| 1 |
commit: 8d91f54dcb67c1e6c02e9539839070e50d1c8c1d |
| 2 |
Author: Donnie Berkholz <dberkholz <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Jul 30 19:17:32 2011 +0000 |
| 4 |
Commit: Donnie Berkholz <dberkholz <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Jul 30 19:17:32 2011 +0000 |
| 6 |
URL: http://git.overlays.gentoo.org/gitweb/?p=dev/dberkholz.git;a=commit;h=8d91f54d |
| 7 |
|
| 8 |
namd: bump to 2.8. |
| 9 |
|
| 10 |
--- |
| 11 |
sci-chemistry/namd/Manifest | 6 +- |
| 12 |
sci-chemistry/namd/files/namd-2.8-gentoo.patch | 120 ++++++++++++++++++++ |
| 13 |
sci-chemistry/namd/files/namd-2.8-ldflags.patch | 42 +++++++ |
| 14 |
.../{namd-2.7_beta3.ebuild => namd-2.8.ebuild} | 8 +- |
| 15 |
4 files changed, 170 insertions(+), 6 deletions(-) |
| 16 |
|
| 17 |
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest |
| 18 |
index e9fe216..45c4bb0 100644 |
| 19 |
--- a/sci-chemistry/namd/Manifest |
| 20 |
+++ b/sci-chemistry/namd/Manifest |
| 21 |
@@ -3,11 +3,13 @@ AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 S |
| 22 |
AUX namd-2.7-iml-dec.patch 520 RMD160 f8f33d8e10a7c6933369c3a6b857d44243bb1c74 SHA1 2edd740e3b6cb5514bde0c4742d0ca4bf6b98126 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024 |
| 23 |
AUX namd-2.7-ldflags.patch 1547 RMD160 bfaf2ca893168e1a652e75a186817d8149af94d8 SHA1 a0ce28bcc65e1cb7ff5c61723e602c26f5eef16b SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924 |
| 24 |
AUX namd-2.7_beta2-gentoo.patch 4409 RMD160 301bc17156f10a552eae4c2b3ed91ed2ea9fae6a SHA1 3cb0deb35e690156cf1a41e35482fab42480e3af SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d |
| 25 |
+AUX namd-2.8-gentoo.patch 4083 RMD160 736e9aed3da973b58f01bf57907bf307980b5354 SHA1 3916a0f8dce506e9dfcdf56c34e279eb1c578827 SHA256 c8e5c6b27d32098203709aa898f024b93de590b3a337682252a66cff5b100be5 |
| 26 |
+AUX namd-2.8-ldflags.patch 1735 RMD160 130707ed9c3b91ab069af350d7a5e703515287f6 SHA1 b07e95a2efe999102384da7e99ede609eac3ee14 SHA256 48ea2c9195001c537e013238950a53910c19705f8d4d9e5db9988e5f3fb73ae5 |
| 27 |
AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992 |
| 28 |
AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696 |
| 29 |
AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250 |
| 30 |
AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 |
| 31 |
-DIST NAMD_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67 |
| 32 |
-EBUILD namd-2.7_beta3.ebuild 2996 RMD160 a63b37e03be81128dcc411503bec610d73f5b828 SHA1 613157a497f34edb47733082afe0b53b221aad1d SHA256 e25afb54ca065f0657683088e9dd60543939808f95a22298c0caf71a58637b6d |
| 33 |
+DIST NAMD_2.8_Source.tar.gz 8451502 RMD160 9a3e4122b29fecc273f56feb714681743d494674 SHA1 dcc7124665c44bfce7c4460415c854be97098233 SHA256 729e69c2a60866bc3c9e91c0266238dd8e6fad135693913e06853289be90a4cb |
| 34 |
+EBUILD namd-2.8.ebuild 2988 RMD160 7104c858037aea16e52e51b4545d4029c81b7d4b SHA1 9f5b6723bdde5ef634c996fde5cdcc05f130ffeb SHA256 ab65d05d8b60431e8187204aeb3970293588a3f8b8c7ba92b71f2271372113c6 |
| 35 |
MISC ChangeLog 2797 RMD160 050da7ba2120061612df6321b0ffd2e49c1ae9e6 SHA1 06d5dc422168a91e935ebd7d5596f4a474ce0c53 SHA256 05c0e8e730d8ba7cebcd8bb0435aa8980e686b908713cc340c222d0455ad8421 |
