Hi Brian,
Thanks for the input.
Ig issue is not our case. We did check that already.
Best.
Ying-chieh
-----Original Message-----
From: Brian Radak [mailto:radak004.umn.edu]
Sent: Tuesday, August 5, 2014 2:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input
but got different output (within statistical error)
Another (perhaps non-obvious), but much simpler explanation could be from
the use of a thermostat. The ntt = "2,3" options will only give identical
results if "ig" is set to a specific (positive?) integer value. This is
generally not done for performance reasons as well.
The only times I've ever tried to repeat results exactly is when running NVE
calculations.
Regards,
Brian
On Mon, Aug 4, 2014 at 1:06 PM, sun <sun.ntnu.edu.tw> wrote:
> On Mon, 04 Aug 2014 09:23:06 -0700, Ross Walker wrote
> > Hi Ying-chieh,
> >
> > It's not clear what you are asking here - or what you actually want
> > to
> do.
> > Are you trying to rerun the exact same simulation?
>
> - Yes. and at the first place, we expected to got exact the same
> results but did not. so we digged into old Amber Q&A and found those
> two possible causes in the last email.
>
> - What we did was run 10 ps NTV and followed by 200 ps NTP simulations.
>
> - the very first frame gave the same energy, but after 5 ps (we only
> printed every 5 ps in this case), the energies differed. The numbers
> were reasonable though.
>
> - after 200 NTP run, "Largestsphere to fit in unit cell has radius,
> Direct force subcell size and BOX X, Y, Z" in the output files are
> slightly different.
>
> - I think these results are reasonable then.
>
> > if yes this is NOT
> > possible with the CPU MPI code due to the load balancer.
>
> - Got it. I don't have knowledge of load balancer. ... need to study
> this more.
>
> > You can either 1)
> > Hack the code to turn off the loadbalancer, you may still get
> > divergence due to order of summation issues in other parts of the
> > code, vector libraries etc. 2) use the serial CPU code, 3) use the
> > GPU code - this is deterministic for both single and multi-GPU.
>
> - OK.
>
> - Ross, thanks for prompt reply.
>
> - Best.
>
> - Ying-chieh
> >
> > The FFT is completely controllable through the ewald namelist - you
> > can set the FFT dimensions. NFFT1, NFFT2, NFFT3. You can also
> > specify that it should always use a slab fft instead of switching to
> > columns at a set MPI task count - see the PMEMD section of the manual.
> >
> > With more details about what you actually want to do we can try to
> > help more.
> >
> > All the best
> > Ross
> >
> > On 8/4/14, 8:39 AM, "sun" <sun.ntnu.edu.tw> wrote:
> >
> > >Hi,
> > >
> > >I know this is not new, was discussed years back, and is NOT
> > >considered
> a
> > >problem. But further comments will help us more.
> > >
> > >I think in our case, possible causes are:
> > >
> > >1). order of addition of forces are different due to network
> > >indeterminacy, and the rounding error causes the difference.
> > >2). some verion of FFT which has feature of automatic algorithm
> selection
> > >depending on network condition is used in PME calculation.
> > >
> > >For 1), we are running with 24 cores on the CPUs of 12 cores each.
> > >
> > >Further comments are appreaciated.
> > >
> > >For 2), can someone describe more or point out where ther FFT
> > >source
> code
> > >is?
> > >
> > >Thank you very much.
> > >
> > >Ying-chieh
> > >
> > >
> > >_______________________________________________
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> > >AMBER.ambermd.org
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> >
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>
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
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Received on Mon Aug 04 2014 - 20:00:02 PDT
