AMBER Archive (2004)

Subject: Re: AMBER: Sander problem with different CPU

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Mar 05 2004 - 07:27:22 CST

this seems reasonable to me. with MPI, the calculation
is done differently- things are calculated in different order,
messages are passed, and there is some slight roundoff
difference that, over time, causes the trajectory to diverge
from the single processor result. The same happens on
single cpus of different type.
carlos

----- 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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