[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ - gentoo-commits

From:	Alexey Shvetsov <alexxy@g.o>
To:	gentoo-commits@l.g.o
Subject:	[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
Date:	Mon, 11 Jul 2016 19:40:26
Message-Id:	`1468266006.e505c9758afd89769db26e1c46adce0215a0daea.alexxy@gentoo`

1

commit:     e505c9758afd89769db26e1c46adce0215a0daea

2

Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>

3

AuthorDate: Mon Jul 11 19:40:06 2016 +0000

4

Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>

5

CommitDate: Mon Jul 11 19:40:06 2016 +0000

6

URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e505c975

7

8

sci-chemistry/gromacs: Add 2016 RC1

9

10

Package-Manager: portage-2.3.0

11

12

 sci-chemistry/gromacs/gromacs-2016.9999.ebuild                 | 10 ++++------

13

 .../{gromacs-2016.9999.ebuild => gromacs-2016_rc1.ebuild}      | 10 ++++------

14

 sci-chemistry/gromacs/gromacs-9999.ebuild                      | 10 ++++------

15

 sci-chemistry/gromacs/metadata.xml                             |  3 ++-

16

 4 files changed, 14 insertions(+), 19 deletions(-)

17

18

diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild

19

index b30ff55..1ca0343 100644

20

--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild

21

+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild

22

@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then

23

 	KEYWORDS=""

24

 else

25

 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz

26

-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"

27

+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"

28

 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"

29

fi

30

31

@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"

32

 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib

33

 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"

34

 SLOT="0/${PV}"

35

-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

36

+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

37

38

 CDEPEND="

39

 	X? (

40

@@ -43,6 +43,7 @@ CDEPEND="

41

 	blas? ( virtual/blas )

42

 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )

43

 	fftw? ( sci-libs/fftw:3.0 )

44

+	hwloc? ( sys-apps/hwloc )

45

 	lapack? ( virtual/lapack )

46

 	mkl? ( sci-libs/mkl )

47

 	mpi? ( virtual/mpi )

48

@@ -149,15 +150,13 @@ src_configure() {

49

 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)

50

 		-DGMX_OPENMP=$(usex openmp)

51

 		-DGMX_COOL_QUOTES=$(usex offensive)

52

-		-DGMX_EXTERNAL_BOOST=$(usex boost)

53

 		-DGMX_USE_TNG=$(usex tng)

54

 		-DGMX_BUILD_MANUAL=$(usex doc)

55

+		-DGMX_HWLOC=$(usex hwloc)

56

 		-DGMX_DEFAULT_SUFFIX=off

57

 		-DGMX_SIMD="$acce"

58

 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"

59

 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"

60

-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF

61

-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF

62

 		-DBUILD_TESTING=OFF

63

 		-DGMX_BUILD_UNITTESTS=OFF

64

 		${extra}

65

@@ -179,7 +178,6 @@ src_configure() {

66

 			-DGMX_MPI=OFF

67

 			-DGMX_THREAD_MPI=$(usex threads)

68

 			"${cuda[@]}"

69

-			-DGMX_OPENMM=OFF

70

 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"

71

 			-DGMX_BINARY_SUFFIX="${suffix}"

72

 			-DGMX_LIBS_SUFFIX="${suffix}"

73

74

diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild

75

similarity index 96%

76

copy from sci-chemistry/gromacs/gromacs-2016.9999.ebuild

77

copy to sci-chemistry/gromacs/gromacs-2016_rc1.ebuild

78

index b30ff55..1ca0343 100644

79

--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild

80

+++ b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild

81

@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then

82

 	KEYWORDS=""

83

 else

84

 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz

85

-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"

86

+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"

87

 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"

88

fi

89

90

@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"

91

 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib

92

 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"

93

 SLOT="0/${PV}"

94

-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

95

+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

96

97

 CDEPEND="

98

 	X? (

99

@@ -43,6 +43,7 @@ CDEPEND="

100

 	blas? ( virtual/blas )

101

 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )

102

 	fftw? ( sci-libs/fftw:3.0 )

