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commit: 726d5118d71546b6c8a190ad39b179ca39fdeced |
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Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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AuthorDate: Sun May 1 15:13:35 2011 +0000 |
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Commit: Christoph Junghans <kleiner_otti <AT> gmx <DOT> de> |
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CommitDate: Sun May 1 15:13:35 2011 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=726d5118 |
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|
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[sci-chemistry/gromacs] sync with tree |
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|
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(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586) |
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|
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--- |
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sci-chemistry/gromacs/gromacs-4.5.9999.ebuild | 27 ++++++----------- |
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sci-chemistry/gromacs/gromacs-9999.ebuild | 39 +++++++++++-------------- |
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2 files changed, 26 insertions(+), 40 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |
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index 8d3c8f8..469f604 100644 |
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--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |
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+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |
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@@ -2,17 +2,16 @@ |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: $ |
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|
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-EAPI="3" |
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+EAPI="4" |
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|
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LIBTOOLIZE="true" |
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TEST_PV="4.0.4" |
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-MANUAL_PV="4.5.3" |
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+MANUAL_PV="4.5.4" |
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|
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inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs |
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|
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SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) |
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- doc? ( |
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- http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )" |
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+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )" |
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|
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if [ "${PV%9999}" != "${PV}" ]; then |
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EGIT_REPO_URI="git://git.gromacs.org/gromacs" |
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@@ -29,7 +28,8 @@ LICENSE="GPL-2" |
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SLOT="0" |
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KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" |
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IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack |
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-mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion" |
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+mpi +single-precision sse2 static-libs test +threads +xml zsh-completion" |
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+REQUIRED_USE="fkernels? ( !threads )" |
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|
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CDEPEND=" |
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X? ( |
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@@ -51,10 +51,6 @@ RDEPEND="${CDEPEND} |
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|
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RESTRICT="test" |
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|
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-#gromacs has gnu exec stacks for speedup |
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-QA_EXECSTACK="usr/lib/libgmx.so.* |
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- usr/lib/libgmx_d.so.*" |
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- |
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src_prepare() { |
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if use mpi && use threads; then |
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elog "mdrun uses only threads OR mpi, and gromacs favours the" |
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@@ -96,10 +92,8 @@ src_configure() { |
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|
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#note for gentoo-PREFIX on apple: use --enable-apple-64bit |
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|
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- #fortran will gone in gromacs 5.0 anyway |
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#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster |
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if use fkernels; then |
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- use threads && eerror "You cannot compile fortran kernel with threads" |
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ewarn "Fortran kernels are usually not faster than C kernels and assembly" |
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ewarn "I hope, you know what are you doing..." |
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fi |
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@@ -126,22 +120,19 @@ src_configure() { |
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fi |
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|
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# if we need external blas or lapack |
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- use blas && export LIBS+=" $(pkg-config blas cblas --libs)" |
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+ use blas && export LIBS+=" $(pkg-config blas --libs)" |
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use lapack && export LIBS+=" $(pkg-config lapack --libs)" |
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local sseflag="x86-64-sse" |
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use x86 && sseflag="ia32-sse" |
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|
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- #a bug in gromacs autotools |
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- use sse && append-flags -msse |
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+ #missing flag in autotools (bug #339837) |
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use sse2 && append-flags -msse2 |
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|
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for x in ${GMX_DIRS}; do |
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- local suffix="" sse="sse" |
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+ local suffix="" |
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#if we build single and double - double is suffixed |
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use double-precision && use single-precision && \ |
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[ "${x}" = "double" ] && suffix="_d" |
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- #double uses sse2, single sse |
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- [ "${x}" = "double" ] && sse="sse2" |
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myeconfargs=( |
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--bindir="${EPREFIX}"/usr/bin |
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--docdir="${EPREFIX}"/usr/share/doc/"${PF}" |
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@@ -162,7 +153,7 @@ src_configure() { |
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--disable-power6 |
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--disable-ia32-sse |
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--disable-x86-64-sse |
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- $(use_enable $sse $sseflag) |
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+ $(use_enable sse2 $sseflag) |
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) |
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#disable ia32-sse and x86-64-sse and enable what we really need in last line |
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|
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|
