sync with sci overlay

Package-Manager: portage-2.2.0_alpha149/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

4 files changed, 44 insertions, 20 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 3b92ed0c2520..66978318d7f7 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.114 2012/12/22 19:41:32 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.115 2012/12/26 22:57:12 ottxor Exp $
+
+*gromacs-4.6_beta3-r1 (26 Dec 2012)
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org>
+  +gromacs-4.6_beta3-r1.ebuild, -gromacs-4.6_beta3.ebuild, metadata.xml:
+  sync with sci overlay
 
 *gromacs-4.6_beta3 (22 Dec 2012)
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 91b3cc0571c2..5288ac5a9c14 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -11,17 +11,17 @@ DIST gromacs-4.6-beta3.tar.gz 10238128 SHA256 4ec708c0def71435d513fba01fe0d71f0c
 DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 SHA512 957995333163f6f28568a18d5423a75dc6c315215692da94d0916f09b6221e2a875c5ff4b05385ad6604bd8ae38f0cb61c740cd734c76b360aa4b598cd2c3380 WHIRLPOOL 07077d81ea89bc02207e45e56c77a668375a7284bf6f4a3cc7fe637f1f53ce4ab687c722f13f208cdd2c056b9d766ebfcbe5ea9579ce7649ec9e088371e7db8d
 DIST gromacs-manual-4.6-beta1.pdf 5527287 SHA256 788a424720b149d905d236d3c792d72c3f5af1c054f6ef19192bd12f44fe1fb9 SHA512 5a76aa847a865bfa8ca77bbad67eec18e8328c3db8af411a609a7039f48bcc1973ac6af0201c78f1428ed05040102cbe96638399413520bb1f1c1013031662c6 WHIRLPOOL 1c189bc1cc1da42bcb7332c45c13789ca822e57dbbff6452be7328163a95ed29b678a201250018a214a95e23fb43258d7cc6a58bdde88afcdf718db0c80cf45a
 EBUILD gromacs-4.5.5-r1.ebuild 7808 SHA256 ffedeea7d72e555a7ee13232b252c536d917ea9f428558386e72ccc010779b01 SHA512 1c21a6b55611c7aff88bf67a5519e5926cb9277bba44db36eebdf4e22f9fcc733a157ae2e2643123f1e38f998fd8d1524a5440b20de5c041d832567e12976497 WHIRLPOOL 7a2664e943bbd2eac9e095a37946794a32f843ec90dcc3c05209a77c454a17c61ea19ed5105bd81ccc1014f500ac434f4a2e73802decbbed0041a298f1c7dc54
-EBUILD gromacs-4.6_beta3.ebuild 6867 SHA256 309333a6d7ed257106d0256fd2ecedb1dd4ce30818be710f9817b427060c8aa4 SHA512 991009e41ae2808ecaac8b97792b3442ad281e7ada702c8e97182da646943287830f35fec4272bfe32e92299da1a4b454f7b388c15dcb9717c0b8441713ee8fc WHIRLPOOL f702d3a97108e2fd0963ce015249d1a18260d3fb8ef85050f482760a2897530907749d1e41c486058a0b6f78dc9437de22abbc0861d45389f30d016c733040e3
-MISC ChangeLog 19193 SHA256 91b9e0d852dea688f27d461c844b924e8a673a957960b2abbc2324482f824002 SHA512 b26792ccde3355c2d07cd196eeafae9ca0d8b8467341c718a7f6159240c5fba48e1bb92a3d47169701b54b81c541899b324f9d7eed46e95a778dc77808dc82cc WHIRLPOOL a436a41a4d93c98926b1a06a6151e189cf42acf14b2dcda97472290b22262f7651e30cdabd44a4aa3e13870fcf35d669c24c74a38d3222fbae40640f2f343b13
-MISC metadata.xml 1025 SHA256 06243b817d8d4f9c3c391da58acb870fb1a4fb52627723968b15c975dfe57647 SHA512 7c1a532274bd74d186fdd6db7bccb7542f1642e75ed648277fb4ec89f83d5dc8706d135d973435ded6fc9826263860c0b536b306d60b97b6275e0bc4c78b6f8d WHIRLPOOL 5b4337a167d29a5e741449de7763526b382309c3b59d4de8d76e352f5460dfd08acae364cbdea042d9a1e8d452e56fac4ab8cad39cbcb403faff9b5586a8ddf3
+EBUILD gromacs-4.6_beta3-r1.ebuild 7260 SHA256 c667428c0697b6e73d0d899d86cc7edaea28782b58a773a7ecc5f5e92902324a SHA512 cf7d707afdc06fd7b000ef1fd0651b336a991434860223c0ace71133ce2b070df0cd14cf0ebde1513bd18ea87873d76197b9cc9db9ac5fbf7b013613bea73622 WHIRLPOOL 6fc0dc5ad7d9cbb819839b635197e015e210880821ca340add048eb40bbc2e2fc271ee68b8853d1c5a3d0c0ec373632fd32927f41c51b0bc52b6aa7666234036
+MISC ChangeLog 19382 SHA256 c8ba7c4304e143c12efb2fd734c31724848a174af780a0b267824160d45b3d2d SHA512 45be585c99583b4739e784b6fff0e770e7f07e10ca6258b085874cc082f22e02940a637455e069f08f6ed154ff352b92f3f500dad711669584ea5cea70511d37 WHIRLPOOL 4a6aae3a300ce82bba6932eae9d3fe09ef5d1db488d9a6e62c5a35d793906d07cf1b22b858c6e70c3b83a3c4f41d31c7055e6486e2f4f8779f406bc3db1c5546
+MISC metadata.xml 1110 SHA256 816a9baa47b63fab420ffa1c6dce9891c6af14245d8ed21fc702fffe2dc32ca4 SHA512 361377fc02ceba7137ae1f53f92d35868e468716597c6cefbab109555089f76ce4943ecd618a09f60673fac532a11ac1db3023814cd085c443b17551b64bcc95 WHIRLPOOL 51f8ee400c771a4f84dee95afa5554edf37990ebc3eeb6b325375073b97fbf80099242e41f33843e2bd8243cd41afd3a5b5b4eb38c3e6dc02e4cda9545f74704
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
 
