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152 lines
5.4 KiB
152 lines
5.4 KiB
diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm
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--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700
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+++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600
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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-6.4.0 or charm in the NAMD base directory.
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-CHARMBASE = /Projects/namd2/charm-6.4.0
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+CHARMBASE = /usr/include/charm-6.4.0
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diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile
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--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600
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+++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600
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@@ -344,10 +344,10 @@
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$(DSTDIR)/stringhash.o
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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/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
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+CHARMLIB = /usr/gentoo-libdir
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CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
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#CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
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#MSA = -DCHARM_HAS_MSA
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@@ -370,7 +370,7 @@
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# Add new executables here.
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-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
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+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
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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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@@ -386,7 +386,7 @@
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namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
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$(MAKEBUILDINFO)
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- $(CHARMC) -verbose -ld++-option \
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+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \
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"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
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"$(CHARM_MODULES)" -language charm++ \
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$(BUILDINFO).o \
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@@ -402,16 +402,9 @@
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$(EXTRALINKLIBS) \
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-lm -o namd2
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-charmrun: $(CHARM)/bin/charmrun # XXX
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- $(COPY) $(CHARM)/bin/charmrun $@
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-
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$(LIBCUDARTSO):
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$(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
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-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe
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-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
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-windowsbinaries: $(WINDOWSBINARIES)
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-
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namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
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$(MAKEBUILDINFO)
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$(CHARMC) -verbose \
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@@ -434,11 +427,8 @@
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charmd_faceless.exe:
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$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
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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: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
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- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
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+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
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psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
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$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
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@@ -456,7 +446,7 @@
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$(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
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flipdcd: $(SRCDIR)/flipdcd.c
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- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
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echo "#!/bin/sh\necho unavailable on this platform" > $@; \
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chmod +x $@
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@@ -466,7 +456,7 @@
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chmod +x $@
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fixdcd: $(SRCDIR)/fixdcd.c
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- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
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dumpdcd: $(SRCDIR)/dumpdcd.c
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$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
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@@ -665,9 +655,7 @@
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DOC_FILES = README.txt announce.txt license.txt notes.txt
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-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
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-
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-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
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+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
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release: all
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$(ECHO) Creating release $(RELEASE_DIR_NAME)
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@@ -678,17 +666,9 @@
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for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
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/bin/rm -rf $$f; \
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done
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- if [ -r $(CHARM)/bin/charmd ]; then \
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- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
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- fi
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- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
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- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
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- fi
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chmod -R a+rX $(RELEASE_DIR_NAME)
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tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
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gzip $(RELEASE_DIR_NAME).tar
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- echo $(CHARM)
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- ls -l $(CHARM)/lib
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-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
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winrelease: winall
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diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw
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--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700
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+++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600
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@@ -1,7 +1,7 @@
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-FFTDIR=/Projects/namd2/fftw/linux-x86_64
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+FFTDIR=/usr
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FFTINCL=-I$(FFTDIR)/include
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-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
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+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
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FFTFLAGS=-DNAMD_FFTW
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FFT=$(FFTINCL) $(FFTFLAGS)
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diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl
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--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600
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+++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600
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@@ -1,9 +1,9 @@
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#TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
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-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
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+TCLDIR=/usr
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TCLINCL=-I$(TCLDIR)/include
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#TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
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-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
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+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
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TCLFLAGS=-DNAMD_TCL
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TCL=$(TCLINCL) $(TCLFLAGS)
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