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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)
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