To add a few more information
My system consists of some peptides attached with adamantane group in
methanol solvent which I minimized through amber itself and the energies are
fine there as well.
On 27 October 2011 14:06, Ashutosh Shandilya <izerokelvin.gmail.com> wrote:
> Dear Sir
> This problem occur both with GPU (Amber11) and CPU(Amber10) code. In the
> beginning of simulation I am only heating for that the input file is as
> follows
> since I am increasing temprature gradually so I took a time step of 5ps and
> the equilibrating for 5ps
>
> &cntrl
> imin = 0, irest = 1, ntx=5, ntb=2, ntp = 1,
> taup=2.0, cut = 10, ntc = 2, ntf = 2, tempi = 295.0,
> temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 2500, dt = 0.001,
> ntpr =2500, ntwx = 2500, ntwr = 5000
> /
>
> In CPU with Amber 10 job stops around 87 to 97ps saying ERROR: max pair
> list cutoff must be less than unit cell max sphere radius! where as in GPUs
> it stops around 20ps of heating saying "STOP PMEMD Terminated Abnormally!"
> and the reason for that is Nan values in the coordiante file and the
> outfile.
> Energies are quite reasonable before getting the energy value as Nan in
> case of GPU.
>
> My job is not running both on CPU and GPU and yes GPU runs cant be started
> due to NaNs in the coordinate file.
> I think the there is some problem with my system but could not figure out
> as such may be something is missing. I have ran similar system without any
> problem.
>
> Looking forward for some suggestions.
>
> Thanks and Regards
> Ashtuosh Shandilya
>
> On 25 October 2011 21:59, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Ashutosh
>>
>> > I went through the mailing archives and found out the suggestions as
>> > adding
>> > bugfix 12 . I checked that by printing one step. Without the bugfix my
>> > job
>> > was terminated at 77ps for so many times after using bugfix 12 it
>> > terminated at 92ps and this was reproduced so many times tried with
>> > ntpr=1
>> > as well there seems to be no problem with that.
>>
>> I suspect your problem is actually with the system you are simulating
>> rather
>> than a bug in the code. But with so few clear details to go on it is
>> difficult to know. Does this problem occur purely with the GPU code or are
>> you also running on CPU?
>>
>> What type of simulation are you running, what does your input file look
>> like? - I would also suggest looking carefully at your output file, are
>> the
>> energies reasonable? What if you visualize it, did it blow up?
>>
>> > I am running my job in methanol solvent earlier I did not find any
>> > problem
>> > with it. I tried with GPU as well again there is some problem that
>> > could not
>> > read the coordinate file as cordinate file is all NaN.
>>
>> I am not sure I understand you here. Are you saying it runs fine on the
>> CPU
>> but not on the GPU? OR that the GPU run cannot be started due to the NaNs
>> in
>> the coordinate file?
>>
>> Note there have been numerous fixes for the GPU code so if you find the
>> problem is purely with the GPU code then you need to apply all the latest
>> bugfixes up to and including bugfix 17. After applying the bugfixes you
>> need
>> to make clean and then reinstall.
>>
>> 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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>
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Received on Thu Oct 27 2011 - 02:00:04 PDT
