[sci-chemistry/gromacs] sync with tree

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

1 files changed, 9 insertions, 18 deletions

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 8d3c8f813..469f60402 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -2,17 +2,16 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI="4"
 
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
+MANUAL_PV="4.5.4"
 
 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-${MANUAL_PV}.pdf )"
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 if [ "${PV%9999}" != "${PV}" ]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
@@ -29,7 +28,8 @@ 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"
+mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
 	X? (
@@ -51,10 +51,6 @@ RDEPEND="${CDEPEND}
 
 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"
@@ -96,10 +92,8 @@ src_configure() {
 
 	#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
@@ -126,22 +120,19 @@ src_configure() {
 	fi
 
 	# if we need external blas or lapack
-	use blas && export LIBS+=" $(pkg-config blas cblas --libs)"
+	use blas && export LIBS+=" $(pkg-config blas --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
+	#missing flag in autotools (bug #339837)
 	use sse2 && append-flags -msse2
 
 	for x in ${GMX_DIRS}; do
-		local suffix="" sse="sse"
+		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
-		#double uses sse2, single sse
-		[ "${x}" = "double" ] && sse="sse2"
 		myeconfargs=(
 			--bindir="${EPREFIX}"/usr/bin
 			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
@@ -162,7 +153,7 @@ src_configure() {
 			--disable-power6
 			--disable-ia32-sse
 			--disable-x86-64-sse
-			$(use_enable $sse $sseflag)
+			$(use_enable sse2 $sseflag)
 		)
 		#disable ia32-sse and x86-64-sse and enable what we really need in last line