Gentoo Archives: gentoo-commits

From: David Seifert <soap@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/namd/files/
Date: Tue, 31 Jan 2017 08:42:17
Message-Id: 1485852081.a3f27ec55f4a824d1e083154df1514fa7987b63c.soap@gentoo
1 commit: a3f27ec55f4a824d1e083154df1514fa7987b63c
2 Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com>
3 AuthorDate: Mon Jan 30 17:51:30 2017 +0000
4 Commit: David Seifert <soap <AT> gentoo <DOT> org>
5 CommitDate: Tue Jan 31 08:41:21 2017 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a3f27ec5
7
8 sci-chemistry/namd: remove unused patches
9
10 Closes: https://github.com/gentoo/gentoo/pull/3730
11
12 sci-chemistry/namd/files/namd-2.6-gentoo.patch | 107 -----------------
13 sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 -------------------
14 sci-chemistry/namd/files/namd-2.7-ldflags.patch | 41 -------
15 .../namd/files/namd-2.7_beta2-gentoo.patch | 126 ---------------------
16 .../namd/files/namd-barrier-fix-gentoo.patch | 61 ----------
17 .../namd/files/namd-fftw-lib-gentoo.patch | 15 ---
18 .../namd/files/namd-makefile-gentoo.patch | 88 --------------
19 sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch | 16 ---
20 8 files changed, 571 deletions(-)
21
22 diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
23 deleted file mode 100644
24 index 9a71de8..00000000
25 --- a/sci-chemistry/namd/files/namd-2.6-gentoo.patch
26 +++ /dev/null
27 @@ -1,107 +0,0 @@
28 -diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile
29 ---- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400
30 -+++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400
31 -@@ -232,10 +232,10 @@
32 - $(DSTDIR)/stringhash.o
33 -
34 - # definitions for Charm routines
35 --CHARMC = $(CHARM)/bin/charmc
36 --CHARMXI = $(CHARM)/bin/charmc
37 --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
38 --CHARMLIB = $(CHARM)/lib
39 -+CHARMC = /usr/bin/charmc
40 -+CHARMXI = /usr/bin/charmc
41 -+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
42 -+CHARMLIB = /usr/lib
43 -
44 - # Libraries we may have changed
45 - LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
46 -@@ -255,7 +255,7 @@
47 -
48 - # Add new executables here.
49 -
50 --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
51 -+BINARIES = namd2 psfgen flipdcd flipbinpdb
52 -
53 - # This should be rebuilt at every compile, but not on Win32.
54 - BUILDINFO = $(DSTDIR)/buildinfo
55 -@@ -284,11 +284,6 @@
56 - $(CHARMOPTS) \
57 - -lm -o namd2
58 -
59 --charmrun: $(CHARM)/bin/charmrun # XXX
60 -- $(COPY) $(CHARM)/bin/charmrun $@
61 --
62 --windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
63 --
64 - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
65 - $(MAKEBUILDINFO)
66 - $(CHARMC) -verbose \
67 -@@ -309,9 +304,6 @@
68 - charmd_faceless.exe:
69 - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
70 -
71 --charmrun.exe:
72 -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
73 --
74 - psfgen: $(DSTDIR) $(SBOBJS)
75 - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
76 -
77 -@@ -571,9 +563,7 @@
78 -
79 - DOC_FILES = README.txt announce.txt license.txt notes.txt
80 -
81 --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
82 --
83 --WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
84 -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
85 -
86 - release: all
87 - $(ECHO) Creating release $(RELEASE_DIR_NAME)
88 -@@ -582,17 +572,9 @@
89 - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
90 - cp -r .rootdir/lib $(RELEASE_DIR_NAME)
91 - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
92 -- if [ -r $(CHARM)/bin/charmd ]; then \
93 -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
94 -- fi
95 -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
96 -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
97 -- fi
98 - chmod -R a+rX $(RELEASE_DIR_NAME)
99 - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
100 - gzip $(RELEASE_DIR_NAME).tar
101 -- echo $(CHARM)
102 -- ls -l $(CHARM)/lib
103 - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
104 -
105 - winrelease: winall
106 -diff -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw
107 ---- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500
108 -+++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400
109 -@@ -1,7 +1,7 @@
110 -
111 --FFTDIR=/Projects/namd2/fftw/linux
112 --FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
113 --FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
114 -+#FFTDIR=/Projects/namd2/fftw/linux
115 -+FFTINCL=-I/usr/include
