Dear AMBER users,
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
BUT numpack also increased by 1000! faint! so the
problem remains same. To increase maxnblst in
ew_setup.f will result in same problem.
Of course I have UGLY method to deal with it, but
could anybody give me a better advice?
Thank you very much!
Best Regards,
Jian Zhang
p.s. this error seems only occur when running sander
in parallel.
=====
Jian Zhang, Dr
Institute for Biophysics
Nanjing University
22 Hankou Road, Nanjing 210093
P. R. China
Tel: 86-25-3594476
Fax: 86-25-3595535
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Received on Wed Nov 13 2002 - 02:56:39 PST
