On Wed, Nov 13, 2002, Zhang Jian wrote:
>
> I run sander in parallel to calculate a protein with
> 36 residues and about 3000 waters, totally 8864 atoms.
>
> I gave the following command in a SGI IRIX machine,
> ==============================================
> mpirun -np 8 sander -O -i ...
> ==============================================
> then got
> ==============================================
> * NB pairs 206 317419 exceeds capacity
> ( 317571) 4
> SIZE OF NONBOND LIST = 317571
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in locmem.f
> ==============================================
> I examined the file locmem.f, ew_direct.f and
> ew_setup.f, then know that it is because
> num+numpack>maxnblst (206+317419>317571)
> in ew_direct.f.
> Since maxnblst=MAXPR, I changed the line
> MAXPR=MAXPR/numtasks
> to
> MAXPR=MAXPR/numtasks+1000
You probably need to change MAXPR by much more than 1000. Look for line
479 in locmem.f:
maxpr_float = natom * (cutoffnb + skinnb)**3 / 3.5d0
and change the denominator to a smaller value (say 3.0 or 2.5).
However, the fact that you have many more non-bonded interactions than the
program expects suggests that something is wrong with your coordinates (maybe
lots of things are on top of each other?? or the system is very
inhomogeneous??) Check (visually or otherwise) that the coordinates are OK.
"Ordinary" sets of coordinates should not have this sort of error.
> To increase maxnblst in ew_setup.f will result in same problem.
No; as the message indicates, you need to work with MAXPR in locmem.f.
>
> p.s. this error seems only occur when running sander
> in parallel.
Try a short minimization or equilibration on a single processor, then see
if those coords work OK in parallel. I suspect that somehow, you have a
fairly inhomogeneous system, so that the nonbonds are not being divided
roughly equally among processors.
..good luck...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
==================================================================
Received on Wed Nov 13 2002 - 16:51:07 PST
