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Subject: Re: [OMPI devel] mpirun oddity w/ PBS on an SGI UV
From: Ralph Castain (rhc_at_[hidden])
Date: 2014-01-31 19:33:01


No worries about PBS itself - better to allow you to just run this way. Easy to add a switch for this purpose.

For now, just add --oversubscribe to the command line

On Jan 31, 2014, at 3:32 PM, Paul Hargrove <phhargrove_at_[hidden]> wrote:

> Ralph,
>
> The mods may have been done by the staff at PSC rather than by SGI.
> Note the "_psc" suffix:
> $ which pbsnodes
> /usr/local/packages/torque/2.3.13_psc/bin/pbsnodes
>
> Their sources appear to be available in the f/s too.
> Using "tar -d" to compare that to the pristine torque-2.3.13 tarball show the following files were modified:
> torque-2.3.13/src/resmom/job_func.c
> torque-2.3.13/src/resmom/mom_main.c
> torque-2.3.13/src/resmom/requests.c
> torque-2.3.13/src/resmom/linux/mom_mach.h
> torque-2.3.13/src/resmom/linux/mom_mach.c
> torque-2.3.13/src/resmom/linux/cpuset.c
> torque-2.3.13/src/resmom/start_exec.c
> torque-2.3.13/src/scheduler.tcl/pbs_sched.c
> torque-2.3.13/src/cmds/qalter.c
> torque-2.3.13/src/cmds/qsub.c
> torque-2.3.13/src/cmds/qstat.c
> torque-2.3.13/src/server/resc_def_all.c
> torque-2.3.13/src/server/req_quejob.c
> torque-2.3.13/torque.spec
>
> I'll provide what assistance I can in testing.
> That includes providing (off-list) the actual diffs of PSC's torque against the tarball, if desired.
>
> In the meantime, since -npernode didn't work, what is the right way to say:
> "I have 1 slot but I want to overcommit and run 16 mpi ranks".
>
> -Paul
>
>
> On Fri, Jan 31, 2014 at 3:20 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>
> On Jan 31, 2014, at 3:13 PM, Paul Hargrove <phhargrove_at_[hidden]> wrote:
>
>> Ralph,
>>
>> As I said this is NOT a cluster - it is a 4k-core shared memory machine.
>
> I understood - that wasn't the nature of my question
>
>> TORQUE is allocating cpus (time-shared mode, IIRC), not nodes.
>> So, there is always exactly one line in $PBS_NODESFILE.
>
> Interesting - because that isn't the standard way Torque behaves. It is supposed to put one line/slot in the nodefile, each line containing the name of the node. Clearly, SGI has reconfigured Torque to do something different.
>
>>
>> The system runs as 2 partitions of 2k-cores each.
>> So, the contents odf$PBS_NODESFILE has exactly 2 possible values, each 1 line.
>>
>> The values of PBS_PPN and PBS_NCPUS both reflect the size of the allocation.
>>
>> At a minimum, shouldn't Open MPI be multiplying the lines in $PBS_NODESFILE by the value of $PBS_PPN?
>
> No, as above, that isn't the way Torque generally behaves. It would appear that we need a "switch" here to handle SGI's modifications. Should be doable - just haven't had anyone using an SGI machine before :-)
>
>>
>> Additionally, when I try "mpirun -npernode 16 ./ring_c" I am still told there are not enough slots.
>> Shouldn't that be working with 1 line is $PBS_NODESFILE?
>>
>> -Paul
>>
>>
>>
>>
>> On Fri, Jan 31, 2014 at 2:47 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>> We read the nodes from the PBS_NODEFILE, Paul - can you pass that along?
>>
>> On Jan 31, 2014, at 2:33 PM, Paul Hargrove <phhargrove_at_[hidden]> wrote:
>>
>>> I am trying to test the trunk on an SGI UV (to validate Nathan's port of btl:vader to SGI's variant of xpmem).
>>>
>>> At configure time, PBS's TM support was correctly located.
>>>
>>> My PBS batch script includes
>>> #PBS -l ncpus=16
>>> because that is what this installation requires (not nodes, mppnodes, or anything like that).
>>> One is allocating cpus on a large shared-memory machine, not a set of nodes in a cluster.
>>>
>>> However, this appears to be causing mpirun to think I have just 1 slot:
>>>
>>> + mpirun -np 2 ./ring_c
>>> --------------------------------------------------------------------------
>>> There are not enough slots available in the system to satisfy the 2 slots
>>> that were requested by the application:
>>> ./ring_c
>>>
>>> Either request fewer slots for your application, or make more slots available
>>> for use.
>>> --------------------------------------------------------------------------
>>>
>>> In case they contain useful info, here are the PBS env vars in the job:
>>>
>>> PBS_HT_NCPUS=32
>>> PBS_VERSION=TORQUE-2.3.13
>>> PBS_JOBNAME=qs
>>> PBS_ENVIRONMENT=PBS_BATCH
>>> PBS_HOME=/var/spool/torque
>>> PBS_O_WORKDIR=/usr/users/6/hargrove/SCRATCH/OMPI/openmpi-trunk-linux-x86_64-uv-trunk/BLD/examples
>>> PBS_PPN=16
>>> PBS_TASKNUM=1
>>> PBS_O_HOME=/usr/users/6/hargrove
>>> PBS_MOMPORT=15003
>>> PBS_O_QUEUE=debug
>>> PBS_O_LOGNAME=hargrove
>>> PBS_O_LANG=en_US.UTF-8
>>> PBS_JOBCOOKIE=9EEF5DF75FA705A241FEF66EDFE01C5B
>>> PBS_NODENUM=0
>>> PBS_O_SHELL=/usr/psc/shells/bash
>>> PBS_SERVER=tg-login1.blacklight.psc.teragrid.org
>>> PBS_JOBID=314827.tg-login1.blacklight.psc.teragrid.org
>>> PBS_NCPUS=16
>>> PBS_O_HOST=tg-login1.blacklight.psc.teragrid.org
>>> PBS_VNODENUM=0
>>> PBS_QUEUE=debug_r1
>>> PBS_O_MAIL=/var/mail/hargrove
>>> PBS_NODEFILE=/var/spool/torque/aux//314827.tg-login1.blacklight.psc.teragrid.org
>>> PBS_O_PATH=[...removed...]
>>>
>>> If any additional info is needed to help make mpirun "just work", please let me know.
>>>
>>> However, at this point I am mostly interested in any work-arounds that will let me run something other than a singleton on this system.
>>>
>>> -Paul
>>>
>>> --
>>> Paul H. Hargrove PHHargrove_at_[hidden]
>>> Future Technologies Group
>>> Computer and Data Sciences Department Tel: +1-510-495-2352
>>> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
>>> _______________________________________________
>>> devel mailing list
>>> devel_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>>
>> _______________________________________________
>> devel mailing list
>> devel_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>>
>>
>> --
>> Paul H. Hargrove PHHargrove_at_[hidden]
>> Future Technologies Group
>> Computer and Data Sciences Department Tel: +1-510-495-2352
>> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
>> _______________________________________________
>> devel mailing list
>> devel_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>
>
> _______________________________________________
> devel mailing list
> devel_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>
>
>
> --
> Paul H. Hargrove PHHargrove_at_[hidden]
> Future Technologies Group
> Computer and Data Sciences Department Tel: +1-510-495-2352
> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
> _______________________________________________
> devel mailing list
> devel_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/devel