commit: a3f27ec55f4a824d1e083154df1514fa7987b63c Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com> AuthorDate: Mon Jan 30 17:51:30 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Jan 31 08:41:21 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a3f27ec5
sci-chemistry/namd: remove unused patches Closes: https://github.com/gentoo/gentoo/pull/3730 sci-chemistry/namd/files/namd-2.6-gentoo.patch | 107 ----------------- sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 ------------------- sci-chemistry/namd/files/namd-2.7-ldflags.patch | 41 ------- .../namd/files/namd-2.7_beta2-gentoo.patch | 126 --------------------- .../namd/files/namd-barrier-fix-gentoo.patch | 61 ---------- .../namd/files/namd-fftw-lib-gentoo.patch | 15 --- .../namd/files/namd-makefile-gentoo.patch | 88 -------------- sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch | 16 --- 8 files changed, 571 deletions(-) diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch deleted file mode 100644 index 9a71de8..00000000 --- a/sci-chemistry/namd/files/namd-2.6-gentoo.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile ---- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400 -+++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400 -@@ -232,10 +232,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/lib - - # Libraries we may have changed - LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -255,7 +255,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -284,11 +284,6 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- --windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe -- - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) - $(CHARMC) -verbose \ -@@ -309,9 +304,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -571,9 +563,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 -- --WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -582,17 +572,9 @@ - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done - - winrelease: winall -diff -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw ---- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500 -+++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux --FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include --FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw -+#FFTDIR=/Projects/namd2/fftw/linux -+FFTINCL=-I/usr/include -+FFTLIB=-L/usr/lib -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl ---- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400 -+++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400 -@@ -1,8 +1,8 @@ - --TCLDIR=/Projects/namd2/tcl/linux -+#TCLDIR=/Projects/namd2/tcl/linux - #TCLDIR=$(HOME)/tcl/cray-xt3 --TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include --TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl -+TCLINCL=-I/usr/include -+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl - TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST - TCL=$(TCLINCL) $(TCLFLAGS) - diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch deleted file mode 100644 index 28a580e..00000000 --- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch +++ /dev/null @@ -1,117 +0,0 @@ -diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm ---- NAMD_2.7b1_Source.orig/Make.charm 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/Make.charm 2009-06-07 15:15:11.000000000 -0500 -@@ -2,5 +2,5 @@ - # The config script will override this setting if there is a directory - # called charm-6.1 or charm in the NAMD base directory. - --CHARMBASE = /Projects/namd2/charm-6.1 -+CHARMBASE = /usr/include/charm-6.1.2 - -diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile ---- NAMD_2.7b1_Source.orig/Makefile 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/Makefile 2009-06-07 15:15:11.000000000 -0500 -@@ -297,10 +297,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/gentoo-libdir - - # Libraries we may have changed - LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -320,7 +320,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -351,14 +351,6 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- --WINDOWSBINARIES = namd2.exe psfgen.exe --# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe -- --windowsbinaries: $(WINDOWSBINARIES) -- - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) - $(MAKEBUILDINFO) - $(CHARMC) -verbose \ -@@ -381,9 +373,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -700,9 +689,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 -- --WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -711,17 +698,9 @@ - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done - - winrelease: winall -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux-x86_64 -+FFTDIR=/usr - FFTINCL=-I$(FFTDIR)/include --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl 2009-06-07 18:25:07.000000000 -0500 -@@ -1,7 +1,7 @@ - --TCLDIR=/Projects/namd2/tcl/linux-x86_64 -+TCLDIR=/usr - TCLINCL=-I$(TCLDIR)/include --TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl -+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl -ldl - TCLFLAGS=-DNAMD_TCL - TCL=$(TCLINCL) $(TCLFLAGS) - diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch deleted file mode 100644 index 686eba8..00000000 --- a/sci-chemistry/namd/files/namd-2.7-ldflags.patch +++ /dev/null @@ -1,41 +0,0 @@ -diff --git a/Makefile b/Makefile -index fd20f12..0821bed 100644 ---- a/Makefile -+++ b/Makefile -@@ -339,7 +339,7 @@ all: $(BINARIES) $(LIBCUDARTSO) - - namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) -- $(CHARMC) -verbose -ld++-option \ -+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ - "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ - -module NeighborLB -module commlib -language charm++ \ - $(BUILDINFO).o \ -@@ -394,23 +394,23 @@ charmrun.exe: - $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe - - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) -- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm -+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - - psfgen.exe: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - - flipdcd: $(SRCDIR)/flipdcd.c -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ - echo "#!/bin/sh\necho unavailable on this platform" > $@; \ - chmod +x $@ - - flipbinpdb: $(SRCDIR)/flipbinpdb.c -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ - echo "#!/bin/sh\necho unavailable on this platform" > $@; \ - chmod +x $@ - - fixdcd: $(SRCDIR)/fixdcd.c -- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c - - dumpdcd: $(SRCDIR)/dumpdcd.c - $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch deleted file mode 100644 index 898d6b5..00000000 --- a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw ---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw 2010-04-23 14:40:54.566510874 -0500 -+++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw 2010-04-23 14:41:08.106528893 -0500 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux-x86_64 -+FFTDIR=/usr - FFTINCL=-I$(FFTDIR)/include --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl ---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl 2010-04-23 14:40:54.566510874 -0500 -+++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl 2010-04-23 14:41:08.106528893 -0500 -@@ -1,7 +1,7 @@ - --TCLDIR=/Projects/namd2/tcl/linux-x86_64 -+TCLDIR=/usr - TCLINCL=-I$(TCLDIR)/include --TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl -+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl - TCLFLAGS=-DNAMD_TCL - TCL=$(TCLINCL) $(TCLFLAGS) - -diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm ---- NAMD_2.7b2_Source.orig//Make.charm 2010-04-23 14:40:54.556517020 -0500 -+++ NAMD_2.7b2_Source//Make.charm 2010-04-23 14:42:16.026530011 -0500 -@@ -2,5 +2,5 @@ - # The config script will override this setting if there is a directory - # called charm-6.1 or charm in the NAMD base directory. - --CHARMBASE = /Projects/namd2/charm-6.1.3 -+CHARMBASE = /usr/include/charm-6.1.3 - -Only in NAMD_2.7b2_Source/: Make.charm.~1~ -Only in NAMD_2.7b2_Source/: Make.charm.porig -diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile ---- NAMD_2.7b2_Source.orig//Makefile 2010-04-23 14:40:54.556517020 -0500 -+++ NAMD_2.7b2_Source//Makefile 2010-04-23 14:42:59.446523306 -0500 -@@ -300,10 +300,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/gentoo-libdir - - # Libraries we may have changed - LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -323,7 +323,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -354,9 +354,6 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- - $(LIBCUDARTSO): - if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \ - $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \ -@@ -364,10 +361,6 @@ - $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \ - fi - --WINDOWSBINARIES = namd2.exe psfgen.exe --# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe --windowsbinaries: $(WINDOWSBINARIES) -- - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) - $(MAKEBUILDINFO) - $(CHARMC) -verbose \ -@@ -390,9 +383,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -716,9 +706,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2 -- --WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) -+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -727,17 +715,9 @@ - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done - - winrelease: winall -Only in NAMD_2.7b2_Source/: Makefile.porig diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch deleted file mode 100644 index 40e8e68..00000000 --- a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch +++ /dev/null @@ -1,61 +0,0 @@ -# patch to fix compile error on gcc-3.x - -diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C ---- NAMD_2.6b1_Source/src/BackEnd.C 2003-12-31 06:37:15.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/src/BackEnd.C 2005-08-22 18:59:59.000000000 +0000 -@@ -162,7 +162,7 @@ - } - - // start QD and scheduler --void BackEnd::barrier(void) { -+void BackEnd::namd_barrier(void) { - awaken(); - suspend(); - } -diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h ---- NAMD_2.6b1_Source/src/BackEnd.h 2000-01-29 00:20:05.