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bas (12 matches)

Ticket Summary Component Milestone Type Created
Description
#29 Connection expiry and maximum connection number issues pbs defect 10/19/11

Hi again,

We seem to be having trouble maitaining open connections to Torque server from within pbs bindings in python.

  • if an invalid connection id is passed, for a connection that is probably no longer active, methods like pbs_statjob/statserver/statnode return an empty list instead of raising an exception or returning an error code
  • error raised after that is 15022 - "No access permission for queue"
  • most common error code we get otherwise is a 15033 - "No free connections"
  • after connection id is invalid, and running pbs.pbs_connect(pbs.pbs_default()) again, the pbs.get_error() still reports error 15033 but a query to pbs.pbs_statjob(c, None, [], None) returns all jobs in batch_result, then pbs.get_error() returns 0 so either pbs_error is not cleared at pbs.pbs_connect() or a connection is successfully established but an error is reported

Best way to diagnose it is to run python in console, connect to torque server and query it from time to time. You shoud notice that an empty list is returned from pbs.pbs_statnode() once the connection is invalid (we have queued jobs so I know for sure that the result is wrong)

We use Torque 2.5.8 (2.5.5 before, no change). The connection limit was raised from 5 to 10 in 2.5.6.

It seems that once the connection limit is reached in interpreter there is no way of connecting again (I tried a reconection decorator to auto reconnect, no luck there either).

Limits are defined in src/include/server_limits.h in Torque

CCd myself this time, any suggestions?

Thanks in advance,

Łukasz Czuja

#44 Problem with pbs_submit() pbs defect 08/04/14

Hi i need a little help with pbs_submit My python script:

import pbs server_name = pbs.pbs_default() c = pbs.pbs_connect(server_name) #c = 1

attropl = pbs.new_attropl(1)

attropl[0].name = pbs.ATTR_N attropl[0].value = "test"

job_id = pbs.pbs_submit(c, attropl, "simple.pbs", 'batch', 'NULL')

e, e_txt = pbs.error() if e:

print e,e_txt

print job_id

Error report is: 15025 Queue already exists job_id = None

My simple.pbs file:

#!/bin/sh

for i in seq 1 60 ; do

echo $i sleep 1

done

#57 pbs_submit - OutputPath syntax pbs defect 05/23/15

Hi all. How can i specify custom output_path when i submit a job with pbs_submit function??

#62 job submission fails in pbs_python but works fine with qsub pbs defect 09/17/15

Hello,

I am trying to set-up galaxy server on our compute cluster and run into a problem: job submission to pbs is very unreliable, in few cases it works but more often it fails. Restarting pbs_server fixes the problem for some time but later it starts again. We have production system with many users and galaxy is a tiny fraction of them, so restarting pbs_server can not be a solution. Errors in Galaxy are completely irrelevant, but trying a simple python script calling pbs.pbs_submit(...) from command line gives:

15044 Resources temporarily unavailable

In pbs logs I see corresponding entry:

PBS_Server.20463;Svr;PBS_Server;LOG_ERROR::Unauthorized Request (15007) in req_jobscript, cannot authorize request (0-Success)

Other commands from examples like ha_server.py or pbsnodes-a.py are working fine. Google brought this report which sounds similar to our problem: ​http://www.supercluster.org/pipermail/torqueusers/2014-January/016735.html

Is it indeed the case that pbs_python uses pbs_submit and not pbs_submit_hash? Are there any plans to move to pbs_submit_hash? ( in assumption that it will fix this problem)

We use moab/pbs, pbs/tourque version 4.2.9 Python 2.6.6

Let me know if you need any additional information.
Thank you
Kind regards

Elena

#63 pbs_python-4.6.0 memory leak pbs defect 10/07/15

Hi,

I am using pbs_python-4.6.0 with torque-5.1.1.2. We found a memory leak for this module. Simply run the following program and hopefully you can reproduce this issue. It gradually takes more and more memory during the run until it takes all available physical memory of our server and crashes.