| 36 |
MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349 |
| 37 |
|
| 38 |
diff --git a/sci-chemistry/namd/files/namd-2.8-gentoo.patch b/sci-chemistry/namd/files/namd-2.8-gentoo.patch |
| 39 |
new file mode 100644 |
| 40 |
index 0000000..c4f2e0a |
| 41 |
--- /dev/null |
| 42 |
+++ b/sci-chemistry/namd/files/namd-2.8-gentoo.patch |
| 43 |
@@ -0,0 +1,120 @@ |
| 44 |
+diff -ur NAMD_2.8_Source.orig/Make.charm NAMD_2.8_Source/Make.charm |
| 45 |
+--- NAMD_2.8_Source.orig/Make.charm 2011-07-30 13:11:21.052330641 -0500 |
| 46 |
++++ NAMD_2.8_Source/Make.charm 2011-07-30 13:13:16.412798831 -0500 |
| 47 |
+@@ -2,5 +2,5 @@ |
| 48 |
+ # The config script will override this setting if there is a directory |
| 49 |
+ # called charm-6.3.2 or charm in the NAMD base directory. |
| 50 |
+ |
| 51 |
+-CHARMBASE = /Projects/namd2/charm-6.3.2 |
| 52 |
++CHARMBASE = /usr/include/charm-6.2.1 |
| 53 |
+ |
| 54 |
+Only in NAMD_2.8_Source: Make.charm.~1~ |
| 55 |
+diff -ur NAMD_2.8_Source.orig/Makefile NAMD_2.8_Source/Makefile |
| 56 |
+--- NAMD_2.8_Source.orig/Makefile 2011-07-30 13:11:21.052330641 -0500 |
| 57 |
++++ NAMD_2.8_Source/Makefile 2011-07-30 13:15:48.003410162 -0500 |
| 58 |
+@@ -323,10 +323,10 @@ |
| 59 |
+ $(DSTDIR)/stringhash.o |
| 60 |
+ |
| 61 |
+ # definitions for Charm routines |
| 62 |
+-CHARMC = $(CHARM)/bin/charmc |
| 63 |
+-CHARMXI = $(CHARM)/bin/charmc |
| 64 |
+-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 |
| 65 |
+-CHARMLIB = $(CHARM)/lib |
| 66 |
++CHARMC = /usr/bin/charmc |
| 67 |
++CHARMXI = /usr/bin/charmc |
| 68 |
++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 |
| 69 |
++CHARMLIB = /usr/gentoo-libdir |
| 70 |
+ |
| 71 |
+ # Libraries we may have changed |
| 72 |
+ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) |
| 73 |
+@@ -346,7 +346,7 @@ |
| 74 |
+ |
| 75 |
+ # Add new executables here. |
| 76 |
+ |
| 77 |
+-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb |
| 78 |
++BINARIES = namd2 psfgen flipdcd flipbinpdb |
| 79 |
+ |
| 80 |
+ # This should be rebuilt at every compile, but not on Win32. |
| 81 |
+ BUILDINFO = $(DSTDIR)/buildinfo |
| 82 |
+@@ -378,16 +378,9 @@ |
| 83 |
+ $(EXTRALINKLIBS) \ |
| 84 |
+ -lm -o namd2 |
| 85 |
+ |
| 86 |
+-charmrun: $(CHARM)/bin/charmrun # XXX |
| 87 |
+- $(COPY) $(CHARM)/bin/charmrun $@ |
| 88 |
+- |
| 89 |
+ $(LIBCUDARTSO): |
| 90 |
+ $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@; |
| 91 |
+ |
| 92 |
+-WINDOWSBINARIES = namd2.exe psfgen.exe |
| 93 |
+-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe |
| 94 |
+-windowsbinaries: $(WINDOWSBINARIES) |
| 95 |
+- |
| 96 |
+ namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) |
| 97 |
+ $(MAKEBUILDINFO) |
| 98 |
+ $(CHARMC) -verbose \ |
| 99 |
+@@ -410,9 +403,6 @@ |
| 100 |
+ charmd_faceless.exe: |
| 101 |
+ $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe |
| 102 |
+ |
| 103 |
+-charmrun.exe: |
| 104 |
+- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe |
| 105 |
+- |
| 106 |
+ psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) |
| 107 |
