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commit: a3f27ec55f4a824d1e083154df1514fa7987b63c |
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Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com> |
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AuthorDate: Mon Jan 30 17:51:30 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Tue Jan 31 08:41:21 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a3f27ec5 |
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|
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sci-chemistry/namd: remove unused patches |
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|
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Closes: https://github.com/gentoo/gentoo/pull/3730 |
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|
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sci-chemistry/namd/files/namd-2.6-gentoo.patch | 107 ----------------- |
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sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 ------------------- |
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sci-chemistry/namd/files/namd-2.7-ldflags.patch | 41 ------- |
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.../namd/files/namd-2.7_beta2-gentoo.patch | 126 --------------------- |
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.../namd/files/namd-barrier-fix-gentoo.patch | 61 ---------- |
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.../namd/files/namd-fftw-lib-gentoo.patch | 15 --- |
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.../namd/files/namd-makefile-gentoo.patch | 88 -------------- |
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sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch | 16 --- |
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8 files changed, 571 deletions(-) |
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|
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diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch |
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deleted file mode 100644 |
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index 9a71de8..00000000 |
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--- a/sci-chemistry/namd/files/namd-2.6-gentoo.patch |
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+++ /dev/null |
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@@ -1,107 +0,0 @@ |
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-diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile |
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---- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400 |
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-+++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400 |
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-@@ -232,10 +232,10 @@ |
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- $(DSTDIR)/stringhash.o |
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- |
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- # definitions for Charm routines |
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--CHARMC = $(CHARM)/bin/charmc |
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--CHARMXI = $(CHARM)/bin/charmc |
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--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 |
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--CHARMLIB = $(CHARM)/lib |
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-+CHARMC = /usr/bin/charmc |
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-+CHARMXI = /usr/bin/charmc |
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-+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1 |
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-+CHARMLIB = /usr/lib |
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- |
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- # Libraries we may have changed |
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- LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) |
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-@@ -255,7 +255,7 @@ |
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- |
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- # Add new executables here. |
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- |
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--BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb |
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-+BINARIES = namd2 psfgen flipdcd flipbinpdb |
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- |
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- # This should be rebuilt at every compile, but not on Win32. |
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- BUILDINFO = $(DSTDIR)/buildinfo |
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-@@ -284,11 +284,6 @@ |
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- $(CHARMOPTS) \ |
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- -lm -o namd2 |
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- |
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--charmrun: $(CHARM)/bin/charmrun # XXX |
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-- $(COPY) $(CHARM)/bin/charmrun $@ |
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-- |
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--windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe |
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-- |
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- namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) |
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- $(MAKEBUILDINFO) |
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- $(CHARMC) -verbose \ |
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-@@ -309,9 +304,6 @@ |
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- charmd_faceless.exe: |
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- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe |
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- |
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--charmrun.exe: |
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-- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe |
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-- |
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- psfgen: $(DSTDIR) $(SBOBJS) |
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- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm |
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- |
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-@@ -571,9 +563,7 @@ |
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- |
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- DOC_FILES = README.txt announce.txt license.txt notes.txt |
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- |
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--RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 |
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-- |
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--WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) |
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-+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 |
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- |
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- release: all |
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- $(ECHO) Creating release $(RELEASE_DIR_NAME) |
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-@@ -582,17 +572,9 @@ |
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- for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done |
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- cp -r .rootdir/lib $(RELEASE_DIR_NAME) |
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- /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS |
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-- if [ -r $(CHARM)/bin/charmd ]; then \ |
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-- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ |
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-- fi |
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-- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ |
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-- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ |
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-- fi |
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- chmod -R a+rX $(RELEASE_DIR_NAME) |
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- tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) |
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- gzip $(RELEASE_DIR_NAME).tar |
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-- echo $(CHARM) |
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-- ls -l $(CHARM)/lib |
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- -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done |
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- |
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- winrelease: winall |
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-diff -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw |
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---- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500 |
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-+++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400 |
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-@@ -1,7 +1,7 @@ |
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- |
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--FFTDIR=/Projects/namd2/fftw/linux |
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--FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include |
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--FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw |
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-+#FFTDIR=/Projects/namd2/fftw/linux |
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-+FFTINCL=-I/usr/include |
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-+FFTLIB=-L/usr/lib -lsrfftw -lsfftw |
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- FFTFLAGS=-DNAMD_FFTW |
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- FFT=$(FFTINCL) $(FFTFLAGS) |
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- |
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-diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl |
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---- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400 |
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-+++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400 |
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-@@ -1,8 +1,8 @@ |
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- |
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--TCLDIR=/Projects/namd2/tcl/linux |
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-+#TCLDIR=/Projects/namd2/tcl/linux |
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- #TCLDIR=$(HOME)/tcl/cray-xt3 |
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--TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include |
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--TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl |
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-+TCLINCL=-I/usr/include |
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-+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl |
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- TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST |
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- TCL=$(TCLINCL) $(TCLFLAGS) |
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- |
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|
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diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch |
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deleted file mode 100644 |
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index 28a580e..00000000 |
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--- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch |
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+++ /dev/null |
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@@ -1,117 +0,0 @@ |
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-diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm |
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---- NAMD_2.7b1_Source.orig/Make.charm 2009-06-07 15:15:11.000000000 -0500 |
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-+++ NAMD_2.7b1_Source/Make.charm 2009-06-07 15:15:11.000000000 -0500 |
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-@@ -2,5 +2,5 @@ |
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- # The config script will override this setting if there is a directory |
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- # called charm-6.1 or charm in the NAMD base directory. |
148 |
- |
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--CHARMBASE = /Projects/namd2/charm-6.1 |
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-+CHARMBASE = /usr/include/charm-6.1.2 |
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- |
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-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 |
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-+++ NAMD_2.7b1_Source/Makefile 2009-06-07 15:15:11.000000000 -0500 |
155 |
-@@ -297,10 +297,10 @@ |
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- $(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 |
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--CHARMLIB = $(CHARM)/lib |
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-+CHARMC = /usr/bin/charmc |
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-+CHARMXI = /usr/bin/charmc |
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-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 |
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-+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 |
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-@@ -351,14 +351,6 @@ |
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- $(CHARMOPTS) \ |
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- -lm -o namd2 |
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- |
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--charmrun: $(CHARM)/bin/charmrun # XXX |
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-- $(COPY) $(CHARM)/bin/charmrun $@ |
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-- |
186 |
--WINDOWSBINARIES = namd2.exe psfgen.exe |
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--# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe |
188 |
-- |
189 |
--windowsbinaries: $(WINDOWSBINARIES) |
190 |
-- |
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- namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) |
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- $(MAKEBUILDINFO) |
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- $(CHARMC) -verbose \ |
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-@@ -381,9 +373,6 @@ |
195 |
- charmd_faceless.exe: |
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- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe |
197 |
- |
198 |
--charmrun.exe: |
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-- $(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 |
- |