We also used torque-5.1.0 but the result is the same. Any suggestion or advice would be gratefully appreciated. 

import pbs
import time
server_name = pbs.pbs_default()
print "Sername name",server_name
c = pbs.pbs_connect(server_name)
attropl = pbs.new_attropl(1)
attropl[0].name  = pbs.ATTR_N
attropl[0].value = 'test'
job_id = pbs.pbs_submit(c, attropl, 'A1.tsk', '', 'NULL')
e, e_txt = pbs.error()
if e:
     print e,e_txt
print job_id
pbs.pbs_disconnect( c )
j=0
while 1:
     time.sleep( 1 )
     j=j+1
     if j >= 200:
       break
     c = pbs.pbs_connect(server_name)
     stat_attrl = pbs.new_attrl(3)
     stat_attrl[0].name = pbs.ATTR_state
     stat_attrl[1].name = pbs.ATTR_used
     stat_attrl[2].name = pbs.ATTR_exitstat
     jobs = pbs.pbs_statjob( c, None, stat_attrl, None )
     pbs.pbs_disconnect( c )

Cheers, Ata

#41 Make pbs_python work s.t. we can install using python setup.py install pbs enhancement 02/25/14

Some tools require that we can merely run python setup.py install. e.g. If pbs_python is a dependency for a project using tox. This improvement would also mean we no longer have to look at autotools generated code. :)

I already have a patch to do this:

​https://github.ugent.be/ehiggs/pbs-python/commit/518b59e8f070f3d1d35dbf981b9cbbeafbeed033

#48 User job submission pbs enhancement 01/12/15

How can i implement the -A option in qsub, in pbs python?

#54 pbs_submit_hash() pbs enhancement 03/27/15

We've found that pbs_submit() has not been reliable. Occasionally pbs_server gets into a state that causes all jobs submitted via pbs_submit() to fail (this is not a problem with pbs_python -- the problem exists even with the C API directly). However, pbs_submit_hash() continues to work in this case. Since Torque moved to pbs_submit_hash(), I don't feel that pbs_submit() is as well tested.

We'd like to move our applications from pbs_submit() to pbs_submit_hash(), but I don't think all the functionality we need is in pbs_python.

Here is a short snippet of C code using pbs_submit_hash:

int fd = pbs_connect(0); char *new_jobid; memmgr* mm; job_data* job_attrs = 0;

memmgr_init(&mm, 0);

/* pass empty ATTR_v, just to show use of hash_add_or_exit */ hash_add_or_exit(&mm, &job_attrs, ATTR_v, "", ENV_DATA);

pbs_submit_hash(fd, &mm, job_attrs, NULL, "/tmp/test.sh", NULL, NULL, &new_jobid, NULL);

#60 Fix bug in _lis_2_dict split and exec_host pbs enhancement 07/09/15

the current code needs following patch to resolve issues with multinode ranges

#66 Python 3 branch pbs enhancement 07/07/16

Is there a Python 3 branch of this package?

#52 PBSQuery + uWSGI pbs task 03/18/15

When i use Django embbedded server everything is fine but when i use uwsgi i get this error:

Could not make a connection with jim-Aspire-5742G

Request Method: GET Request URL: ​http://localhost:8000/ Django Version: 1.6 Exception Type: PBSError Exception Value:

Could not make a connection with jim-Aspire-5742G

Exception Location: /usr/local/lib/python2.7/dist-packages/PBSQuery.py in _connect, line 103 Python Executable: /usr/local/bin/uwsgi Python Version: 2.7.6 Python Path:

['/usr/local/lib/python2.7/dist-packages/',

'.', , '/home/jim/Documents/dbikas/lib/python2.7', '/home/jim/Documents/dbikas/lib/python2.7/plat-x86_64-linux-gnu', '/home/jim/Documents/dbikas/lib/python2.7/lib-tk', '/home/jim/Documents/dbikas/lib/python2.7/lib-old', '/home/jim/Documents/dbikas/lib/python2.7/lib-dynload', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/home/jim/Documents/dbikas/local/lib/python2.7/site-packages', '/home/jim/Documents/dbikas/lib/python2.7/site-packages']

Any ideas???

#10 PBSQuery module enhancement PBSQuery enhancement 09/21/07

we now only can query keywords, eg: 

 l = ['state', 'np' ]
nodes = p.getnodes(l)
}}

Nut sometimes we want only nodes that have, eg np=2. That is imposible for this moment.
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