AMBER Archive (2006)

Subject: Re: AMBER: paralelization and sander problems

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Fri Feb 17 2006 - 04:07:37 CST

Dear Carlos,
The ntpr is set to 1000, my problem was that i killed the two jobs (4p 8p) in
the first steps because i noticed that the error between the energies grew
up,
Now I carried out the jobs to the final and the errors only oscilates between
5 to 107 of 157,000 Kcal/mol and in an aleatory way.
This variations in the total energy in 4/8 processors can be normal,
I'm right ??

Thanks in advance.

Cristian Obiol
Biological Systems Modelling and Drug Design
Research Group
University of Barcelona

> in the third MD step (of ~1fs each) or third time that the
> energy is written in the output (which could be longer)?
> I get identical output for different # of cpus up to a few hundred
> steps of 1fs each.
>
> cristian obiol wrote:
> > Dear AMBER users,
> >
> > We have running a cluster of 12 processors in linux Debian platform
> > (mpich 1.2.6. and fortran intel_fc_80 compiler), and our results in
> > sander8 outputs are different depending the queue (4 or 8) that we are
> > using, around 0.0001 % in the final energy in the third step.
> >
> > We are disturbed because the test factor_ix for sander 8 is well passed
> > in both queues.
> >
> > Any comments are welcome,
> > Thanks in advance.
> >
> > Cristian Obiol
> > Biological Systems Modelling and Drug Design
> > Research Group
> > University of Barcelona
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