103

+	hwloc? ( sys-apps/hwloc )

104

 	lapack? ( virtual/lapack )

105

 	mkl? ( sci-libs/mkl )

106

 	mpi? ( virtual/mpi )

107

@@ -149,15 +150,13 @@ src_configure() {

108

 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)

109

 		-DGMX_OPENMP=$(usex openmp)

110

 		-DGMX_COOL_QUOTES=$(usex offensive)

111

-		-DGMX_EXTERNAL_BOOST=$(usex boost)

112

 		-DGMX_USE_TNG=$(usex tng)

113

 		-DGMX_BUILD_MANUAL=$(usex doc)

114

+		-DGMX_HWLOC=$(usex hwloc)

115

 		-DGMX_DEFAULT_SUFFIX=off

116

 		-DGMX_SIMD="$acce"

117

 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"

118

 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"

119

-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF

120

-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF

121

 		-DBUILD_TESTING=OFF

122

 		-DGMX_BUILD_UNITTESTS=OFF

123

 		${extra}

124

@@ -179,7 +178,6 @@ src_configure() {

125

 			-DGMX_MPI=OFF

126

 			-DGMX_THREAD_MPI=$(usex threads)

127

 			"${cuda[@]}"

128

-			-DGMX_OPENMM=OFF

129

 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"

130

 			-DGMX_BINARY_SUFFIX="${suffix}"

131

 			-DGMX_LIBS_SUFFIX="${suffix}"

132

133

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild

134

index b30ff55..1ca0343 100644

135

--- a/sci-chemistry/gromacs/gromacs-9999.ebuild

136

+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild

137

@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then

138

 	KEYWORDS=""

139

 else

140

 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz

141

-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"

142

+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"

143

 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"

144

fi

145

146

@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"

147

 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib

148

 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"

149

 SLOT="0/${PV}"

150

-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

151

+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"

152

153

 CDEPEND="

154

 	X? (

155

@@ -43,6 +43,7 @@ CDEPEND="

156

 	blas? ( virtual/blas )

157

 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )

158

 	fftw? ( sci-libs/fftw:3.0 )

159

+	hwloc? ( sys-apps/hwloc )

160

 	lapack? ( virtual/lapack )

161

 	mkl? ( sci-libs/mkl )

162

 	mpi? ( virtual/mpi )

163

@@ -149,15 +150,13 @@ src_configure() {

164

 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)

165

 		-DGMX_OPENMP=$(usex openmp)

166

 		-DGMX_COOL_QUOTES=$(usex offensive)

167

-		-DGMX_EXTERNAL_BOOST=$(usex boost)

168

 		-DGMX_USE_TNG=$(usex tng)

169

 		-DGMX_BUILD_MANUAL=$(usex doc)

170

+		-DGMX_HWLOC=$(usex hwloc)

171

 		-DGMX_DEFAULT_SUFFIX=off

172

 		-DGMX_SIMD="$acce"

173

 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"

174

 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"

175

-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF

176

-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF

177

 		-DBUILD_TESTING=OFF

178

 		-DGMX_BUILD_UNITTESTS=OFF

179

 		${extra}

180

@@ -179,7 +178,6 @@ src_configure() {

181

 			-DGMX_MPI=OFF

182

 			-DGMX_THREAD_MPI=$(usex threads)

183

 			"${cuda[@]}"

184

-			-DGMX_OPENMM=OFF

185

 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"

186

 			-DGMX_BINARY_SUFFIX="${suffix}"

187

 			-DGMX_LIBS_SUFFIX="${suffix}"

188

189

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml

190

index 0c7b107..e98cd51 100644

191

--- a/sci-chemistry/gromacs/metadata.xml

192

+++ b/sci-chemistry/gromacs/metadata.xml

193

@@ -17,7 +17,8 @@

194

     <flag name="cuda">Enable cuda non-bonded kernels</flag>

195

     <flag name="double-precision">More precise calculations at the expense of speed</flag>

196

     <flag name="single-precision">Single precision version of gromacs (default)</flag>

