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
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Received on Thu Oct 27 2011 - 02:00:03 PDT
