pbs_python compilation error message

[vipin@…]

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

[bas]

The quick answer is to copy the provided log.h from the pbs_python package to /opt/torque/include/. log.h will be included in a next release of torque.

The compilation/installation errors will be fixed

[vipin@…]

Thanks! There are two log.h files under pbs_python package. Which one should I take to move to /opt/torque/include.

./pbs_python-4.4.0/src/C/log.h ./pbs_python-4.4.0/src/C++/log.h

[bas]

Replying to vipin@…:

Thanks! There are two log.h files under pbs_python package. Which one should I take to move to /opt/torque/include.

./pbs_python-4.4.0/src/C/log.h ./pbs_python-4.4.0/src/C++/log.h

The C++ one this is for torque version 4 and higher, C is for torque version 2

[vipin@…]

Hi, I have tried to compile pbs_python package after copying ./pbs_python-4.4.0/src/C++/log.h to /opt/torque/include. The make step was successful. Then the make install step was partially successful (as described above, some manual editing is needed, till the below line it was fine) creating //share/software/lib64/python2.6/site-packages/pbs.pth

Now when I try to import the pbs module it shows the same error message as reported before. /share/software/lib/python2.6/site-packages/pbs/_pbs.so: undefined symbol: _Z13log_availablei In conclusion the copying of log.h didn't help much.

I have suspicion in the make step that somehow missed the ordering of libraries

[bas]

Did you a make:

• make distclean
• make
• cd build/lib.linux-x86_64-*
• python/ipython
• import pbs

[vipin@…]

Yes I did that, still no luck.

In [1]: import pbs

---

ImportError? Traceback (most recent call last)

/share/software/pbs_python/pbs_python-4.4.0/build/lib.linux-x86_64-2.6/<ipython console> in <module>()

/share/software/pbs_python/pbs_python-4.4.0/build/lib.linux-x86_64-2.6/pbs.py in <module>()

24 fp.close() 25 return _mod

---> 26 _pbs = swig_import_helper()

27 del swig_import_helper 28 else:

/share/software/pbs_python/pbs_python-4.4.0/build/lib.linux-x86_64-2.6/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?: ./_pbs.so: undefined symbol: _Z13log_availablei

[bas]

I am on holiday from 15 Feb till 23 Feb. The test that i run was with torque version 4.2.6 and higher.

[anonymous]

I am working on Version: 4.2.5

[bas]

Replying to anonymous:

I am working on Version: 4.2.5

I know. I have read your logs ;-)

[bas]

Will close this ticket. The main effort will be for 5.X versions.