-iQEcBAEBCAAGBQJQ1gz5AAoJEOeBhlrCAAWG03YIAJ+IpkGwYzWQTiSFkayQ61Md
-d+mMO+X+jZphbfs0BZp3Rbml0UrTSuRtDBrpjzHPy0BlmO6lKLyUbUX/SlOZ35UI
-3Mpychn9phhEWd+779JG4JXW4VYWSVDWSt+Q/EeRWEUAM2vlHj4k9u8IvWqt9Y30
-ueLvWpeg5xJEoaXwHJSYWBDHFWA+2/RS2iajVDIHxYC8mjhDAIpAkjVdYyodnvH6
-kAVvQjkICKo7q1iE+d/j3HzF3+DjxbhsjpZGaDM5ck8L3oT1rzT6/YOY/WlOHXw0
-Rq1UxO9GJUOxr9nFdI1zg8ZBRVVo7IzkebrDNnrTVe0fTnF4CiiOKEsk/R5YTHw=
-=aKef
+iQEcBAEBCAAGBQJQ24DJAAoJEOeBhlrCAAWGO4YH/A8U9OlA5Ph6jnLqAthqtL/q
+0+Jxpk6ar1MdhzpOnkGvIAimhakX+cK8ai3MfGhS2DAVo9dlZaem/k3mo4tgtSJD
+JyPI2F/iGNLOsw+CnTUM0Tt+R9MmQ1pN0EyaVQellBuG0KmcbfmzLWcxN+18QidZ
+a6tMkBAi2/lUUKi90zEju/23Et4ZvxO8oaSLmiGDJNAnH9bIccgXCnZDAshWjvww
+29w+sN1qrF7OaiU2wJNaxvWrgq1Ahap2dKBusyFCBB18Blz2m+02imCrgF/oJoIr
+tD6p3+vPIDIa637PLo5TzX6wybNqmps6wxlZEe3VmuU6XXPlCbjfOuV8yfjXUUY=
+=Abka
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild b/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild
index 746dba40ba5b..cae588c690b1 100644
--- a/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild,v 1.1 2012/12/22 19:41:32 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild,v 1.1 2012/12/26 22:57:12 ottxor Exp $
 
 EAPI=5
 
@@ -38,7 +38,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -51,15 +51,22 @@ CDEPEND="
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
-	openmm? ( sci-libs/openmm[cuda,opencl] )"
+	openmm? (
+		dev-util/nvidia-cuda-toolkit
+		sci-libs/openmm[cuda,opencl]
+	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( single-precision ) openmm? ( single-precision cuda )"
+REQUIRED_USE="
+	cuda? ( single-precision )
+	openmm? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -70,7 +77,6 @@ pkg_pretend() {
 src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
-	# -mkl support
 
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
@@ -89,7 +95,7 @@ src_prepare() {
 }
 
 src_configure() {
-	local mycmakeargs_pre=( ) extra
+	local mycmakeargs_pre=( ) extra fft_opts=( )
 
 	#go from slowest to fastest acceleration
 	local acce="None"
@@ -102,8 +108,19 @@ src_configure() {
 	[[ ${CHOST} = *-darwin* ]] && \
 		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
 
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
 	mycmakeargs_pre+=(
-		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
+		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)
@@ -113,7 +130,7 @@ src_configure() {
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
-	    -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		${extra}
 	)
 
@@ -135,7 +152,7 @@ src_configure() {
 			einfo "Configuring for openmm build"
 			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
+				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
 			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
 		fi
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 24ddf421224b..1360fcbfd3d6 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -17,5 +17,6 @@
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
 		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
 	</use>
 </pkgmetadata>