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
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
|
import os
import os.path
#compilation mode: please choose between debug and release
compile_mode = "release"
#compile_mode = "debug"
#users may overide these settings if SCons cannot automatically locate some library:
#PATH to g77 or gfortran:
user_path_fortrancompiler = ""
#libg2c.a (or .so) or libgfortran.a PATH:
user_path_libg2cgfortran = ""
#boost libraries PATH:
user_path_boost = ""
#if you add a file in this list, please make sure that
#this .cpp file begins with " //$Id$"
#and type: svn propset svn:keywords Id filename
COMMON_CPP = Split ("""atom.cpp
basetypes.cpp
rigidbody.cpp
attractrigidbody.cpp
coord3d.cpp
pdbio.cpp
geometry.cpp
atomselection.cpp
rmsd.cpp
forcefield.cpp
pairlist.cpp
minimizers/lbfgs_interface.cpp
minimizers/routines.f
minimizers/lbfgs_wrapper/lbfgsb_wrapper.cpp
mcopff.cpp
surface.cpp
coordsarray.cpp
superpose.cpp
version.cpp
attractforcefield.cpp
""")
COMMON_LIBS=[""]
#COMMON_LIBS=["gfortran"]
#COMMON_CPPPATH=['.', '/sw/include/boost-1_33_1']
COMMON_CPPPATH=['.']
FFLAGS="-g"
def FIND_FILE(name,path, useEnvPath=False):
if useEnvPath:
additional_path = os.environ['PATH'].split(':')
path.extend(additional_path)
for p in path:
if os.path.exists(p+'/'+name):
return p+'/'+name
return None
def FIND_HEADER(names, paths, useEnvPath=False):
#find a library in a given set of directories
if useEnvPath:
additional_path = os.environ['PATH'].split(':')
paths.extend(additional_path)
for p in paths:
if os.path.exists(p):
files=os.listdir(p)
for n in names:
if os.path.exists(p+"/"+n):
return p
return None
#find g++ / g77 or g++/gfortran:
FORTRANPROG = ""
LIB_PATH=['.']
print "Searching for compilers..."
gpp = FIND_FILE("g++", ["/usr/bin"], True)
if gpp is None:
print "Error: cannot locate g++, compilation aborted"
Exit(1)
else:
print "g++ found here: ", gpp
g77 = FIND_FILE("g77", [user_path_fortrancompiler,"/usr/bin","/sw/bin/"], True)
if g77 is None:
print "Cannot locate g77 fortran compiler, trying gfortran:"
gfortran=FIND_FILE("gfortran", [user_path_fortrancompiler,"/usr/bin"], True)
if gfortran is None:
print "Error: no fortran compiler found, aborting"
Exit(1)
else: #gfortran compiler, try to locate libgfortran
print "using fortran compiler: gfortran"
FORTRANPROG="gfortran -O2 -g -fPIC"
gfortranlib=FIND_HEADER(["libgfortran.a", "libgfortran.la",\
"libgfortran.so", "libgfortran.so.3"], [user_path_libg2cgfortran,"/usr/lib","/usr/lib64","/sw/lib",\
"/usr/lib/gcc/x86_64-redhat-linux/3.4.6/","/usr/lib64/gcc/x86_64-suse-linux/4.1.2/"], True)
if gfortranlib is not None:
print "libgfortran found here: ", gfortranlib
LIB_PATH.append(gfortranlib)
COMMON_LIBS.append("gfortran")
else:
print "WARNING: libgfortran not found, may not compile..."
COMMON_LIBS.append("gfortran")
else: #g77 compiler
print "using fortran compiler: g77"
FORTRANPROG="g77 -O2 -g -fPIC"
g2clib = FIND_HEADER(["libg2c.a", "libg2c.so", "libg2c.la","libg2c.so.0"], [user_path_libg2cgfortran,"/usr/lib",\
"/usr/local/lib/", "/sw/lib/","/usr/lib/gcc/x86_64-redhat-linux/3.4.6/"], True)
if g2clib is None:
print "Warning: libg2c not found, may not compile..."
