Hi Noel,
Just an update on my failing struggles.
So I've restored the initial setting of my CentOS machine, meaning I removed
all version of Python (tricky).
and reinstalled the system python which is python2.4 (and not
-enable-shared).
wget
http://mirror.centos.org/centos/5/os/x86_64/CentOS/python-2.4.3-56.el5.x86_6
4.rpm
rpm -ivh python-2.4.3-56.el5.x86_64.rpm
compile openbabel against this resulted in a lot of errors as attached.
For the program I want to test I need python 2.6 or higher anyway so next I
tried to download a rpm as Riccardo suggested.
#################################################
wget
http://dl.fedoraproject.org/pub/epel/5/x86_64/python26-2.6.8-2.el5.x86_64.rp
m
rpm -ivh python26-2.6.8-2.el5.x86_64.rpm
cd ~/downloads/openbabel/build
make clean
cmake ../openbabel-2.3.2
-DEIGEN2_INCLUDE_DIR=/home/peter/lib/eigen-eigen-b23437e61a07
-DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=/home/peter/tools/openbabel
-DCMAKE_BUILD_TYPE=DEBUG
### Check the python settings in CMakeCache.txt
# //Path to a program.
# PYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python2.6
#
# //Path to a file.
# PYTHON_INCLUDE_PATH:PATH=/usr/local/include/python2.6
#
# //Path to a library.
# PYTHON_LIBRARY:FILEPATH=/usr/local/lib/python2.6/config/libpython2.6.a
ERROR:
Linking CXX shared module ../lib/_openbabel.so
/usr/local/lib/python2.6/config/libpython2.6.a(posixmodule.o): In function
`posix_forkpty':
/home/peter/downloads/Python-2.6.6/./Modules/posixmodule.c:3811: undefined
reference to `forkpty'
/usr/local/lib/python2.6/config/libpython2.6.a(posixmodule.o): In function
`posix_openpty':
/home/peter/downloads/Python-2.6.6/./Modules/posixmodule.c:3751: undefined
reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2
I also checked the phython version from the rpm and it was NOT compiled
using -enabled-shared.
(http://stackoverflow.com/questions/9193773/is-there-a-way-to-tell-if-python
-was-configured-and-compiled-with-with-thread)
##############################################
So now I started to compile python in an alternative location:
wget http://www.python.org/ftp/python/3.2.3/Python-3.2.3.tgz
tar -xvf Python-3.2.3.tgz
cd Python-3.2.3
./configure --prefix=/opt/python3 --enable-shared LDFLAGS="-Wl,-rpath
/opt/python3/lib"
make -j
su root
make install
/opt/python3/bin/python3 -V
cmake ../openbabel-2.3.2
-DEIGEN2_INCLUDE_DIR=/home/peter/lib/eigen-eigen-b23437e61a07
-DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/opt/python3/bin/python3
-DPYTHON_LIBRARY=/opt/python3/lib/python3.2/config-3.2m/libpython3.2m.a
-DPYTHON_INCLUDE_PATH=/opt/python3/include/python3.2m
-DCMAKE_INSTALL_PREFIX=/home/peter/tools/openbabel -DCMAKE_BUILD_TYPE=DEBUG
ERROR
Linking CXX shared module ../lib/_openbabel.so
/opt/python3/lib/python3.2/config-3.2m/libpython3.2m.a(posixmodule.o): In
function `posix_forkpty':
/home/peter/downloads/Python-3.2.3/./Modules/posixmodule.c:4262: undefined
reference to `forkpty'
/opt/python3/lib/python3.2/config-3.2m/libpython3.2m.a(posixmodule.o): In
function `posix_openpty':
/home/peter/downloads/Python-3.2.3/./Modules/posixmodule.c:4202: undefined
reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2
################################
So unless somebody has a bright idea, I'm giving up.
Peter
make clean
cmake ../openbabel-2.3.2
-DEIGEN2_INCLUDE_DIR=/home/peter/lib/eigen-eigen-b23437e61a07
-DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python2.4
-DPYTHON_LIBRARY=/usr/lib/python2.4/config/libpython2.4.a
-DPYTHON_LIBRARY=/usr/lib/python2.4/config/libpython2.4.a
-DCMAKE_INSTALL_PREFIX=/home/peter/tools/openbabel -DCMAKE_BUILD_TYPE=DEBUG
make
Linking CXX shared module ../lib/_openbabel.so
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(abstract.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(boolobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(classobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(cobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(floatobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(intobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(iterobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(listobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(longobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(dictobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(moduleobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(object.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(obmalloc.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(sliceobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(stringobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(tupleobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(typeobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(weakrefobject.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(unicodeobject.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(unicodectype.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(exceptions.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(ceval.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(compile.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(codecs.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(errors.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(future.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getargs.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(import.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(importdl.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(marshal.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(modsupport.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(mystrtoul.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(mysnprintf.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(pystate.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(pythonrun.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(random.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(symtable.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(sysmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(traceback.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(pystrtod.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(dynload_shlib.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(thread.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(config.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getpath.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(gcmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(threadmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(signalmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(posixmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(errnomodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(pwdmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(_sre.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(_codecsmodule.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(zipimport.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(symtablemodule.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(acceler.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(grammar1.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(node.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(parsetok.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(tokenizer.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(bufferobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(cellobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(complexobject.o)' is incompatible
with i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(descrobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(genobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(fileobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(frameobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(funcobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(methodobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(structseq.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(bltinmodule.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(frozen.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getcopyright.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getmtime.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getplatform.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getversion.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(graminit.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(structmember.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getbuildinfo.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(parser.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(myreadline.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(enumobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(rangeobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(setobject.o)' is incompatible with
i386:x86-64 output
/usr/bin/ld: warning: i386 architecture of input file
`/usr/lib/python2.4/config/libpython2.4.a(getcompiler.o)' is incompatible with
i386:x86-64 output
CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function
`SWIG_From_unsigned_SS_int':
/home/peter/downloads/openbabel/openbabel-2.3.2/scripts/python/openbabel-python.cpp:5037:
undefined reference to `PyInt_FromSize_t'
CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function
`SWIG_Python_SetModule':
/home/peter/downloads/openbabel/openbabel-2.3.2/scripts/python/openbabel-python.cpp:2726:
undefined reference to `Py_InitModule4_64'
CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function
`init_openbabel':
/home/peter/downloads/openbabel/openbabel-2.3.2/scripts/python/openbabel-python.cpp:57631:
undefined reference to `Py_InitModule4_64'
/usr/lib/python2.4/config/libpython2.4.a(posixmodule.o): In function
`posix_forkpty':
(.text+0x2fe9): undefined reference to `forkpty'
/usr/lib/python2.4/config/libpython2.4.a(posixmodule.o): In function
`posix_openpty':
(.text+0x3078): undefined reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2
------------------------------------------------------------------------------
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