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Subject: Re: [OMPI users] programs are segfaulting using Torque & OpenMPI
From: W.Keegstra (W.Keegstra_at_[hidden])
Date: 2009-07-31 13:30:24


Hi,

Sorry to bother you again, but the system limits are default limits
for openSuSE 11.1, which are as far as I can see the same from
OS version `openSuSE 10.0.
Furthermore if I specify the node parameter such that the job is
running on only 1 node (either with 2 or 8 cores) is runs well.
A few weeks ago I put a lot of printf commands in the program that
is executed and and the segfaults are completely random through
the code. Even completely random on the nodes were the process
is running.
Every time tm is used because the process is spread over different
nodes is goes wrong, if tm is not used because either the process
is running on 1 node or openmpi is compiled without tm.
The only thing I can think of is that the environment (??) with tm
is different from that without tm.
May be the fact that the program is using mpi-open, mpi-read and
mpi-write to files has something to do with it. I tried for weeks
to figure out what the problem is and I still have no idea. In
my opinion everthing points to the tm interface.
For me the only solution now is sticking to the older programs,
e.g. torque 2.3.3 and openmpi 1.2.9, in this case tm is still not
needed and everything runs without problems, only 10-15% slower.

kind regards,
Wilko

On Fri, 31 Jul 2009 09:31:55 -0600
  Ralph Castain <rhc_at_[hidden]> wrote:
> You might check with your sys admin - or checkout the "ulimit" cmd.
> Depends on what the sys admin has set for system limits.
>
>
> On Jul 31, 2009, at 9:12 AM, Wilko Keegstra wrote:
>
>> Hi,
>>
>> Sofar I don't have a core file.
>> the weird thing is that the same job will run well when openmpi
>> is compiled without --with-tm.
>> Is the amount of memory, or number of open files different in both
>> cases?
>> How can I force unlimited resources for the job??
>> only then I will get a core file.
>>
>> kind regards,
>> Wilko
>>
>> Ralph Castain wrote:
>>> Ummm...this log indicates that OMPI ran perfectly - it is your
>>> application that segfaulted.
>>>
>>> Can you run gdb (or your favorite debugger) against a core file from
>>> your app? It looks like something in your app is crashing.
>>>
>>> As far as I can tell, everything is working fine. We launch and
>>> wireup
>>> just fine, then detect one of your processes has segfaulted - which
>>> triggers us to kill the remaining processes and terminate the job.
>>>
>>>
>>> On Jul 31, 2009, at 8:35 AM, Wilko Keegstra wrote:
>>>
>>>> Hi,
>>>>
>>>> I have recompiled openmpi with the --enabled-debug and
>>>> --with-tm=/usr/local
>>>> flags, and submitted the job to torque 2.3.7:
>>>>
>>>> #PBS -q cluster2
>>>> #PBS -l nodes=5:ppn=2
>>>> #PBS -N AlignImages
>>>> #PBS -j oe
>>>> /usr/local/bin/mpiexec -v -mca ras_base_verbose 5 -mca
>>>> plm_base_verbose
>>>> 5 --debug-daemons -machinefile $PBS_NODEFILE
>>>> /pcs/programs/grip/bin/RunAlignmentMPI DoAlign
>>>> /pcs/pc00/keegstra/work/hm/hemo-mix-psml.img
>>>> /pcs/pc00/keegstra/work/hm/hemo-mix-psml-ali.img 4 9 14 1 2497
>>>> 360.000
>>>> 64.000 /pcs/pc00/keegstra/work/hm/hemo-mix-pref.img 1 7 0
>>>>
>>>> and the job crashed almost immediately. i have attached:
>>>> tm.3.gz, Job output: AlignImages.o34.gz, momlog-20090731
>>>>
>>>> I hope you can help me,
>>>> kind regards,
>>>> Wilko
>>>>
>>>>
>>>> Ralph Castain wrote:
>>>>> Could you send the contents of a PBS_NODEFILE from a Torque 2.3.7
>>>>> allocation, and the man page for tm_spawn?
>>>>>
>>>>> My only guess would be that something changed in those areas as
>>>>> we don't
>>>>> really use anything else from Torque, and run on Torque-based
>>>>> clusters
>>>>> in production every day. Not sure what version we have here,
>>>>> though I
>>>>> believe it is pretty current (will check).
>>>>>