COMMON_LIBS.append("g2c")
else:
print " libg2c found here:", g2clib
LIB_PATH.append(g2clib)
COMMON_LIBS.append("g2c")
boostdir=FIND_HEADER(["boost/shared_array.hpp"], [user_path_boost,"/usr/include", \
"/sw/include/boost-1_33_1"] )
if boostdir is None:
print "cannot locate Boost hearders directory, still trying to compile..."
else:
print "boost directory found here: ", boostdir
COMMON_CPPPATH.append(boostdir)
python24dir=FIND_HEADER(["Python.h"], ["/usr/include/python2.4", \
"/sw/include/python2.4"])
if python24dir is not None:
print "python2.4 found, configuring path and libs"
PYTHON_CPPPATH=[python24dir]
PYTHON_LIBS=["python2.4"]
if python24dir is None:
print "cannot locate python2.4, tying with python2.5:"
python25dir = FIND_HEADER(["Python.h"], ["/usr/include/python2.5/",
"/sw/include/python2.5/"])
if python25dir is None:
print "cannot locate Python2.5, the library may not compile..."
print "trying to locate Python 2.6:"
python26dir = FIND_HEADER(["Python.h"], ["/usr/include/python2.6/",
"/sw/include/python2.6/"])
if python26dir is not None:
print "Python 2.6 found!"
PYTHON_CPPPATH=[python26dir]
PYTHON_LIBS=["python2.6"]
else:
PYTHON_CPPPATH=[python25dir]
PYTHON_LIBS=["python2.5"]
PYTHON_CPP=[]
import fnmatch
import os
for file in os.listdir("Pybindings"):
if fnmatch.fnmatch(file, "*.cpp"):
PYTHON_CPP.append("Pybindings/%s"%file)
#generate svnrev.h (revision number of the library)
os.system("gcc svnrev.c -o svnrev")
svnrevfiles = [f for f in os.listdir('.') if fnmatch.fnmatch(f, "*.cpp") or fnmatch.fnmatch(f,"*.h") and not fnmatch.fnmatch(f,"svnrev.*") ] #list every .h or .cpp
os.system("./svnrev %s"%(" ".join(svnrevfiles)))
if compile_mode == "release":
ccflags = "-Wall -O2 -fPIC -Woverloaded-virtual -DNDEBUG -ffunction-sections -fvisibility=hidden"
else:
ccflags = "-Wall -O2 -fPIC -g -Woverloaded-virtual"
print "common cpp path:", COMMON_CPPPATH
common=Environment(LIBS=COMMON_LIBS,CPPPATH=COMMON_CPPPATH, CCFLAGS=ccflags, LIBPATH=LIB_PATH, FORTRAN=FORTRANPROG, FORTRANFLAGS="-g -fPIC" )
#common.Append(CCFLAGS='-Wall -O2 -fPIC -Woverloaded-virtual -DNDEBUG') #fastest(?) release
#common.Append(CCFLAGS='-Wall -O2 -g -fPIC -D_GLIBCXX_DEBUG') #debuging high (use with care !)
#common.Append(CCFLAGS='-Wall -O0 -g -pg -fPIC -DNDEBUG ') #profiling
#check for some boost header files:
has_boost=False
conf = Configure(common)
if conf.CheckCXXHeader("boost/shared_array.hpp"):
has_boost=True
if not has_boost:
print "cannot find boost::shared_array include file"
Exit(1)
common = conf.Finish()
python=common.Copy()
nopython=common.Copy()
python.Append(CPPPATH=PYTHON_CPPPATH, LIBS=PYTHON_LIBS)
objects=common.SharedObject(COMMON_CPP)
statics=common.StaticObject(COMMON_CPP) #to make a static library
python.Append(LIBS=['boost_python'])
#check python header file:
conf = Configure(python)
if not conf.CheckCHeader('Python.h'):
print "you must install either python2.4-dev or python2.5-dev"
Exit(1)
env = conf.Finish()
print "using CPPPATH =", python['CPPPATH']
lib1=python.SharedLibrary(File('_ptools.so'),source=[objects,PYTHON_CPP])
#lib2=nopython.SharedLibrary('ptools',source=[objects])
lib2=nopython.StaticLibrary('ptools',source=[statics]) #this makes the pure C++ static library
Alias('python',lib1)
Alias('cpp',[lib2] )
print "BUILD_TARGETS is", map(str, BUILD_TARGETS)
#### old commands. Not needed but kept here for some time #####
#Alias('cpp',[lib2,tst])
|