AMBER Archive (2004)

Subject: Re: AMBER: Sander problem with different CPU

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Sat Mar 06 2004 - 19:40:25 CST

Thanks for you & Carlos Simmerling

  I've compared my MD simulation with different cpu, and the difference
gets larger during the production dynamics. I make a comparison between
them about the RMSd, as follows,
http://bioinfo.ndhu.edu.tw/~yuann/TMP/1.gif

  I'd like to know how to explain my result reasonably, or I have to run
the simulation with only one CPU ?
Thank you very much!

Sincerely,
sychen.

On Fri, 5 Mar 2004 08:39:37 -0500
"Robert Duke" <rduke_at_email.unc.edu> wrote:

> Yuann -
> You should not be surprised. When sander runs on different numbers of
> cpu's, the calculations are done in a different order, because the
> calculations are distributed differently. This causes differences in the
> rounding errors, and ultimately the results will drift around a bit. The
> results you are seeing here are perfectly acceptable, and if you look at the
> pairlist totals, the same sorts of pairlists are being generated, the only
> difference is they are distributed in the 8 processor case.
> I typically see identical output for no more than around 300 steps in MD,
> and for some systems, a value or two will vary in far fewer steps in the
> last digit, due to the fact that the value as printed out is very near the
> "rounding point", and can easily go one way or the other (thus a value
> reported as 1.4378 vs 1.4377 may actually be reflecting an internal
> difference of 1.437750000000001 vs. 1.437749999999999).
> Regards - Bob Duke
> ----- Original Message -----
> From: "yuann" <yuann_at_bioinfo.ndhu.edu.tw>
> To: <amber_at_scripps.edu>
> Sent: Friday, March 05, 2004 7:29 AM
> Subject: AMBER: Sander problem with different CPU
>
>
> > Dear All,
> > Recently, I'm supprised that sander gives me different output
> > when it applies different number of CPU on IBM P690(AIX51). The
> > difference between them initiates at 550steps, and gets larger
> > at the NPT equlibrium stage, and also production dynamics.
> > System administrator for this machine told me all the AMBER bugfix
> > are updated to fix.36.
> >
> > I'm wondering if this is due to the arrangement of 'SIZE OF NONBOND LIST'
> > while running sander with different number of CPU?
> >
> >
> > Here are the output information at the 1st minimization step,
> >
> >
> >
> > ---input for sander minimization---
> > DNA_drug_complex_WAT 11578atoms 1st_Minimization 1000steps
> >
> > &cntrl
> > imin=1, ntx=1, maxcyc=1000, ncyc=200,
> > ntc=1, ntf=1,
> > ntb=1, ntp=0,
> > ntpr=50,
> > cut=9.0,
> > ntr=0,
> > &end
> > &ewald
> > &end
> >
> > --------main difference of output-------
> >
> > (1cpu):
> > | Local SIZE OF NONBOND LIST = 2461494
> > | TOTAL SIZE OF NONBOND LIST = 2461494
> >
> > (8cpu):
> > | Local SIZE OF NONBOND LIST = 370628
> > | TOTAL SIZE OF NONBOND LIST = 2461494
> >
> > ----------------------------------------
> >
> > (1cpu):
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 550 -4.6614E+04 9.7806E-01 2.2339E+01 O5' 543
> >
> > BOND = 3037.9037 ANGLE = 176.5293 DIHED = 555.3168
> > VDWAALS = 7046.6932 EEL = -56278.6230 HBOND = 0.0000
> > 1-4 VDW = 341.6471 1-4 EEL = -1493.6799 RESTRAINT = 0.0000
> >
> > ..........
> >
> > (8cpu):
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 550 -4.6614E+04 9.7805E-01 2.2339E+01 O5' 543
> > BOND = 3037.9031 ANGLE = 176.5292 DIHED = 555.3168
> > VDWAALS = 7046.6917 EEL = -56278.6196 HBOND = 0.0000
> > 1-4 VDW = 341.6471 1-4 EEL = 1493.6799 RESTRAINT = 0.0000
> >
> > ..........
> > --------------------------------------------------------------------------
> -
> >
> >
> > sincerely,
> > sychen.
> >
> > -----------------------------------------------------------------------
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>
>
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