+ $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm |
| 108 |
+ |
| 109 |
+@@ -630,9 +620,7 @@ |
| 110 |
+ |
| 111 |
+ DOC_FILES = README.txt announce.txt license.txt notes.txt |
| 112 |
+ |
| 113 |
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2 |
| 114 |
+- |
| 115 |
+-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) |
| 116 |
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2 |
| 117 |
+ |
| 118 |
+ release: all |
| 119 |
+ $(ECHO) Creating release $(RELEASE_DIR_NAME) |
| 120 |
+@@ -643,17 +631,9 @@ |
| 121 |
+ for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ |
| 122 |
+ /bin/rm -rf $$f; \ |
| 123 |
+ done |
| 124 |
+- if [ -r $(CHARM)/bin/charmd ]; then \ |
| 125 |
+- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ |
| 126 |
+- fi |
| 127 |
+- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ |
| 128 |
+- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ |
| 129 |
+- fi |
| 130 |
+ chmod -R a+rX $(RELEASE_DIR_NAME) |
| 131 |
+ tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) |
| 132 |
+ gzip $(RELEASE_DIR_NAME).tar |
| 133 |
+- echo $(CHARM) |
| 134 |
+- ls -l $(CHARM)/lib |
| 135 |
+ -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done |
| 136 |
+ |
| 137 |
+ winrelease: winall |
| 138 |
+diff -ur NAMD_2.8_Source.orig/arch/Linux-x86_64.fftw NAMD_2.8_Source/arch/Linux-x86_64.fftw |
| 139 |
+--- NAMD_2.8_Source.orig/arch/Linux-x86_64.fftw 2011-07-30 13:11:21.052330641 -0500 |
| 140 |
++++ NAMD_2.8_Source/arch/Linux-x86_64.fftw 2011-07-30 13:12:25.242589102 -0500 |
| 141 |
+@@ -1,7 +1,7 @@ |
| 142 |
+ |
| 143 |
+-FFTDIR=/Projects/namd2/fftw/linux-x86_64 |
| 144 |
++FFTDIR=/usr |
| 145 |
+ FFTINCL=-I$(FFTDIR)/include |
| 146 |
+-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw |
| 147 |
++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw |
| 148 |
+ FFTFLAGS=-DNAMD_FFTW |
| 149 |
+ FFT=$(FFTINCL) $(FFTFLAGS) |
| 150 |
+ |
| 151 |
+diff -ur NAMD_2.8_Source.orig/arch/Linux-x86_64.tcl NAMD_2.8_Source/arch/Linux-x86_64.tcl |
| 152 |
+--- NAMD_2.8_Source.orig/arch/Linux-x86_64.tcl 2011-07-30 13:11:21.052330641 -0500 |
| 153 |
++++ NAMD_2.8_Source/arch/Linux-x86_64.tcl 2011-07-30 13:12:25.242589102 -0500 |
| 154 |
+@@ -1,7 +1,7 @@ |
| 155 |
+ |
| 156 |
+-TCLDIR=/Projects/namd2/tcl/linux-x86_64 |
| 157 |
++TCLDIR=/usr |
| 158 |
+ TCLINCL=-I$(TCLDIR)/include |
| 159 |
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl |
| 160 |
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl |
| 161 |
+ TCLFLAGS=-DNAMD_TCL |
| 162 |
+ TCL=$(TCLINCL) $(TCLFLAGS) |
| 163 |
+ |
| 164 |
|
| 165 |
diff --git a/sci-chemistry/namd/files/namd-2.8-ldflags.patch b/sci-chemistry/namd/files/namd-2.8-ldflags.patch |
| 166 |
new file mode 100644 |
| 167 |
index 0000000..272590d |
| 168 |
--- /dev/null |
| 169 |
+++ b/sci-chemistry/namd/files/namd-2.8-ldflags.patch |
| 170 |
@@ -0,0 +1,42 @@ |
| 171 |
+diff -ur NAMD_2.8_Source.orig/Makefile NAMD_2.8_Source/Makefile |
| 172 |
+--- NAMD_2.8_Source.orig/Makefile 2011-07-30 13:17:02.513705293 -0500 |
| 173 |
++++ NAMD_2.8_Source/Makefile 2011-07-30 13:18:03.363943762 -0500 |
| 174 |