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diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild |
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index a2718f0..817444e 100644 |
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--- a/sci-chemistry/gromacs/gromacs-9999.ebuild |
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+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild |
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@@ -2,9 +2,8 @@ |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: $ |
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|
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-EAPI="3" |
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+EAPI="4" |
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|
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-LIBTOOLIZE="true" |
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TEST_PV="4.0.4" |
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|
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EGIT_REPO_URI="git://git.gromacs.org/gromacs" |
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@@ -20,9 +19,10 @@ LICENSE="GPL-2" |
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SLOT="0" |
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KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" |
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IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack |
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-mpi +single-precision sse sse2 test +threads xml zsh-completion" |
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+mpi +single-precision sse2 test +threads xml zsh-completion" |
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+REQUIRED_USE="fkernels? ( !threads )" |
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|
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-DEPEND=" |
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+CDEPEND=" |
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X? ( |
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x11-libs/libX11 |
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x11-libs/libSM |
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@@ -34,16 +34,14 @@ DEPEND=" |
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lapack? ( virtual/lapack ) |
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mpi? ( virtual/mpi ) |
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xml? ( dev-libs/libxml2:2 )" |
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-RDEPEND="${DEPEND} |
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+DEPEND="${CDEPEND} |
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+ dev-util/pkgconfig" |
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+RDEPEND="${CDEPEND} |
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app-shells/tcsh" |
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PDEPEND="doc? ( app-doc/gromacs-manual )" |
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|
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RESTRICT="test" |
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|
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-#gromacs has gnu exec stacks for speedup |
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-QA_EXECSTACK="usr/lib/libgmx.so.* |
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- usr/lib/libgmx_d.so.*" |
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- |
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src_prepare() { |
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#add user patches from /etc/portage/patches/sci-chemistry/gromacs |
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epatch_user |
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@@ -88,10 +86,8 @@ src_configure() { |
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|
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#note for gentoo-PREFIX on apple: use --enable-apple-64bit |
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|
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- #fortran will gone in gromacs 5.0 anyway |
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#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster |
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if use fkernels; then |
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- use threads && eerror "You cannot compile fortran kernel with threads" |
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ewarn "Fortran kernels are usually not faster than C kernels and assembly" |
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ewarn "I hope, you know what are you doing..." |
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fi |
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@@ -117,11 +113,12 @@ src_configure() { |
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elog "libmd with and without mpi support." |
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fi |
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|
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- #go from slowest to faster acceleration |
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- local acce_pre="none" |
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- use fkernels && acce_pre="fortran" |
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- use altivec && acce_pre="altivec" |
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- use ia64 && acce_pre="ia64" |
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+ #go from slowest to fasterest acceleration |
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+ local acce="none" |
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+ use fkernels && acce="fortran" |
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+ use altivec && acce="altivec" |
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+ use ia64 && acce="ia64" |
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+ use sse2 && acce="sse" |
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|
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mycmakeargs_pre+=( |
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$(cmake-utils_use X GMX_X11) |
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@@ -131,25 +128,23 @@ src_configure() { |
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$(cmake-utils_use threads GMX_THREADS) |
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$(cmake-utils_use xml GMX_XML) |
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-DGMX_DEFAULT_SUFFIX=off |
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+ -DGMX_ACCELERATION="$acce" |
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) |
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|
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for x in ${GMX_DIRS}; do |
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einfo "Configuring for ${x} precision" |
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- local suffix="" acce="$acce_pre" |
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+ local suffix="" |
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#if we build single and double - double is suffixed |
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use double-precision && use single-precision && \ |
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[ "${x}" = "double" ] && suffix="_d" |
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- #double uses sse2, single sse |
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- [ "${x}" = "float" ] && use sse && acce="sse" |
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- [ "${x}" = "double" ] && use sse2 && acce="sse" |
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local p |
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[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
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- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_ACCELERATION="$acce" |
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+ mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF |
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-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) |
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
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use mpi || continue |
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einfo "Configuring for ${x} precision with mpi" |
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- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON -DGMX_ACCELERATION="$acce" |
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+ mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON |
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-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) |
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure |
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done |
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