116 -+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
117 - FFTFLAGS=-DNAMD_FFTW
118 - FFT=$(FFTINCL) $(FFTFLAGS)
119 -
120 -diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl
121 ---- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400
122 -+++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400
123 -@@ -1,8 +1,8 @@
124 -
125 --TCLDIR=/Projects/namd2/tcl/linux
126 -+#TCLDIR=/Projects/namd2/tcl/linux
127 - #TCLDIR=$(HOME)/tcl/cray-xt3
128 --TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
129 --TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
130 -+TCLINCL=-I/usr/include
131 -+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
132 - TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
133 - TCL=$(TCLINCL) $(TCLFLAGS)
134 -
135
136 diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
137 deleted file mode 100644
138 index 28a580e..00000000
139 --- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch
140 +++ /dev/null
141 @@ -1,117 +0,0 @@
142 -diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm
143 ---- NAMD_2.7b1_Source.orig/Make.charm 2009-06-07 15:15:11.000000000 -0500
144 -+++ NAMD_2.7b1_Source/Make.charm 2009-06-07 15:15:11.000000000 -0500
145 -@@ -2,5 +2,5 @@
146 - # The config script will override this setting if there is a directory
147 - # called charm-6.1 or charm in the NAMD base directory.
148 -
149 --CHARMBASE = /Projects/namd2/charm-6.1
150 -+CHARMBASE = /usr/include/charm-6.1.2
151 -
152 -diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile
153 ---- NAMD_2.7b1_Source.orig/Makefile 2009-06-07 15:15:11.000000000 -0500
154 -+++ NAMD_2.7b1_Source/Makefile 2009-06-07 15:15:11.000000000 -0500
155 -@@ -297,10 +297,10 @@
156 - $(DSTDIR)/stringhash.o
157 -
158 - # definitions for Charm routines
159 --CHARMC = $(CHARM)/bin/charmc
160 --CHARMXI = $(CHARM)/bin/charmc
161 --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
162 --CHARMLIB = $(CHARM)/lib
163 -+CHARMC = /usr/bin/charmc
164 -+CHARMXI = /usr/bin/charmc
165 -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
166 -+CHARMLIB = /usr/gentoo-libdir
167 -
168 - # Libraries we may have changed
169 - LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
170 -@@ -320,7 +320,7 @@
171 -
172 - # Add new executables here.
173 -
174 --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
175 -+BINARIES = namd2 psfgen flipdcd flipbinpdb
176 -
177 - # This should be rebuilt at every compile, but not on Win32.
178 - BUILDINFO = $(DSTDIR)/buildinfo
179 -@@ -351,14 +351,6 @@
180 - $(CHARMOPTS) \
181 - -lm -o namd2
182 -
183 --charmrun: $(CHARM)/bin/charmrun # XXX
184 -- $(COPY) $(CHARM)/bin/charmrun $@
185 --
186 --WINDOWSBINARIES = namd2.exe psfgen.exe
187 --# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
188 --
189 --windowsbinaries: $(WINDOWSBINARIES)
190 --
191 - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
192 - $(MAKEBUILDINFO)
193 - $(CHARMC) -verbose \
194 -@@ -381,9 +373,6 @@
195 - charmd_faceless.exe:
196 - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
197 -
198 --charmrun.exe:
199 -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
200 --
201 - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
202 - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
203 -
204 -@@ -700,9 +689,7 @@
205 -
206 - DOC_FILES = README.txt announce.txt license.txt notes.txt
207 -
208 --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
209 --
210 --WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
211 -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
212 -
213 - release: all
214 - $(ECHO) Creating release $(RELEASE_DIR_NAME)
215 -@@ -711,17 +698,9 @@
216 - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
217 - cp -r .rootdir/lib $(RELEASE_DIR_NAME)
218 - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
219 -- if [ -r $(CHARM)/bin/charmd ]; then \
220 -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
221 -- fi
222 -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
223 -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
224 -- fi
225 - chmod -R a+rX $(RELEASE_DIR_NAME)
226 - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
227 - gzip $(RELEASE_DIR_NAME).tar
228 -- echo $(CHARM)
229 -- ls -l $(CHARM)/lib
230 - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
231 -
232 - winrelease: winall
233 -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw
234 ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500
235 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500
