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Ticket Resolution Summary Owner Reporter
#24 fixed pbs_python and python3 support. bas steve.traylen@…
Description

Hi,

As part of adding to Fedora:

https://bugzilla.redhat.com/show_bug.cgi?id=631964

I will build a python3 variant if its possible but alas there looks to be problems.

Steps to reproduce working on Fedora13 box.

tar zxvf pbs_python-4.3.0.tar.gz

cd pbs_python-4.3.0

2to3 --write --nobackups .

./configure --with-python=python3 checking for pbs-config... /usr/bin/pbs-config Found torque version: 2.1.8 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: creating setup.py

# Note the 2.6 above

2to3 --write --nobackups setup.py

$ python3 setup.py build Please specify where the PBS libraries are!! edit setup.py and fill in the PBS_LIB_DIR variable

This I understand and is caused by old pbs-config present on Fedora 13 so you can ignore this one, I've fixed this past Fedora 13.

But still build fails.

See attachment.

#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
#34 fixed pbs_python does not work with most recent TORQUE 4.2.0 bas glen.beane@…
Description

TORQUE has switched to using g++ to compile. It appears there are some name mangling issues now as pbs_python is unable to find symbols:

ImportError?: /opt/compsci/python/2.7.3/lib/python2.7/site-packages/pbs/_pbs.so: undefined symbol: log_record

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