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

[XAvier Periole]

OK, I'll try to get that tomorrow if not next week. 

In my case the issue was not to be able to run a mixture of 23 and 24 threads on a set of nodes with 24 CPUs. A few nodes had 23 threads assigned, the rest 24, per node. moving to 23 or 24 threads per node for all nodes fixed the issue.

XAvier.

On Nov 26, 2013, at 6:43 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> OK, thanks. We would like to fix that so that it does not hang, but we
> might need to know some more details. So far, I have failed to replicate
> your symptoms using 30 threads across 2 nodes with 32 total cores. However,
> my mpirun and/or OpenMP library was setting thread affinities for me. That
> may or may not have been the case for you. Can you please open an issue at
> redmine.gromacs.org with .tpr, .log, stdout, stderr for both a working and
> failing case?
> 
> Mark
> 
> 
> On Mon, Nov 25, 2013 at 3:25 PM, XAvier Periole <x.periole at rug.nl> wrote:
> 
>> 
>> 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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