236 -@@ -1,7 +1,7 @@
237 -
238 --FFTDIR=/Projects/namd2/fftw/linux-x86_64
239 -+FFTDIR=/usr
240 - FFTINCL=-I$(FFTDIR)/include
241 --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
242 -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
243 - FFTFLAGS=-DNAMD_FFTW
244 - FFT=$(FFTINCL) $(FFTFLAGS)
245 -
246 -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl
247 ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl 2009-06-07 15:15:11.000000000 -0500
248 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl 2009-06-07 18:25:07.000000000 -0500
249 -@@ -1,7 +1,7 @@
250 -
251 --TCLDIR=/Projects/namd2/tcl/linux-x86_64
252 -+TCLDIR=/usr
253 - TCLINCL=-I$(TCLDIR)/include
254 --TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
255 -+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl -ldl
256 - TCLFLAGS=-DNAMD_TCL
257 - TCL=$(TCLINCL) $(TCLFLAGS)
258 -
259
260 diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
261 deleted file mode 100644
262 index 686eba8..00000000
263 --- a/sci-chemistry/namd/files/namd-2.7-ldflags.patch
264 +++ /dev/null
265 @@ -1,41 +0,0 @@
266 -diff --git a/Makefile b/Makefile
267 -index fd20f12..0821bed 100644
268 ---- a/Makefile
269 -+++ b/Makefile
270 -@@ -339,7 +339,7 @@ all: $(BINARIES) $(LIBCUDARTSO)
271 -
272 - namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
273 - $(MAKEBUILDINFO)
274 -- $(CHARMC) -verbose -ld++-option \
275 -+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \
276 - "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
277 - -module NeighborLB -module commlib -language charm++ \
278 - $(BUILDINFO).o \
279 -@@ -394,23 +394,23 @@ charmrun.exe:
280 - $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
281 -
282 - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
283 -- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
284 -+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
285 -
286 - psfgen.exe: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
287 - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
288 -
289 - flipdcd: $(SRCDIR)/flipdcd.c
290 -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
291 -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
292 - echo "#!/bin/sh\necho unavailable on this platform" > $@; \
293 - chmod +x $@
294 -
295 - flipbinpdb: $(SRCDIR)/flipbinpdb.c
296 -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
297 -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
298 - echo "#!/bin/sh\necho unavailable on this platform" > $@; \
299 - chmod +x $@
300 -
301 - fixdcd: $(SRCDIR)/fixdcd.c
302 -- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
303 -+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
304 -
305 - dumpdcd: $(SRCDIR)/dumpdcd.c
306 - $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
307
308 diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
309 deleted file mode 100644
310 index 898d6b5..00000000
311 --- a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
312 +++ /dev/null
313 @@ -1,126 +0,0 @@
314 -diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw
315 ---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw 2010-04-23 14:40:54.566510874 -0500
316 -+++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw 2010-04-23 14:41:08.106528893 -0500
317 -@@ -1,7 +1,7 @@
318 -
319 --FFTDIR=/Projects/namd2/fftw/linux-x86_64
320 -+FFTDIR=/usr
321 - FFTINCL=-I$(FFTDIR)/include
322 --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
323 -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
324 - FFTFLAGS=-DNAMD_FFTW
325 - FFT=$(FFTINCL) $(FFTFLAGS)
326 -
327 -diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl
328 ---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl 2010-04-23 14:40:54.566510874 -0500
329 -+++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl 2010-04-23 14:41:08.106528893 -0500
330 -@@ -1,7 +1,7 @@
331 -
332 --TCLDIR=/Projects/namd2/tcl/linux-x86_64
333 -+TCLDIR=/usr
334 - TCLINCL=-I$(TCLDIR)/include
335 --TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
336 -+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
337 - TCLFLAGS=-DNAMD_TCL
338 - TCL=$(TCLINCL) $(TCLFLAGS)
339 -
340 -diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm
341 ---- NAMD_2.7b2_Source.orig//Make.charm 2010-04-23 14:40:54.556517020 -0500
342 -+++ NAMD_2.7b2_Source//Make.charm 2010-04-23 14:42:16.026530011 -0500
343 -@@ -2,5 +2,5 @@
344 - # The config script will override this setting if there is a directory
345 - # called charm-6.1 or charm in the NAMD base directory.