+@@ -362,7 +362,7 @@ |
| 175 |
+ |
| 176 |
+ namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) |
| 177 |
+ $(MAKEBUILDINFO) |
| 178 |
+- $(CHARMC) -verbose -ld++-option \ |
| 179 |
++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ |
| 180 |
+ "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ |
| 181 |
+ -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \ |
| 182 |
+ $(BUILDINFO).o \ |
| 183 |
+@@ -404,7 +404,7 @@ |
| 184 |
+ $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe |
| 185 |
+ |
| 186 |
+ psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) |
| 187 |
+- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm |
| 188 |
++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm |
| 189 |
+ |
| 190 |
+ psfgen.exe: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) |
| 191 |
+ $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm |
| 192 |
+@@ -413,17 +413,17 @@ |
| 193 |
+ $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm |
| 194 |
+ |
| 195 |
+ flipdcd: $(SRCDIR)/flipdcd.c |
| 196 |
+- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ |
| 197 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ |
| 198 |
+ echo "#!/bin/sh\necho unavailable on this platform" > $@; \ |
| 199 |
+ chmod +x $@ |
| 200 |
+ |
| 201 |
+ flipbinpdb: $(SRCDIR)/flipbinpdb.c |
| 202 |
+- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ |
| 203 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ |
| 204 |
+ echo "#!/bin/sh\necho unavailable on this platform" > $@; \ |
| 205 |
+ chmod +x $@ |
| 206 |
+ |
| 207 |
+ fixdcd: $(SRCDIR)/fixdcd.c |
| 208 |
+- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c |
| 209 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c |
| 210 |
+ |
| 211 |
+ dumpdcd: $(SRCDIR)/dumpdcd.c |
| 212 |
+ $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c |
| 213 |
|
| 214 |
diff --git a/sci-chemistry/namd/namd-2.7_beta3.ebuild b/sci-chemistry/namd/namd-2.8.ebuild |
| 215 |
similarity index 94% |
| 216 |
rename from sci-chemistry/namd/namd-2.7_beta3.ebuild |
| 217 |
rename to sci-chemistry/namd/namd-2.8.ebuild |
| 218 |
index 2ef08e4..b8d8d2b 100644 |
| 219 |
--- a/sci-chemistry/namd/namd-2.7_beta3.ebuild |
| 220 |
+++ b/sci-chemistry/namd/namd-2.8.ebuild |
| 221 |
@@ -9,7 +9,7 @@ LICENSE="namd" |
| 222 |
HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" |
| 223 |
|
| 224 |
MY_PN="NAMD" |
| 225 |
-MY_PV="2.7b2" |
| 226 |
+MY_PV="2.8" |
| 227 |
|
| 228 |
SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz" |
| 229 |
|
| 230 |
@@ -51,10 +51,10 @@ src_unpack() { |
| 231 |
|
| 232 |
# apply a few small fixes to make NAMD compile and |
| 233 |
# link to the proper libraries |
| 234 |
- epatch "${FILESDIR}"/namd-2.7_beta2-gentoo.patch |
| 235 |
- epatch "${FILESDIR}"/namd-2.7-ldflags.patch |
| 236 |
+ epatch "${FILESDIR}"/namd-2.8-gentoo.patch |
| 237 |
+ epatch "${FILESDIR}"/namd-2.8-ldflags.patch |
| 238 |
epatch "${FILESDIR}"/namd-2.7-iml-dec.patch |
| 239 |
- sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \ |
| 240 |
+ sed -e "s:charm-6.2.1:charm-${CHARM_VERSION}:" \ |
| 241 |
Make.charm || \ |
| 242 |
die |
Archives