch "${FILESDIR}/${PN}-4.0.9999-configure-gfortran.patch"
 
 	filter-ldflags -Wl,--as-needed
 	eautoreconf