pbs_python does not work with most recent TORQUE 4.2.0

[glen.beane@…]

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

[anonymous]

I was able to get it to work by doing the following:

removing these functions from pbs_wrap.c and pbs.py in pbs_python:

log_record log_close log_open log_err log_event log_roll log_size chk_file_sec setup_env

[bas]

Glen,

It is still on my todo list to port pbs_python to 4.2.0. The files are generated by swig. So i have to some work. It is good to know that some function do not exists anymore.

regards

PS) Currently we are evaluating slurm to replace our torque/maui setup

[glen.beane@…]

If you do use Slurm to replace torque/maui is there a chance you could turn pbs_python over to someone that will be willing to maintain it and update it for recent versions of Torque? We have built a mission critical application around pbs_python and really need to see it maintained.

[bas]

Replying to glen.beane@…:

If you do use Slurm to replace torque/maui is there a chance you could turn pbs_python over to someone that will be willing to maintain it and update it for recent versions of Torque? We have built a mission critical application around pbs_python and really need to see it maintained.

We still running torque/maui, but the old torque version. I have to setup torque 4.2 and then test the pbs_python stuff. I stiil make patches but that is also for the old toque versions.

Maybe there are volunteers to help port it to torque version 4.X

[glen.beane@…]

there is no reason to call these functions from pbs_python anyway, so I think it would be safe to just remove them -- it shouldn't hurt anyone using an old version of torque.

[bas]

Glen i am bit swamped lately but we use the log_ functions in our utilities. I need some time to port it to 4.X versions. we just upgraded to the latest 2.5 version. I know it is also end of release.

[anonymous]

I think the porting issues to 4.2.4 are a little more involved.. I just noticed that calling get_mom_values against a worker causes pbs_mom to shut down.

Doesn't seem to be a crash.. it looks like a clean shutdown to me?

08/13/2013 16:15:47;0002; pbs_mom.29227;n/a;rm_request;shutdown 08/13/2013 16:15:47;0002; pbs_mom.29227;n/a;dep_cleanup;dependent cleanup 08/13/2013 16:15:47;0002; pbs_mom.29227;Svr;Log;Log closed

[anonymous]

For what it is worth, I can confirm that the chages specified in the post regarding pbs_wrap.c and pbs.py for pbs_python fix pbs_python for Galaxy when using pbs_python-4.1.0 and pbs_python-4.3.5 for TORQUE 4.2.2 Some of the files appear to be named a little bit differently in the source folder (i.e. pbs_wrap_2.1.c and pbs_wrap_2.4.c). I could get this working by stripping out the functions from the files as described.

[anonymous]

I'm the one that posted the work-around above.

pbs_wrap.c is a symlink that points to either pbs_wrap_2.1.c or pbs_wrap_2.4.c, so you need to edit the correct pbs_wrap_*.c and pbs*.py for your system (I think there was a bug in the version pbs_python TORQUE version detection that would cause it to chose pbs_wrap_2.1.c for modern versions of TORQUE. I'm not sure if this is still the case)

[anonymous]

i posted some patches for 4.2 support in https://oss.trac.surfsara.nl/pbs_python/ticket/36. hope this helps things forward.

[bas]

As today i have just installed 4.2-dev on a test node and succeeded in porting pbs_python to this torque release. I will release an updated pbs_python version shortly.

[bas]

support is added in the trunk version that will shortly be released as version 4.4.0

[bas]

Version 4.4.0 is released