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/src/BackEnd.h 2005-08-22 18:59:47.000000000 +0000 -@@ -17,7 +17,7 @@ - - static void suspend(void); // Let message code run... - static void awaken(void); // ...then return -- static void barrier(void); // Let message code run, then return -+ static void namd_barrier(void); // Let message code run, then return - static void ExitSchedOn(int pe); // Tell a remote processor to stop - // his scheduler - -diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C ---- NAMD_2.6b1_Source/src/ScriptTcl.C 2005-06-23 18:47:00.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C 2005-08-22 19:00:21.000000000 +0000 -@@ -56,7 +56,7 @@ - } - - void ScriptTcl::barrier() { -- BackEnd::barrier(); -+ BackEnd::namd_barrier(); - } - - void ScriptTcl::initcheck() { -diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C ---- NAMD_2.6b1_Source/src/main.C 2005-05-27 22:56:49.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/src/main.C 2005-08-22 19:17:34.000000000 +0000 -@@ -67,7 +67,9 @@ - - #ifndef NOHOSTNAME - iout << iINFO << -- "Sending usage information to NAMD developers via UDP. Sent data is:\n" -+ "Markus says: I don't want to send usage information \n" -+ << endi; -+ iout << iINFO << "to NAMD developers :) Data not sent is:\n" - << endi; - - char sendbuf[TBSOFT_TRACK_MAXLEN]; -@@ -88,7 +90,7 @@ - sprintf(sendbuf, "1 %s %s %s %s %s %s %s", - program, versionnum, platform, numcpus, miscinfo, host, user); - iout << iINFO << sendbuf << "\n" << endi; -- send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); -+ //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); - - #endif - return 0; diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch deleted file mode 100644 index 731ea23..00000000 --- a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch +++ /dev/null @@ -1,15 +0,0 @@ -# adjust paths for proper linking to fftw libs - ---- NAMD_2.6b1_Source/arch/Linux-i686.fftw 2004-02-20 22:38:36.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw 2005-08-22 18:50:38.000000000 +0000 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux --FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include --FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw -+#FFTDIR=/Projects/namd2/fftw/linux -+FFTINCL=-I/usr/include -+FFTLIB=-L/usr/lib -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - diff --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch deleted file mode 100644 index 4ee5822..00000000 --- a/sci-chemistry/namd/files/namd-makefile-gentoo.patch +++ /dev/null @@ -1,88 +0,0 @@ -# provide paths for charm++ provided includes/libraries/binaries - ---- NAMD_2.6b1_Source-patched/Makefile 2005-07-22 18:50:58.000000000 +0000 -+++ NAMD_2.6b1_Source/Makefile 2005-09-30 02:28:35.000000000 +0000 -@@ -227,10 +227,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/lib - - # Libraries we may have changed - LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -250,7 +250,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -279,10 +279,7 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- --win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe -+win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe - - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) -@@ -304,9 +301,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -565,9 +559,9 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb -+RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb - --WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) -+WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL) - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -575,18 +569,18 @@ - cp $(RELEASE_FILES) $(RELEASE_DIR_NAME) - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -+ if [ -r /usr/bin/charmd ]; then \ -+ $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \ - fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -+ if [ -r /usr/bin/charmd_faceless ]; then \ -+ $(COPY) /usr/bin/charmd_faceless $(RELEASE_DIR_NAME); \ - fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib -- echo $(CHARM) -+ echo /usr -+ ls -l /usr/lib -+ echo /usr - file $(RELEASE_FILES) - - winrelease: winall diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch deleted file mode 100644 index 0e6f0dd..00000000 --- a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch +++ /dev/null @@ -1,16 +0,0 @@ -# adjust paths for proper linking to tcl libs - ---- NAMD_2.6b1_Source/arch/Linux-i686.tcl 2004-10-27 21:40:55.000000000 +0000 -+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl 2005-09-14 20:50:14.000000000 +0000 -@@ -1,8 +1,8 @@ - --TCLDIR=/Projects/namd2/tcl/linux -+#TCLDIR=/Projects/namd2/tcl/linux - #TCLDIR=$(HOME)/tcl/cray-xt3 --TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include --TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl -+TCLINCL=-I/usr/include -+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl - TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST - TCL=$(TCLINCL) $(TCLFLAGS) -