>>>>> You also might want to configure OMPI 1.3.3 with --enable-debug.
>>>>> You
>>>>> could then do a run with -mca ras_base_verbose 5 -mca
>>>>> plm_base_verbose 5
>>>>> --debug-daemons on your mpirun cmd line to get a step-by-step
>>>>> diagnostic
>>>>> output of the interaction with Torque. Should give us some idea
>>>>> of where
>>>>> the failure is occurring.
>>>>>
>>>>> Ralph
>>>>>
>>>>> On Jul 31, 2009, at 7:20 AM, Wilko Keegstra wrote:
>>>>>
>>>>>> hi,
>>>>>>
>>>>>> I have the following problem:
>>>>>>
>>>>>> I am using openmpi 1.3.3
>>>>>>
>>>>>> programs (directly and from scripts) submitted with mpiexec are
>>>>>> running
>>>>>> fine.
>>>>>>
>>>>>> programs (directly and from scripts) submitted through Torque
>>>>>> 2.3.7
>>>>>> with openmpi compiled with --with-tm (and torque-devel) installed
>>>>>> give segfaulting of the programs.
>>>>>>
>>>>>> programs submitted through Torque 2.3.7 directly with openmpi
>>>>>> compiled without --with-tm (and NO torque-devel installed) run
>>>>>> fine
>>>>>> however mpiexec programs from script (script submiited through
>>>>>> torque)
>>>>>> are only running on 1 node, so I need openmpi compiled with --
>>>>>> with-tm
>>>>>>
>>>>>> We also have a cluster running with openmpi 1.2.9 compiled without
>>>>>> --with-tm in combination with torque 2.3.3 and everything is
>>>>>> running
>>>>>> fine, so NO segfaults and mpiexec from script also running on the
>>>>>> nodes selected at submitting time.
>>>>>>
>>>>>> I don't have errors on log files only on the job log file:
>>>>>>
>>>>>> ---------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> mpiexec noticed that process rank 7 with PID 3150 on node
>>>>>> rugem21.chem.rug.nl exited on signal 11 (Segmentation fault).
>>>>>> --------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>> Could anyone please help me,
>>>>>> many thanks in advance
>>>>>> Wilko Keegstra
>>>>>>
>>>>>> --
>>>>>> +-------------------------------------------------------------+
>>>>>> | Dr. Wilko Keegstra priv.phone: +31594514153,+31610477915 |
>>>>>> | Groningen University email: W.Keegstra_at_[hidden] |
>>>>>> | Groningen Biomolecular Sciences and Biotechnology Institute |
>>>>>> | Nijenborgh 4 phone: +31503634224 |
>>>>>> | 9747 AG GRONINGEN fax : +31503634800 |
>>>>>> | The Netherlands |
>>>>>> +-------------------------------------------------------------+
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> users_at_[hidden]
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>
>>>>> _______________________________________________
>>>>> users mailing list
>>>>> users_at_[hidden]
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>
>>>> --
>>>> +-------------------------------------------------------------+
>>>> | Dr. Wilko Keegstra priv.phone: +31594514153,+31610477915 |
>>>> | Groningen University email: W.Keegstra_at_[hidden] |
>>>> | Groningen Biomolecular Sciences and Biotechnology Institute |
>>>> | Nijenborgh 4 phone: +31503634224 |
>>>> | 9747 AG GRONINGEN fax : +31503634800 |
>>>> | The Netherlands |
>>>> +-------------------------------------------------------------+
>>>> <tm.
>>>> 3
>>>> .gz
>>>> >
>>>> <
>>>> AlignImages
>>>> .o34
>>>> .gz
>>>> ><momlog-20090731.gz>_______________________________________________
>>>>
>>>> users mailing list
>>>> users_at_[hidden]
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>> --
>> +-------------------------------------------------------------+
>> | Dr. Wilko Keegstra priv.phone: +31594514153,+31610477915 |
>> | Groningen University email: W.Keegstra_at_[hidden] |
>> | Groningen Biomolecular Sciences and Biotechnology Institute |
>> | Nijenborgh 4 phone: +31503634224 |
>> | 9747 AG GRONINGEN fax : +31503634800 |
>> | The Netherlands |
>> +-------------------------------------------------------------+
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
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