346 -
347 --CHARMBASE = /Projects/namd2/charm-6.1.3
348 -+CHARMBASE = /usr/include/charm-6.1.3
349 -
350 -Only in NAMD_2.7b2_Source/: Make.charm.~1~
351 -Only in NAMD_2.7b2_Source/: Make.charm.porig
352 -diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile
353 ---- NAMD_2.7b2_Source.orig//Makefile 2010-04-23 14:40:54.556517020 -0500
354 -+++ NAMD_2.7b2_Source//Makefile 2010-04-23 14:42:59.446523306 -0500
355 -@@ -300,10 +300,10 @@
356 - $(DSTDIR)/stringhash.o
357 -
358 - # definitions for Charm routines
359 --CHARMC = $(CHARM)/bin/charmc
360 --CHARMXI = $(CHARM)/bin/charmc
361 --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
362 --CHARMLIB = $(CHARM)/lib
363 -+CHARMC = /usr/bin/charmc
364 -+CHARMXI = /usr/bin/charmc
365 -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
366 -+CHARMLIB = /usr/gentoo-libdir
367 -
368 - # Libraries we may have changed
369 - LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
370 -@@ -323,7 +323,7 @@
371 -
372 - # Add new executables here.
373 -
374 --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
375 -+BINARIES = namd2 psfgen flipdcd flipbinpdb
376 -
377 - # This should be rebuilt at every compile, but not on Win32.
378 - BUILDINFO = $(DSTDIR)/buildinfo
379 -@@ -354,9 +354,6 @@
380 - $(CHARMOPTS) \
381 - -lm -o namd2
382 -
383 --charmrun: $(CHARM)/bin/charmrun # XXX
384 -- $(COPY) $(CHARM)/bin/charmrun $@
385 --
386 - $(LIBCUDARTSO):
387 - if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \
388 - $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \
389 -@@ -364,10 +361,6 @@
390 - $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \
391 - fi
392 -
393 --WINDOWSBINARIES = namd2.exe psfgen.exe
394 --# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
395 --windowsbinaries: $(WINDOWSBINARIES)
396 --
397 - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
398 - $(MAKEBUILDINFO)
399 - $(CHARMC) -verbose \
400 -@@ -390,9 +383,6 @@
401 - charmd_faceless.exe:
402 - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
403 -
404 --charmrun.exe:
405 -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
406 --
407 - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
408 - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
409 -
410 -@@ -716,9 +706,7 @@
411 -
412 - DOC_FILES = README.txt announce.txt license.txt notes.txt
413 -
414 --RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
415 --
416 --WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
417 -+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2
418 -
419 - release: all
420 - $(ECHO) Creating release $(RELEASE_DIR_NAME)
421 -@@ -727,17 +715,9 @@
422 - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
423 - cp -r .rootdir/lib $(RELEASE_DIR_NAME)
424 - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
425 -- if [ -r $(CHARM)/bin/charmd ]; then \
426 -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
427 -- fi
428 -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
429 -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
430 -- fi
431 - chmod -R a+rX $(RELEASE_DIR_NAME)
432 - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
433 - gzip $(RELEASE_DIR_NAME).tar
434 -- echo $(CHARM)
435 -- ls -l $(CHARM)/lib
436 - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
437 -
438 - winrelease: winall
439 -Only in NAMD_2.7b2_Source/: Makefile.porig
440
441 diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
442 deleted file mode 100644
443 index 40e8e68..00000000
444 --- a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
445 +++ /dev/null
446 @@ -1,61 +0,0 @@
447 -# patch to fix compile error on gcc-3.x
448 -
449 -diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C
450 ---- NAMD_2.6b1_Source/src/BackEnd.C 2003-12-31 06:37:15.000000000 +0000
451 -+++ NAMD_2.6b1_Source_patched/src/BackEnd.C 2005-08-22 18:59:59.000000000 +0000
452 -@@ -162,7 +162,7 @@
453 - }
454 -
455 - // start QD and scheduler
456 --void BackEnd::barrier(void) {
457 -+void BackEnd::namd_barrier(void) {
458 - awaken();
459 - suspend();
460 - }
461 -diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h
462 ---- NAMD_2.6b1_Source/src/BackEnd.h 2000-01-29 00:20:05.000000000 +0000
463 -+++ NAMD_2.6b1_Source_patched/src/BackEnd.h 2005-08-22 18:59:47.000000000 +0000
464 -@@ -17,7 +17,7 @@
465 -
466 - static void suspend(void); // Let message code run...
