1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
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)
|