[torqueusers] Torque 4.0 and job arrays

Rhys Hill rhys.hill at adelaide.edu.au
Tue Apr 24 00:23:55 MDT 2012


Hi David,

Thanks for that. I've just found and fixed some other bugs which I've added to
bugzilla. The one issue that remains is odd. It seems that we have a situation
where an array is stuck, when all of it's component jobs are finished.

For instance, qstat -f says this:

Job Id: 678[].moby.cs.adelaide.edu.au
    Job_Name = YZ_Oxford_group
    Job_Owner = yanzhichen at moby.cs.adelaide.edu.au
    job_state = Q
    queue = batch
    server = moby.cs.adelaide.edu.au
    Checkpoint = u
    ctime = Tue Apr 24 09:26:10 2012
    Error_Path = moby.cs.adelaide.edu.au:/home/yanzhichen/moby/oxbuilding_voca
	bulary/out.e.txt
    Hold_Types = n
    Join_Path = n
    Keep_Files = n
    Mail_Points = a
    mtime = Tue Apr 24 09:26:10 2012
    Output_Path = moby.cs.adelaide.edu.au:/home/yanzhichen/moby/oxbuilding_voc
	abulary/out.o.txt
    Priority = 0
    qtime = Tue Apr 24 09:26:10 2012
    Rerunable = True
    Resource_List.mem = 5gb
    Resource_List.nodect = 1
    Resource_List.nodes = 1:ppn=1
    Resource_List.pmem = 5gb
    Resource_List.pvmem = 8gb
    Resource_List.walltime = 48:00:00
    etime = Tue Apr 24 09:26:10 2012
    submit_args = -t 2-11 ./job_dogroup
    job_array_request = 2-11
    fault_tolerant = False
    job_radix = 0
    submit_host = moby.cs.adelaide.edu.au
    init_work_dir = /home/yanzhichen/moby/oxbuilding_vocabulary

whereas qstat -ft has no mention of 678[x] at all. qdel and qdel -p have no effect
on jobs like these. I think I've submitted a fix for the problem that leads to the
job getting into this state, but it would be handy if qdel could remove it.

Thanks,

On 24/04/2012, at 2:52 AM, David Beer wrote:

> Rhys,
> 
> I'm surprised that you say you haven't seen this message before, as the check exists in both places and has been there since 2.5 was released. There must've been a bug that allowed it before. In this case, please try the attached patch to see if it resolves your problem for 4.0. This patch only requires you to rebuild and restart the server (dependencies are unknown to pbs_moms).
> 
> David
> 
> On Sun, Apr 22, 2012 at 9:31 PM, Rhys Hill <rhys.hill at adelaide.edu.au> wrote:
> Hi everyone,
> 
> I recently upgraded to torque 4.0 alongside moab 7.0, mostly because we'd been
> having some trouble with cpusets and I'd hoped that the support for hwloc would
> resolve the problem. cpusets are now working very well, but I'm having a lot of
> trouble with job arrays, which form a very large part of our workload.
> 
> Torque 4.0.0 would regularly lock-up when processing job arrays, so I upgraded to
> the most recent 4.0.1 snapshot, and that behaves much better, but still seems
> unstable compared to 2.5.9.
> 
> One concrete issue is that many of our jobs that worked fine with 2.5.9 are now
> stalling with 4.0.1 with the following message:
> 
> "Arrays may only be given array dependencies"
> 
> which only seems to appear in the server logs and is otherwise invisible. This
> was certainly never true before, and doesn't really make sense. We frequently
> use array->single job dependencies for scatter-gather type operations.
> 
> Once the above message has been printed, the job arrays sit in a hold state forever.
> They can't be removed using qdel and if I try to break the hold using qrls or
> mjobctl, they move into the queued state, but they disappear from moab and never
> actually start, and still can't be removed. The only way I can get rid of them
> is to bring down pbs_server, which has to killed via `killall -QUIT pbs_server`
> since the init script cannot stop the process properly, and delete the job
> files manually.
> 
> I'm currently thinking of just reverting to the old, working version of torque,
> but has anyone else had trouble with job arrays and can the above problems be
> fixed somehow?
> 
> Thanks,
> 
> --------------------------------------------------------------------------------
> Rhys Hill,                                             Senior Research Associate
> Australian Centre for Visual Technologies                 University of Adelaide
> 
> Phone: +61 8 8313 6197                           Mail:
> Fax:   +61 8 8313 4366                           School of Computer Science
>                                                 University of Adelaide
>                                                 Adelaide, Australia
> http://www.cs.adelaide.edu.au/~rhys/             5005
> --------------------------------------------------------------------------------
> 
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> 
> 
> 
> -- 
> David Beer | Software Engineer
> Adaptive Computing
> 
> <ArrayDeps.patch>_______________________________________________
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--------------------------------------------------------------------------------
Rhys Hill,                                             Senior Research Associate
Australian Centre for Visual Technologies                 University of Adelaide

Phone: +61 8 8313 6197                           Mail:
Fax:   +61 8 8313 4366                           School of Computer Science
                                                 University of Adelaide
                                                 Adelaide, Australia
http://www.cs.adelaide.edu.au/~rhys/             5005
--------------------------------------------------------------------------------



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