467 - static void awaken(void); // ...then return
468 -- static void barrier(void); // Let message code run, then return
469 -+ static void namd_barrier(void); // Let message code run, then return
470 - static void ExitSchedOn(int pe); // Tell a remote processor to stop
471 - // his scheduler
472 -
473 -diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C
474 ---- NAMD_2.6b1_Source/src/ScriptTcl.C 2005-06-23 18:47:00.000000000 +0000
475 -+++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C 2005-08-22 19:00:21.000000000 +0000
476 -@@ -56,7 +56,7 @@
477 - }
478 -
479 - void ScriptTcl::barrier() {
480 -- BackEnd::barrier();
481 -+ BackEnd::namd_barrier();
482 - }
483 -
484 - void ScriptTcl::initcheck() {
485 -diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C
486 ---- NAMD_2.6b1_Source/src/main.C 2005-05-27 22:56:49.000000000 +0000
487 -+++ NAMD_2.6b1_Source_patched/src/main.C 2005-08-22 19:17:34.000000000 +0000
488 -@@ -67,7 +67,9 @@
489 -
490 - #ifndef NOHOSTNAME
491 - iout << iINFO <<
492 -- "Sending usage information to NAMD developers via UDP. Sent data is:\n"
493 -+ "Markus says: I don't want to send usage information \n"
494 -+ << endi;
495 -+ iout << iINFO << "to NAMD developers :) Data not sent is:\n"
496 - << endi;
497 -
498 - char sendbuf[TBSOFT_TRACK_MAXLEN];
499 -@@ -88,7 +90,7 @@
500 - sprintf(sendbuf, "1 %s %s %s %s %s %s %s",
501 - program, versionnum, platform, numcpus, miscinfo, host, user);
502 - iout << iINFO << sendbuf << "\n" << endi;
503 -- send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
504 -+ //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
505 -
506 - #endif
507 - return 0;
508
509 diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
510 deleted file mode 100644
511 index 731ea23..00000000
512 --- a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
513 +++ /dev/null
514 @@ -1,15 +0,0 @@
515 -# adjust paths for proper linking to fftw libs
516 -
517 ---- NAMD_2.6b1_Source/arch/Linux-i686.fftw 2004-02-20 22:38:36.000000000 +0000
518 -+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw 2005-08-22 18:50:38.000000000 +0000
519 -@@ -1,7 +1,7 @@
520 -
521 --FFTDIR=/Projects/namd2/fftw/linux
522 --FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
523 --FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
524 -+#FFTDIR=/Projects/namd2/fftw/linux
525 -+FFTINCL=-I/usr/include
526 -+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
527 - FFTFLAGS=-DNAMD_FFTW
528 - FFT=$(FFTINCL) $(FFTFLAGS)
529 -
530
531 diff --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch
532 deleted file mode 100644
533 index 4ee5822..00000000
534 --- a/sci-chemistry/namd/files/namd-makefile-gentoo.patch
535 +++ /dev/null
536 @@ -1,88 +0,0 @@
537 -# provide paths for charm++ provided includes/libraries/binaries
538 -
539 ---- NAMD_2.6b1_Source-patched/Makefile 2005-07-22 18:50:58.000000000 +0000
540 -+++ NAMD_2.6b1_Source/Makefile 2005-09-30 02:28:35.000000000 +0000
541 -@@ -227,10 +227,10 @@
542 - $(DSTDIR)/stringhash.o
543 -
544 - # definitions for Charm routines
545 --CHARMC = $(CHARM)/bin/charmc
546 --CHARMXI = $(CHARM)/bin/charmc
547 --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
548 --CHARMLIB = $(CHARM)/lib
549 -+CHARMC = /usr/bin/charmc
550 -+CHARMXI = /usr/bin/charmc
551 -+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
552 -+CHARMLIB = /usr/lib
553 -
554 - # Libraries we may have changed
555 - LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
556 -@@ -250,7 +250,7 @@
557 -
558 - # Add new executables here.
