AMBER Archive (2006)

Subject: Re: AMBER: Different results between serial and parallel runs in AMBER 8

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Mar 07 2006 - 07:45:01 CST

Dear Carlos,

I started from scratch, copied the files from original AMBER 8 CD, applied
all the patches, and compiled in both serial and parallel versions.

I used the following md.in file for serial and parallel runs (mpirun -np
2):

----------------------------- md.in ---------------------------------
    10 fs simulation
     &cntrl
      imin=0,
      ntx=1,irest=0,
      ntpr=1,ntwr=1,ntwx=1,
      ntc=2,ntf=2,ntb=1,cut=8,
      igb=0,
      ntr=0,
      nstlim=10,dt=0.001,nscm=5000,nrespa=1,
      ntt=1,
      tempi=300,temp0=300,ig=233,
      ntp=0,taup=2.0,pres0=1
     /
---------------------------------------------------------------------

As u suggested, I set ntt=1. The inpcrd did not have any velocity info in
it, and indeed all two .out files have exactly the same values in them.
This means that ntt=3 has some kind of a bug (or if it is called as a bug).
Thanks for the suggestions. Hope this can be fixed.

Best,

On Mon, 6 Mar 2006, Carlos Simmerling wrote:

> try not using Langevin (set ntt=1).
> have you applied all bug fixes?
> it may be that the random number sequence isn't the same for
> multiple cpus.
>
> Ilyas Yildirim wrote:
>
> >Dear All,
> >
> >I have a question on parallel and serial MD runs in AMBER 8. I have
> >created a system, which is a 4X4 base paired RNA, solvated in water. I
> >have created ordinary prmtop and inpcrd files. I compiled AMBER 8 both in
> >serial and parallel versions (renamed them as sander.serial and
> >sander.parallel). Then, I did a short run on this system, using
> >sander.serial and sander.parallel. Here are the first two step results:
> >
> >--------------------------- parallel run -------------------------------
> >.
> >.
> >.
> > 10 fs simulation
> > &cntrl
> > imin=0,
> > ntx=1,irest=0,
> > ntpr=1,ntwr=1,ntwx=1,
> > ntc=2,ntf=2,ntb=1,cut=8,
> > igb=0,
> > ntr=0,
> > nstlim=10,dt=0.001,nscm=5000,nrespa=1,
> > ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
> > ntp=0,taup=2.0,pres0=1
> > /
> >.
> >.
> >.
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 439.42 PRESS = 0.0
> > Etot = 4337.6493 EKtot = 6803.5776 EPtot = -2465.9282
> > BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
> > 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
> > EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
> > Ewald error estimate: 0.1351E-02
> > ------------------------------------------------------------------------
> > NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 345.43 PRESS = 0.0
> > Etot = 2882.4294 EKtot = 5348.3577 EPtot = -2465.9282
> > BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
> > 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
> > EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
> > Ewald error estimate: 0.1351E-02
> >.
> >.
> >.
> >-------------------------------------------------------------------------
> >
> >------------------------------ serial run -------------------------------
> >.
> >.
> >.
> > 10 fs simulation
> > &cntrl
> > imin=0,
> > ntx=1,irest=0,
> > ntpr=1,ntwr=1,ntwx=1,
> > ntc=2,ntf=2,ntb=1,cut=8,
> > igb=0,
> > ntr=0,
> > nstlim=10,dt=0.001,nscm=5000,nrespa=1,
> > ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
> > ntp=0,taup=2.0,pres0=1
> > /
> >.
> >.
> >.
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 439.42 PRESS = 0.0
> > Etot = 4337.6493 EKtot = 6803.5776 EPtot = -2465.9282
> > BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
> > 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
> > EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
> > Ewald error estimate: 0.1351E-02
> >-------------------------------------------------------------------------
> > NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 332.09 PRESS = 0.0
> > Etot = 2675.8869 EKtot = 5141.8152 EPtot = -2465.9282
> > BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
> > 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
> > EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
> > Ewald error estimate: 0.1351E-02
> >.
> >.
> >.
> >-------------------------------------------------------------------------
> >
> >I have used the same md.in file. In the above results, the NSTEP = 0 have
> >the same values (which is expected because the structures are exactly the
> >same). But when it becomes NSTEP = 1, the temp. values changes; in one
> >case it is 345.43 and in the other case it is 332.09. And as a result, the
> >rest of the NSTEPs have different values when serial and parallel runs are
> >compared. Is this an expected behavior?
> >
> >Best,
> >
> >
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu