[gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

For the record.

gmx-4.6.4 hangs when number of threads is not a multiple of the number of nodes. 

XAvier.

On Nov 22, 2013, at 7:14 PM, XAvier Periole <x.periole at rug.nl> wrote:

> 
> Ok, tks. I'll try then :))
> 
> XAvier.
> 
> On Nov 22, 2013, at 4:31 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
>> Hardware detection and management of the results is greatly improved since
>> 4.6.1, so we would expect relevant changes, particularly if -pin off makes
>> it work (very slowly)
>> 
>> Mark
>> On Nov 21, 2013 7:37 PM, "XAvier Periole" <x.periole at rug.nl> wrote:
>> 
>>> 
>>> For the record:
>>> 
>>> I do not expect this issue to be affected by an update to gmx4.6.4 …
>>> 
>>> But the problem is fixed by turning the pin option off.
>>> 
>>> XAvier.
>>> 
>>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> It's not expected, but instead of trying to figure out what the issues
>>>> is with 4.6.1, you should really update to the latest version. If the
>>>> problem persists with 4.6.4, we shall have a closer look.
>>>> 
>>>> Cheers,
>>>> --
>>>> Szilárd
>>>> 
>>>> 
>>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole <x.periole at rug.nl>
>>> wrote:
>>>>> 
>>>>> Dears,
>>>>> 
>>>>> When running on multiple nodes I get GMX-461 hanging if the number of
>>> threads is not a multiple of the number of cores.
>>>>> 
>>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23
>>> threads per node) or 264 threads (24 threads per node) would work but
>>> defining 256 threads would result in mdrun to hang for long time.
>>>>> 
>>>>> That might be expected and not really an issue but that be nice if
>>> anyone knows why.
>>>>> 
>>>>> Thanks,
>>>>> XAvier.
>>>>> --
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