[Openmd-users] Update
Dan Gezelter
gezelter at nd.edu
Fri Sep 3 13:47:17 EDT 2010
Brett,
I'm having trouble reproducing this here with the files you sent. Any chance you can give me details on OS version, compiler version, MPI version, etc.? I can try on a couple of more architectures, but I want to get as close as possible to what you are running on.
--Dan
On Sep 1, 2010, at 11:14 AM, Brett Donovan wrote:
> Hi Dan
>
> These are what I am using. Let me know if you want more details on the
> actual machines/compilers etc etc. As far as I know these are the gcc
> compiled compiled libraries. not intel. Thanks.
>
> Best wishes
>
> Brett
>
> On Wed, Sep 1, 2010 at 1:33 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>> Brett,
>>
>> Can you send me the md / frc files you used for this? It sounds like a bug in the computation of the conserved quantity, although it should be using the MPI-safe routines from SimInfo and Thermo for the necessary quantities. Why it would pop up in NPTxyz and not the other integrators is a bit of a mystery. Do you also get this problem if you use NPTi?
>>
>> --Dan
>>
>>
>> On Aug 31, 2010, at 6:44 AM, Brett Donovan wrote:
>>
>>> No problem, they start pretty early over there, many have another
>>> month here or so before they come back.
>>>
>>> Just noticed a little feature here is that when running on our server
>>> [this time with the new update], I get the following difference
>>> between running in a single processor and on the MPI version.
>>>
>>> The single processor [non MPI] runs whilst the MPI version gives the following:
>>>
>>> StatWriter detected a numerical error writing: Conserved Quantity
>>>
>>> Any ideas what this might be? Its on the NPTxyz ensemble that this is
>>> occuring - where I have changed over from NVT to NPTxyz
>>>
>>> Thanks
>>>
>>> Brett
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Fri, Aug 27, 2010 at 7:09 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>>>> Brett,
>>>>
>>>> Sorry I've been out of touch lately. The freshman chemistry students have descended en masse, and I'm still a little swamped.
>>>>
>>>> --JDG
>>>>
>>>> On Aug 27, 2010, at 10:36 AM, Brett Donovan wrote:
>>>>
>>>>> Hi Dan
>>>>>
>>>>> I think we might have sourced the problems with the different versions
>>>>> of OMD running on different machines. I think the issues of the
>>>>> energies blowing up was possibly down to the code not updating on the
>>>>> super computing cluster and us running an old copy. I am told by the
>>>>> guys in charge of the cluster they were using the tarballs [not the
>>>>> SVN] and that they might not have been the latest version to update
>>>>> from. They have now updated and built from the SVN copy and that seems
>>>>> all good.
>>>>>
>>>>> I cannot seem to recreate any issues with the sin term in the cosine
>>>>> bend, and my calculation from my development version does not differ
>>>>> so hopefully...all is well and the original implementation should hold
>>>>> well.
>>>>>
>>>>> Best wishes
>>>>>
>>>>>
>>>>> Brett
>>>>>
>>>>> Have a great weekend!
>>>>
>>>> ***********************************************
>>>> J. Daniel Gezelter
>>>> Associate Professor of Chemistry
>>>> Director of Graduate Admissions
>>>> Department of Chemistry and Biochemistry
>>>> 251 Nieuwland Science Hall
>>>> University of Notre Dame
>>>> Notre Dame, IN 46556-5670
>>>>
>>>> phone: +1 (574) 631-7595
>>>> fax: +1 (574) 631-6652
>>>> e-mail: gezelter at nd.edu
>>>> web: http://www.nd.edu/~gezelter
>>>> ************************************************
>>>>
>>>>
>>>>
>>
>> ***********************************************
>> J. Daniel Gezelter
>> Associate Professor of Chemistry
>> Director of Graduate Admissions
>> Department of Chemistry and Biochemistry
>> 251 Nieuwland Science Hall
>> University of Notre Dame
>> Notre Dame, IN 46556-5670
>>
>> phone: +1 (574) 631-7595
>> fax: +1 (574) 631-6652
>> e-mail: gezelter at nd.edu
>> web: http://www.nd.edu/~gezelter
>> ************************************************
>>
>>
>>
> <Membrane_Therm.md><FF_Dipole.frc>
***********************************************
J. Daniel Gezelter
Associate Professor of Chemistry
Director of Graduate Admissions
Department of Chemistry and Biochemistry
251 Nieuwland Science Hall
University of Notre Dame
Notre Dame, IN 46556-5670
phone: +1 (574) 631-7595
fax: +1 (574) 631-6652
e-mail: gezelter at nd.edu
web: http://www.nd.edu/~gezelter
************************************************
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