Hi Mary,
Please read the following page: http://ambermd.org/gpus/
This has all the information you should need for running correctly on GPUs.
All the best
Ross
On 3/14/13 8:20 PM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
>Sir,
>
>Infact this is a single GPU with 24 cores as i understand.
>bugixes have been done.
>But i will try the step u suggested.
>Also this work run without any problem in CPU workstaion.
>Hope the input doesnt contain any variable not compatible with pmemd!
>
>Thanking you
>
>On Thu, Mar 14, 2013 at 9:16 PM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Hi Mary,
>>
>> 8 GPUs is a lot to use you probably won't get optimal scaling unless you
>> have very good interconnect and only 1 GPU per node. Some things to try
>>/
>> consider:
>>
>>
>> >|--------------------- INFORMATION ----------------------
>> >
>> >| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> >
>> >| Version 12.0
>> >
>> >|
>> >
>> >| 03/19/2012
>>
>> You should update your copy of AMBER since there have been many tweaks
>>and
>> bug fixes. Do:
>>
>> cd $AMBERHOME
>> ./patch_amber.py --update
>>
>> Run this until it stops saying there are updates (about 3 or 4 times).
>>Then
>>
>> make clean
>> ./configure gnu
>> make
>> ./configure -mpi gnu
>> make
>> ./configure -cuda gnu
>> make
>> ./configure -cuda -mpi gnu
>> make
>>
>> >begin time read from input coords = 400.000 ps
>> >Number of triangulated 3-point waters found: 35215
>> >Sum of charges from parm topology file = -0.00000042
>> >Forcing neutrality...
>>
>> This happens with the CPU code sometimes - often when the inpcrd /
>>restart
>> file does not contain box information when a periodic simulation is
>> requested. Does it run ok with the CPU code? - Alternatively it may just
>> be running so slow over 8 GPUs that it hasn't even got to 500 steps yet
>>to
>> print anything. Try it with just one GPU and see what happens.
>>
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> ---------------------------------------------------------
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Adjunct Assistant Professor |
>> | Dept. of Chemistry and Biochemistry |
>> | University of California San Diego |
>> | NVIDIA Fellow |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>>not
>> be read every day, and should not be used for urgent or sensitive
>>issues.
>>
>>
>>
>>
>>
>>
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>>
>
>
>
>--
>Mary Varughese
>Research Scholar
>School of Pure and Applied Physics
>Mahatma Gandhi University
>India
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Received on Fri Mar 15 2013 - 09:00:03 PDT
