Hi
could you retry your runs WITHOUT the mpi? just run one gpu please and
let us know.
thanks
adrian
On 4/17/13 2:24 PM, HIMANSHU JOSHI wrote:
> Dear Gustavo,
> Thanks for your kind reply.
>
> I am already using ioufm = 1 (for binary trajectories )and iwrap = 1 .
>
> And the **** in the energy values is also there, eg .
> 1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
> **************
>
> And most importantly the same job is running well in cpu version of pmemd.
> Can it be a bug with pmemd.cuda.MPI ?
>
>
>
> On Wed, Apr 17, 2013 at 11:40 PM, Gustavo Seabra
> <gustavo.seabra.gmail.com>wrote:
>
>> Hi,
>>
>> what you are seeing in the restart file is likely *not* an error: the
>> numbers are just too large for the output format. As you run longer
>> calculations these days, this problem will just get more and more frequent.
>> Its also likely that you will find some "***" in the mdcrd file as well.
>>
>> Some possible solutions are:
>> 1. Use iwrap=1
>> 2. Use binary (NetCDF) files.
>>
>> Please see the manual for the details.
>>
>> Cheers,
>>
>> Gustavo Seabra
>> Professor Adjunto
>> Departamento de Química Fundamental
>> Universidade Federal de Pernambuco
>> Fone: +55-81-2126-7450
>>
>>
>> On Wed, Apr 17, 2013 at 3:03 PM, HIMANSHU JOSHI <himanshuphy87.gmail.com
>>> wrote:
>>> Dear friends,
>>>
>>> I am running pmemd.cuda.MPI for a system with approximately 1/2 million
>>> atoms with dna and wate, After energy min and equilibration, I tried to
>> do
>>> production run with constant pressure (flag : ntb =2 ntp =1) but its
>>> giving error *** in the restart file and energy values in output file
>> after
>>> running few steps (~ 30 ps). The same job with same input files is
>> running
>>> well in cpu version of pmemd (pmemd.mpi).
>>>
>>> Earlier the same system I ran with constant volume simulation (ntb = 1 )
>> in
>>> gpu with same pmemd.cuda.MPI and it ran well.
>>>
>>> So there is some problem with pmemd.cuda.MPI with npt simulation !!!
>>>
>>> Can anyone assure me.
>>>
>>> I have applied the latest bugfixes to amber 12 amber (Version 12.2) dated
>>> (01/10/2013) for both cpu and gpu.
>>>
>>> Looking forward for some constructive comments from amber community .
>>> Thanks for your kind attention.
>>>
>>>
>>> --
>>> *With Regards,
>>> HIMANSHU JOSHI
>>> Graduate Scholar, Center for Condense Matter Theory
>>> Department of Physics IISc.,Bangalore India 560012*
>>> ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
>>> सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
>>> <
>>>
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>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Wed Apr 17 2013 - 11:30:04 PDT
