Fix bug #302048. thanks to Christoph Junghans

(Portage version: 2.2_rc61/cvs/Linux x86_64)

5 files changed, 327 insertions, 1 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1d5480d19dd6..0cdd35a9a8fb 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.48 2010/01/18 19:16:11 armin76 Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.49 2010/01/24 19:39:09 alexxy Exp $
+
+*gromacs-4.0.7-r1 (24 Jan 2010)
+
+  24 Jan 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r1.ebuild,
+  +files/gromacs-4.0.9999-ccache.patch,
+  +files/gromacs-4.0.9999-configure-gfortran.patch,
+  +files/gromacs-4.0.9999-docdir.patch:
+  Fix bug #302048. thanks to Christoph Junghans
 
   18 Jan 2010; Raúl Porcel <armin76@gentoo.org> gromacs-4.0.5.ebuild:
   alpha stable
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 000000000000..68b6a1e66e1d
--- /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-4.0.9999-configure-gfortran.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
new file mode 100644
index 000000000000..1bf19ddf532e
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
@@ -0,0 +1,19 @@
+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 gcc"
+-    f77_names="fort f77 g77"
++    f77_names="fort f77 g77 gfortran"
+     ;;
+   *) 
+     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"
+     ;;
+ esac
+ # the (non-mpi) c compiler, which is also used for programs executed during build stage
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
new file mode 100644
index 000000000000..e32ddec90291
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
@@ -0,0 +1,36 @@
+diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
+--- gromacs-4.0.5.orig/share/html/Makefile.am	2006-03-06 10:52:20.000000000 +0100
++++ gromacs-4.0.5/share/html/Makefile.am	2009-11-29 22:27:24.000000000 +0100
+@@ -4,7 +4,7 @@
+ #
+ SUBDIRS = .  images  online
+ 
+-htmldir = ${pkgdatadir}/html
++htmldir = @htmldir@/html
+ 
+ html_DATA = online.html gmxfaq.html
+ 
+diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
+--- gromacs-4.0.5.orig/share/html/images/Makefile.am	2006-03-06 10:52:20.000000000 +0100
++++ gromacs-4.0.5/share/html/images/Makefile.am	2009-11-29 23:00:57.000000000 +0100
+@@ -2,7 +2,7 @@
+ #
+ # Don't edit - this file is generated automatically from Makefile.am
+ #
+-imagedir = ${pkgdatadir}/html/images
++imagedir = @htmldir@/html/images
+ 
+ image_DATA = \
+ 	features.gif					\
+diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
+--- gromacs-4.0.5.orig/share/html/online/Makefile.am	2008-08-11 11:46:17.000000000 +0200
++++ gromacs-4.0.5/share/html/online/Makefile.am	2009-11-29 23:01:47.000000000 +0100
+@@ -2,7 +2,7 @@
+ #
+ # Don't edit - this file is generated automatically from Makefile.am
+ #
+-onlinedir = ${pkgdatadir}/html/online
++onlinedir = @htmldir@/html/online
+ 
+ online_DATA = \
+   cpt.html	\
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 000000000000..abc141e621b4
--- /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-r1.ebuild,v 1.1 2010/01/24 19:39:09 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
+}