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Subject: Re: [OMPI users] SGE tight integration and ?tm? protocol for start
From: Sean Davis (sdavis2_at_[hidden])
Date: 2008-10-12 18:55:14


On Sat, Oct 11, 2008 at 6:48 PM, Reuti <reuti_at_[hidden]> wrote:
> Am 12.10.2008 um 00:21 schrieb Sean Davis:
>
>> <snip>
>>
>> Thanks, Pak. There is only one queue on the SGE system. Of course,
>> there are queue instances for each machine, which is the usual for
>> SGE.
>>
>> I'll give the -masterq a look. And the messages files for the
>> involved machines are devoid of anything useful; in fact, there is no
>> mention of these jobs, in general.
>
> Hi,
>
> to see more, you can set "loglevel log_info" in the scheduler configuration.
>
> Do you have more than one network card installed and gave them the same
> name?
> Your defined "tmpdir" is local on each machine?
> Do you redifine $TMPDIR in your .bashrc or anything else therein?

The tmpdir is the same on each machine and is local to the machine.
We do have two interfaces on each machine, one for a local subnet and
the other for an outside connection from each machine. The DNS is
resolved on the outside network. Why would behavior be different on
jobs that are run in a PE and only in $round_robin than for standard
serial jobs or jobs on only one node?

Sean

>>>> Date: Sat, 11 Oct 2008 07:56:02 -0400
>>>> From: Jeff Squyres <jsquyres_at_[hidden]>
>>>> Subject: Re: [OMPI users] SGE tight integration and ?tm? protocol for
>>>> start
>>>> To: Open MPI Users <users_at_[hidden]>
>>>> Message-ID: <3E62159B-14B9-4D44-96F6-0345079BCCE5_at_[hidden]>
>>>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>>>
>>>> I don't know much/anything about SGE (I'll leave that to the Sun folks
>>>> on
>>>> this list to reply), but I can tell you about the tm plugins: tm is the
>>>> protocol used by the PBS/Torque family of launchers. It looks like
>>>> your
>>>> Open MPI was built with TM support, but when you launch, it's likely
>>>> unable
>>>> to find the support libraries that it needs to load those plugins.
>>>>
>>>> This is probably fine in your case, since you want to use SGE, not TM.
>>>>
>>>>
>>>> On Oct 9, 2008, at 4:40 PM, Sean Davis wrote:
>>>>
>>>>> I am relatively new to OpenMPI and Sun Grid Engine parallel
>>>>> integration. I have a small cluster that is running SGE6.2 on linux
>>>>> machines all using Intel Xeon processors. I have installed OpenMPI
>>>>> 1.2.7 from source using the --with-sge switch. Now, I am trying to
>>>>> troubleshoot some problems I am having. I have created a simple job
>>>>> script:
>>>>>
>>>>> The job script looks like:
>>>>> #!/bin/bash
>>>>> #$ -S /bin/bash
>>>>> #$ -cwd
>>>>> mpirun --mca pls_gridengine_verbose 1 -np $NSLOTS hostname
>>>>>
>>>>> And the output on the error stream:
>>>>>>
>>>>>> more junksub.sh.e3574
>>>>>
>>>>> [shakespeare:05720] mca: base: component_find: unable to open ras tm:
>>>>> file not found (ignored)
>>>>> [shakespeare:05720] mca: base: component_find: unable to open pls tm:
>>>>> file not found (ignored)
>>>>> Starting server daemon at host "shakespeare.nci.nih.gov"
>>>>> Starting server daemon at host "octopus.nci.nih.gov"
>>>>> Server daemon successfully started with task id "1.shakespeare"
>>>>> [shakespeare:05733] mca: base: component_find: unable to open ras tm:
>>>>> file not found (ignored)
>>>>> [shakespeare:05733] mca: base: component_find: unable to open pls tm:
>>>>> file not found (ignored)
>>>>> error: executing task of job 3576 failed: failed sending task to
>>>>> execd_at_[hidden]: can't find connecti
>>>>> on
>>>>> [shakespeare:05720] ERROR: A daemon on node octopus.nci.nih.gov failed
>>>>> to start as expected.
>>>>> [shakespeare:05720] ERROR: There may be more information available
>>>>> from
>>>>> [shakespeare:05720] ERROR: the 'qstat -t' command on the Grid Engine
>>>>> tasks.
>>>>> [shakespeare:05720] ERROR: If the problem persists, please restart the
>>>>> [shakespeare:05720] ERROR: Grid Engine PE job
>>>>> [shakespeare:05720] ERROR: The daemon exited unexpectedly with status
>>>>> 1.
>>>>>
>>>>> However, there is no output in any output stream.
>>>>>
>>>>> And if I log into shakespeare and qrsh -q all.q_at_octopus, I immediately
>>>>> get a slot, so there isn't a "direct" problem with connecting.
>>>>>
>>>>> As I got a hint from folks on the SGE mailing list, it appears that
>>>>> qrsh is not being used for job submission. Any suggestions as to why
>>>>> this might be the case (or if it is the case)?
>>>>>
>>>>> Thanks,
>>>>> Sean
>>>>> _______________________________________________
>>>>> users mailing list
>>>>> users_at_[hidden]
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>
>>>>
>>>
>>>
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