[gmx-users] Re: Gromacs 4.6 Installation under Cygwin

[Szilárd Páll]

I've a few more comments. First of all, please upload to redmine the full
mdrun.debug output!

It looks like the detection of the number of cores in your machine does not
work with cygwin because when you only set "-ntmp 1" N OpenMP threads
should be auto-set (N=#cores), but based on your output it seems that only
one is used. Could you please verify this? I am not sure whether this is an
inherent problem with cygwin or a bug (and as I don't have access to cygwin
I can't test).

Cheers,

--
Szilárd


On Tue, Feb 26, 2013 at 10:55 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> Hi,
>
> That is a likely cause. I can not comment with full certainty on the use
> of MARTINI with the Verlet scheme & without shifts, but I know that it is a
> topic that's being investigated and hopefully other can comment on it.
>
> However, the hanging should definitely not happen, but instead an error
> should be triggered, Now that we have quite well-defined problem, could you
> please file a bug report (redmine.gromacs.org)? A brief problem
> description with:
> - inputs;
> - a link to this discussion (
> http://www.mail-archive.com/gmx-users@gromacs.org/msg57828.html);
> - link to mdrun.debug in pastebin
> would be very helpful.
>
> Thanks,
>
> --
> Szilárd
>
>
> On Tue, Feb 26, 2013 at 10:11 PM, <toma0052 at umn.edu> wrote:
>
>> Hello,
>>     It looks like the problem might be in my mdp settings. I am using the
>> MARTINI force field which uses shift functions for both electrostatics and
>> vdw which are only available in the group-based cut-off scheme. OpenMP
>> doesn't seem to run with the group-based cut-off scheme, just Verlet.
>>     If I switch the cut-off scheme to Verlet and change the vdw and
>> coulombtype to cut-off and then add in potential-shift-verlet as modifiers
>> I can get the system to run. However, in doing this, am I mucking up the
>> force field?
>>
>> Thanks,
>> Mike
>>
>>
>>
>> On Feb 26 2013, Mirco Wahab wrote:
>>
>>  Hi Mike
>>>
>>> On 25.02.2013 17:25, toma0052 at umn.edu wrote:
>>>
>>>> ...
>>>> Estimated maximum distance required for P-LINCS: 0.810 nm
>>>> ...
>>>> Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
>>>>
>>>
>>> Do your runs use PME and/or P-LINCS?
>>>
>>> Maybe you could point out the problem by disabling
>>> each or both in yout .mdp file?
>>>
>>> I tested some systems (without PME) on cygwin/gmx
>>> 4.6 that worked ok. Probably glitches with the
>>> cygwin-provided fftw3?
>>>
>>> Maybe you could try to compile fftwf 3.3.3
>>> in single precision from source and link it to
>>> your gromacs build.
>>>
>>  http://www.fftw.org/fftw3_doc/**Installation-on-Unix.html#**
>> Installation-on-Unix<http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix>
>>
>>>
>>>
>>>
>>> M.
>>>
>>>
>>>  --
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>