197

-    <flag name="boost">Enable external boost library</flag>

198

+	<flag name="boost">Enable external boost library</flag>

199

+	<flag name="hwloc">Enable HWLoc lib support</flag>

200

     <flag name="tng">Enable new trajectory format - tng</flag>

201

     <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>

202

     <!-- acceleration optimization flags -->

1	commit: e505c9758afd89769db26e1c46adce0215a0daea
2	Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
3	AuthorDate: Mon Jul 11 19:40:06 2016 +0000
4	Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
5	CommitDate: Mon Jul 11 19:40:06 2016 +0000
6	URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e505c975
7
8	sci-chemistry/gromacs: Add 2016 RC1
9
10	Package-Manager: portage-2.3.0
11
12	sci-chemistry/gromacs/gromacs-2016.9999.ebuild \| 10 ++++------
13	.../{gromacs-2016.9999.ebuild => gromacs-2016_rc1.ebuild} \| 10 ++++------
14	sci-chemistry/gromacs/gromacs-9999.ebuild \| 10 ++++------
15	sci-chemistry/gromacs/metadata.xml \| 3 ++-
16	4 files changed, 14 insertions(+), 19 deletions(-)
17
18	diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
19	index b30ff55..1ca0343 100644
20	--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
21	+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
22	@@ -18,7 +18,7 @@ if [[ $PV = 9999 ]]; then
23	KEYWORDS=""
24	else
25	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
26	- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
27	+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
28	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
29	fi
30
31	@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
32	# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
33	LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
34	SLOT="0/${PV}"
35	-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
36	+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
37
38	CDEPEND="
39	X? (
40	@@ -43,6 +43,7 @@ CDEPEND="
41	blas? ( virtual/blas )
42	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
43	fftw? ( sci-libs/fftw:3.0 )
44	+ hwloc? ( sys-apps/hwloc )
45	lapack? ( virtual/lapack )
46	mkl? ( sci-libs/mkl )
47	mpi? ( virtual/mpi )
48	@@ -149,15 +150,13 @@ src_configure() {
49	-DGMX_EXTERNAL_LAPACK=$(usex lapack)
50	-DGMX_OPENMP=$(usex openmp)
51	-DGMX_COOL_QUOTES=$(usex offensive)
52	- -DGMX_EXTERNAL_BOOST=$(usex boost)
53	-DGMX_USE_TNG=$(usex tng)
54	-DGMX_BUILD_MANUAL=$(usex doc)
55	+ -DGMX_HWLOC=$(usex hwloc)
56	-DGMX_DEFAULT_SUFFIX=off
57	-DGMX_SIMD="$acce"
58	-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
59	-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
60	- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
61	- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
62	-DBUILD_TESTING=OFF
63	-DGMX_BUILD_UNITTESTS=OFF
64	${extra}
65	@@ -179,7 +178,6 @@ src_configure() {
66	-DGMX_MPI=OFF
67	-DGMX_THREAD_MPI=$(usex threads)
68	"${cuda[@]}"
69	- -DGMX_OPENMM=OFF
70	"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
71	-DGMX_BINARY_SUFFIX="${suffix}"
72	-DGMX_LIBS_SUFFIX="${suffix}"
73
74	diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
75	similarity index 96%
76	copy from sci-chemistry/gromacs/gromacs-2016.9999.ebuild
77	copy to sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
78	index b30ff55..1ca0343 100644
79	--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
80	+++ b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
81	@@ -18,7 +18,7 @@ if [[ $PV = 9999 ]]; then
82	KEYWORDS=""
83	else
84	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
85	- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
86	+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
87	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
88	fi
89
90	@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
91	# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
92	LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
93	SLOT="0/${PV}"
94	-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
95	+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
96
97	CDEPEND="
