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Ticket | Resolution | Summary | Owner | Reporter |
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#40 | wontfix | pbs_python compilation error message | bas | vipin@… |
Description |
Hi pbs_python team, I am trying to compile pbs_python module locally (not the system-wide distribution), downloaded a recent stable version pbs_python-4.4.0. In my side I am using, RHEL Linux local 2.6.32-279.14.1.el6.x86_64, python 2.6 and torque version 4.2.5. The configure step gives me a warning message, I think that looks ok. *pbs_python/pbs_python-4.4.0$ ./configure --prefix=/share/software/* checking for pbs-config... /opt/torque/bin//pbs-config Found torque version: 4.2.5 checking for python... /usr/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.6/site-packages configure: creating ./config.status config.status: creating Makefile config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting config.status: creating setup.py Next I went to provide "make" command and which throws me an error message as follows: pbs_python/pbs_python-4.4.0$ make #(cd src; make) python setup.py build Failed to find log.h in inlcude dir /opt/torque/include/. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) make: *** [pythonlib] Error 2 I have set the env PBS_PYTHON_INCLUDEDIR to /opt/torque/include/ where my torque include files. I haven't seen the log.h file in that path but I can see /opt/torque/include/log_event.h /opt/torque/include/pbs_log.h With the /opt/torque/include/pbs_log.h file I updated the setup.py file and run the "make" command, this time it was successful. *pbs_python/pbs_python-4.4.0$ make * #(cd src; make) python setup.py build running build running build_py creating build creating build/lib.linux-x86_64-2.6 copying src/pbs.py -> build/lib.linux-x86_64-2.6 copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 running build_ext building '_pbs' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src creating build/temp.linux-x86_64-2.6/src/C++ g++ -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/opt/torque/include/ -fPIC -DTORQUE_4 -I/usr/include/python2.6 -c src/C++/pbs_wrap.cxx -o build/temp.linux-x86_64-2.6/src/C++/pbs_wrap.o g++ -pthread -shared -I/opt/torque/include/ build/temp.linux-x86_64-2.6/src/C++/pbs_wrap.o -L/opt/torque/lib -L/usr/lib64 -ltorque -lpython2.6 -o build/lib.linux-x86_64-2.6/_pbs.so -L/opt/torque/lib -ltorque -Wl,-rpath -Wl,/opt/torque/lib then I proceed further and gave make install command */pbs_python/pbs_python-4.4.0$ make install* #(cd src; make) python setup.py build running build running build_py running build_ext python ./setup.py install --prefix //share/software ; running install running build running build_py running build_ext running install_lib creating //share/software/lib64/python2.6/site-packages/pbs copying build/lib.linux-x86_64-2.6/pbs.py -> //share/software/lib64/python2.6/site-packages/pbs copying build/lib.linux-x86_64-2.6/PBSQuery.py -> //share/software/lib64/python2.6/site-packages/pbs copying build/lib.linux-x86_64-2.6/_pbs.so -> //share/software/lib64/python2.6/site-packages/pbs byte-compiling //share/software/lib64/python2.6/site-packages/pbs/pbs.py to pbs.pyc byte-compiling //share/software/lib64/python2.6/site-packages/pbs/PBSQuery.py to PBSQuery.pyc running install_egg_info Writing //share/software/lib64/python2.6/site-packages/pbs/pbs_python-4.4.0-py2.6 .egg-info creating //share/software/lib64/python2.6/site-packages/pbs.pth install -D LICENSE.openpbs //share/doc/ /LICENSE.openpbs install: target `/LICENSE.openpbs' is not a directory make: *** [install] Error 1 By looking at the Makefile, I have fixed manually the install -D steps, which I believe the Makefile was not able to get the right path from the defined variables. Of course they are not going to effect much in the core installation of pbs_python, because the steps consists of mainly the licenses and example scripts. The pbs_python installation was successful and I tried to use the "pbs" module and which was not working and throwing me an error message. *In [1]: import pbs* --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /home/vipin/codebase/TaskManager/<ipython console> in <module>() /share/software/lib64/python2.6/site-packages/pbs/pbs.py in <module>() 24 fp.close() 25 return _mod ---> 26 _pbs = swig_import_helper() 27 del swig_import_helper 28 else: /share/software/lib64/python2.6/site-packages/pbs/pbs.py in swig_import_helper() 20 if fp is not None: 21 try: ---> 22 _mod = imp.load_module('_pbs', fp, pathname, description) 23 finally: 24 fp.close() ImportError: /share/software/lib64/python2.6/site-packages/pbs/_pbs.so: undefined symbol: _Z13log_availablei I have also checked the files associated with the shared object _pbs.so, which looks everything fine as here *pbs_python/pbs_python-4.4.0$ ldd /share/software/lib64/python2.6/site-packages/pbs/_pbs.so* linux-vdso.so.1 => (0x00007fff1fff0000) libtorque.so.2 => /opt/torque/lib64/libtorque.so.2 (0x00007f18b85aa000) libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007f18b8203000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f18b7efd000) libm.so.6 => /lib64/libm.so.6 (0x00007f18b7c79000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f18b7a62000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f18b7845000) libc.so.6 => /lib64/libc.so.6 (0x00007f18b74b2000) libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007f18b715f000) libz.so.1 => /lib64/libz.so.1 (0x00007f18b6f49000) libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00007f18b6baf000) libssl.so.10 => /usr/lib64/libssl.so.10 (0x00007f18b6951000) librt.so.1 => /lib64/librt.so.1 (0x00007f18b6749000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f18b6545000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f18b6341000) /lib64/ld-linux-x86-64.so.2 (0x000000306f000000) libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007f18b60fd000) libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007f18b5e16000) libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f18b5c12000) libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007f18b59e6000) libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007f18b57da000) libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007f18b55d7000) libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f18b53bd000) libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f18b519d000) Is there anything you can help the situation with me, I am happy to provide more details from my side. I don't know if I am missing to put the libs to be the last args at the end of the g++ command line in make step? many thanks in advance for the module, Vipin |
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#45 | duplicate | undefined symbols in C++ wrappers | bas | glen.beane@… |
Description |
I had to remove references to two functions: log_available begin_rm_req from src/C++/pbs.py and src/C++/pbs_wrap.cxx otherwise we got undefined symbol errors when importing the module in our python program It appears these had already been removed from src/C/pbs.py and src/C/pbs_wrap.c |
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#23 | worksforme | using pbs_python under windows/cygwin | bas | anonymous |
Description |
Hi! I have a question. Is pbs_python known to work at Windows/Cygwin? platform? Thank you |
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