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Subject: Re: [OMPI users] memory per core/process
From: Reuti (reuti_at_[hidden])
Date: 2013-04-02 09:08:23


Am 30.03.2013 um 15:35 schrieb Gustavo Correa:

> On Mar 30, 2013, at 10:02 AM, Duke Nguyen wrote:
>> On 3/30/13 8:20 PM, Reuti wrote:
>>> Am 30.03.2013 um 13:26 schrieb Tim Prince:
>>>> On 03/30/2013 06:36 AM, Duke Nguyen wrote:
>>>>> On 3/30/13 5:22 PM, Duke Nguyen wrote:
>>>>>> On 3/30/13 3:13 PM, Patrick Bégou wrote:
>>>>>>> I do not know about your code but:
>>>>>>> 1) did you check stack limitations ? Typically intel fortran codes needs large amount of stack when the problem size increase.
>>>>>>> Check ulimit -a
>>>>>> First time I heard of stack limitations. Anyway, ulimit -a gives
>>>>>> $ ulimit -a
>>>>>> core file size (blocks, -c) 0
>>>>>> data seg size (kbytes, -d) unlimited
>>>>>> scheduling priority (-e) 0
>>>>>> file size (blocks, -f) unlimited
>>>>>> pending signals (-i) 127368
>>>>>> max locked memory (kbytes, -l) unlimited
>>>>>> max memory size (kbytes, -m) unlimited
>>>>>> open files (-n) 1024
>>>>>> pipe size (512 bytes, -p) 8
>>>>>> POSIX message queues (bytes, -q) 819200
>>>>>> real-time priority (-r) 0
>>>>>> stack size (kbytes, -s) 10240
>>>>>> cpu time (seconds, -t) unlimited
>>>>>> max user processes (-u) 1024
>>>>>> virtual memory (kbytes, -v) unlimited
>>>>>> file locks (-x) unlimited
>>>>>> So stack size is 10MB??? Does this one create problem? How do I change this?
>>>>> I did $ ulimit -s unlimited to have stack size to be unlimited, and the job ran fine!!! So it looks like stack limit is the problem. Questions are:
>>>>> * how do I set this automatically (and permanently)?
>>>>> * should I set all other ulimits to be unlimited?
>>>> In our environment, the only solution we found is to have mpirun run a script on each node which sets ulimit (as well as environment variables which are more convenient to set there than in the mpirun), before starting the executable. We had expert recommendations against this but no other working solution. It seems unlikely that you would want to remove any limits which work at default.
>>>> Stack size unlimited in reality is not unlimited; it may be limited by a system limit or implementation. As we run up to 120 threads per rank and many applications have threadprivate data regions, ability to run without considering stack limit is the exception rather than the rule.
>>> Even if I would be the only user on a cluster of machines, I would define this in any queuingsystem to set the limits for the job.
>> Sorry if I dont get this correctly, but do you mean I should set this using Torque/Maui (our queuing manager) instead of the system itself (/etc/security/limits.conf and /etc/profile.d/)?

Yes, or per queue/job.

> Hi Duke
> We do both.
> Set memlock and stacksize to unlimited, and increase the maximum number of
> open files in the pbs_mom script in /etc/init.d, and do the same in /etc/security/limits.conf.
> This maybe an overzealous "belt and suspenders" policy, but it works.
> As everybody else said, a small stacksize is a common cause of segmentation fault in
> large codes.

This way it would be fixed in the overall cluster and not per job - or? I saw situations, where with a limited virtual memory for a job, the stack size has to be set to a low value in range of a few ten megabytes only.

Whether such a request is possible depends on the queuingsystem though. In GridEngine it's possible, I'm not sure about Torque/PBS.

-- Reuti

> Basically all codes that we run here have this problem, with too many
> automatic arrays, structures, etc in functions and subroutines.
> But also a small memlock is trouble for OFED/Infinband, and the small (default)
> max number of open file handles may hit the limit easily if many programs
> (or poorly written programs) are running in the same node.
> The default Linux distribution limits don't seem to be tailored for HPC, I guess.
> I hope this helps,
> Gus Correa
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