98	X? (
99	@@ -43,6 +43,7 @@ CDEPEND="
100	blas? ( virtual/blas )
101	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
102	fftw? ( sci-libs/fftw:3.0 )
103	+ hwloc? ( sys-apps/hwloc )
104	lapack? ( virtual/lapack )
105	mkl? ( sci-libs/mkl )
106	mpi? ( virtual/mpi )
107	@@ -149,15 +150,13 @@ src_configure() {
108	-DGMX_EXTERNAL_LAPACK=$(usex lapack)
109	-DGMX_OPENMP=$(usex openmp)
110	-DGMX_COOL_QUOTES=$(usex offensive)
111	- -DGMX_EXTERNAL_BOOST=$(usex boost)
112	-DGMX_USE_TNG=$(usex tng)
113	-DGMX_BUILD_MANUAL=$(usex doc)
114	+ -DGMX_HWLOC=$(usex hwloc)
115	-DGMX_DEFAULT_SUFFIX=off
116	-DGMX_SIMD="$acce"
117	-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
118	-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
119	- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
120	- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
121	-DBUILD_TESTING=OFF
122	-DGMX_BUILD_UNITTESTS=OFF
123	${extra}
124	@@ -179,7 +178,6 @@ src_configure() {
125	-DGMX_MPI=OFF
126	-DGMX_THREAD_MPI=$(usex threads)
127	"${cuda[@]}"
128	- -DGMX_OPENMM=OFF
129	"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
130	-DGMX_BINARY_SUFFIX="${suffix}"
131	-DGMX_LIBS_SUFFIX="${suffix}"
132
133	diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
134	index b30ff55..1ca0343 100644
135	--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
136	+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
137	@@ -18,7 +18,7 @@ if [[ $PV = 9999 ]]; then
138	KEYWORDS=""
139	else
140	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
141	- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
142	+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
143	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
144	fi
145
146	@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
147	# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
148	LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
149	SLOT="0/${PV}"
150	-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
151	+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
152
153	CDEPEND="
154	X? (
155	@@ -43,6 +43,7 @@ CDEPEND="
156	blas? ( virtual/blas )
157	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
158	fftw? ( sci-libs/fftw:3.0 )
159	+ hwloc? ( sys-apps/hwloc )
160	lapack? ( virtual/lapack )
161	mkl? ( sci-libs/mkl )
162	mpi? ( virtual/mpi )
163	@@ -149,15 +150,13 @@ src_configure() {
164	-DGMX_EXTERNAL_LAPACK=$(usex lapack)
165	-DGMX_OPENMP=$(usex openmp)
166	-DGMX_COOL_QUOTES=$(usex offensive)
167	- -DGMX_EXTERNAL_BOOST=$(usex boost)
168	-DGMX_USE_TNG=$(usex tng)
169	-DGMX_BUILD_MANUAL=$(usex doc)
170	+ -DGMX_HWLOC=$(usex hwloc)
171	-DGMX_DEFAULT_SUFFIX=off
172	-DGMX_SIMD="$acce"
173	-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
174	-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
175	- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
176	- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
177	-DBUILD_TESTING=OFF
178	-DGMX_BUILD_UNITTESTS=OFF
179	${extra}
180	@@ -179,7 +178,6 @@ src_configure() {
181	-DGMX_MPI=OFF
182	-DGMX_THREAD_MPI=$(usex threads)
183	"${cuda[@]}"
184	- -DGMX_OPENMM=OFF
185	"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
186	-DGMX_BINARY_SUFFIX="${suffix}"
187	-DGMX_LIBS_SUFFIX="${suffix}"
188
189	diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
190	index 0c7b107..e98cd51 100644
191	--- a/sci-chemistry/gromacs/metadata.xml
192	+++ b/sci-chemistry/gromacs/metadata.xml
193	@@ -17,7 +17,8 @@
194	<flag name="cuda">Enable cuda non-bonded kernels</flag>
195	<flag name="double-precision">More precise calculations at the expense of speed</flag>
196	<flag name="single-precision">Single precision version of gromacs (default)</flag>
197	- <flag name="boost">Enable external boost library</flag>
198	+ <flag name="boost">Enable external boost library</flag>
199	+ <flag name="hwloc">Enable HWLoc lib support</flag>
200	<flag name="tng">Enable new trajectory format - tng</flag>
201	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
202	<!-- acceleration optimization flags -->

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