559 -
560 --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
561 -+BINARIES = namd2 psfgen flipdcd flipbinpdb
562 -
563 - # This should be rebuilt at every compile, but not on Win32.
564 - BUILDINFO = $(DSTDIR)/buildinfo
565 -@@ -279,10 +279,7 @@
566 - $(CHARMOPTS) \
567 - -lm -o namd2
568 -
569 --charmrun: $(CHARM)/bin/charmrun # XXX
570 -- $(COPY) $(CHARM)/bin/charmrun $@
571 --
572 --win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
573 -+win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe
574 -
575 - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
576 - $(MAKEBUILDINFO)
577 -@@ -304,9 +301,6 @@
578 - charmd_faceless.exe:
579 - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
580 -
581 --charmrun.exe:
582 -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
583 --
584 - psfgen: $(DSTDIR) $(SBOBJS)
585 - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
586 -
587 -@@ -565,9 +559,9 @@
588 -
589 - DOC_FILES = README.txt announce.txt license.txt notes.txt
590 -
591 --RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb
592 -+RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb
593 -
594 --WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
595 -+WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL)
596 -
597 - release: all
598 - $(ECHO) Creating release $(RELEASE_DIR_NAME)
599 -@@ -575,18 +569,18 @@
600 - cp $(RELEASE_FILES) $(RELEASE_DIR_NAME)
601 - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
602 - cp -r .rootdir/lib $(RELEASE_DIR_NAME)
603 -- if [ -r $(CHARM)/bin/charmd ]; then \
604 -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
605 -+ if [ -r /usr/bin/charmd ]; then \
606 -+ $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \
607 - fi
608 -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
609 -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
610 -+ if [ -r /usr/bin/charmd_faceless ]; then \
611 -+ $(COPY) /usr/bin/charmd_faceless $(RELEASE_DIR_NAME); \
612 - fi
613 - chmod -R a+rX $(RELEASE_DIR_NAME)
614 - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
615 - gzip $(RELEASE_DIR_NAME).tar
616 -- echo $(CHARM)
617 -- ls -l $(CHARM)/lib
618 -- echo $(CHARM)
619 -+ echo /usr
620 -+ ls -l /usr/lib
621 -+ echo /usr
622 - file $(RELEASE_FILES)
623 -
624 - winrelease: winall
625
626 diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
627 deleted file mode 100644
628 index 0e6f0dd..00000000
629 --- a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
630 +++ /dev/null
631 @@ -1,16 +0,0 @@
632 -# adjust paths for proper linking to tcl libs
633 -
634 ---- NAMD_2.6b1_Source/arch/Linux-i686.tcl 2004-10-27 21:40:55.000000000 +0000
635 -+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl 2005-09-14 20:50:14.000000000 +0000
636 -@@ -1,8 +1,8 @@
637 -
638 --TCLDIR=/Projects/namd2/tcl/linux
639 -+#TCLDIR=/Projects/namd2/tcl/linux
640 - #TCLDIR=$(HOME)/tcl/cray-xt3
641 --TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
642 --TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
643 -+TCLINCL=-I/usr/include
644 -+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
645 - TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
646 - TCL=$(TCLINCL) $(TCLFLAGS)
647 -