From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/namd/files/namd-2.10-gentoo.patch | 124 +++++++++++++++++++ sci-chemistry/namd/files/namd-2.7-iml-dec.patch | 24 ++++ sci-chemistry/namd/files/namd-2.9-gentoo.patch | 151 ++++++++++++++++++++++++ 3 files changed, 299 insertions(+) create mode 100644 sci-chemistry/namd/files/namd-2.10-gentoo.patch create mode 100644 sci-chemistry/namd/files/namd-2.7-iml-dec.patch create mode 100644 sci-chemistry/namd/files/namd-2.9-gentoo.patch (limited to 'sci-chemistry/namd/files') diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch new file mode 100644 index 000000000000..e578c131c36d --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch @@ -0,0 +1,124 @@ +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 +@@ -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) $(FFTFLAGS) + +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + +diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile +--- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 +@@ -389,10 +389,10 @@ + $(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 + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast + #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB +@@ -418,7 +418,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -434,7 +434,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -484,11 +484,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -506,7 +503,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -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 $@ + +@@ -516,7 +513,7 @@ + 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 +@@ -711,9 +708,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -724,17 +719,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch new file mode 100644 index 000000000000..e5ee3bd6c818 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch @@ -0,0 +1,24 @@ +diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c +index 94b71ba..01a2529 100644 +--- a/src/flipbinpdb.c ++++ b/src/flipbinpdb.c +@@ -9,6 +9,7 @@ + #include + #include + #include ++#include + + #ifndef MAP_FILE + #define MAP_FILE 0 +diff --git a/src/flipdcd.c b/src/flipdcd.c +index 8ec85b7..1c23433 100644 +--- a/src/flipdcd.c ++++ b/src/flipdcd.c +@@ -13,6 +13,7 @@ + #include + #include + #include ++#include + + #ifndef MAP_FILE + #define MAP_FILE 0 diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch new file mode 100644 index 000000000000..583cc52645df --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch @@ -0,0 +1,151 @@ +diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm +--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700 ++++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.4.0 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.4.0 ++CHARMBASE = /usr/include/charm-6.4.0 + +diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile +--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600 ++++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600 +@@ -344,10 +344,10 @@ + $(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 + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #MSA = -DCHARM_HAS_MSA +@@ -370,7 +370,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -386,7 +386,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -402,16 +402,9 @@ + $(EXTRALINKLIBS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@; + +-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -434,11 +427,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -456,7 +446,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -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 $@ + +@@ -466,7 +456,7 @@ + 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 +@@ -665,9 +655,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -678,17 +666,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- 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 $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw +--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700 ++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600 +@@ -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) $(FFTFLAGS) + +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl +--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600 ++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + -- cgit v1.2.3