AMBER Archive (2002)

Subject: Re: message during minimization

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Dec 18 2002 - 18:32:21 CST

Dear Iona
I'll guess that your problem is that you have too few atoms per processor.
A 20A water box has probably 1000 or less atoms. That makes
less than 10 atoms per processor. Unfortunately sander e.g. pme sander
may have somewhere some hidden assumptions about system size. Thus rather
than recognize its in trouble with some aspect of the simulation, it
simply dies. PME should I think be fine with that many processors,
although with more atoms.
Hope this helps
Tom Darden
 On Wed, 18 Dec 2002, Ioana Cozmuta wrote:

> Hello,
>
> Thanks for the replies and sorry for not being more explicit. In the
> output file this is the last thing it is written before the job stops.
>
> Here is my input file (it is for a cubic water box L=20A, using PBC and a
> cutoff of 8 A.)
>
> Initial minimization of the water box, 20A, PBC, 8.0 cut
> &cntrl
> ntx = 1, irest = 0, ntxo = 1,
> ntpr = 1,
> ntf = 1, ntb = 1,
> cut = 8.0, scee = 1.2,
> ibelly = 0, ntr = 0,
> imin = 1,
> maxcyc = 300,
> ncyc = 50,
> ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
> &end
>
> I assumed that amber will automatically use PME to calculate the
> electrostatic energy (PME seems to be faster and more accurate than simple
> Ewald) so I did not put anything explicit to ewald.
>
> Here is the command to submit the job:
>
> mpirun -np 128 $AMBERHOME/exe/sander -O -i ./box20Amin.in \
> -o ./box20Amin_128cpu.out \
> -p ./box20A.prmtop \
> -c ./box20A.prmcrd \
> -r ./box20A_128cpu.restrt \
> -ref ./box20A.prmcrd \
> -inf ./box20A.128cpu.mdinfo
> \
> Could this be a problem with the fact that PME is not designed to run on
> 128 processors? What is the limit for PME in terms of CPU's?
> What is the limit for normal ewald calculations in the same terms?
>
> Thank you,
> Ioana
>
>
>
> On Wed, 18 Dec 2002, David A. Case wrote:
>
> > On Tue, Dec 17, 2002, Ioana Cozmuta wrote:
> > >
> > > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > > using 5000.0 points per unit in tabled values
> > > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK
> > > switch(x): max rel err = 0.2088E-14 at 2.598900 | CHECK d/dx switch(x):
> > > max rel err = 0.7671E-11 at 2.757160
> > > ---------------------------------------------------
> >
> > Above is normal, and is not an error message. From the info given, I
> > can't tell why the job stops.
> >
> > ..dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================
> >
> >
>