Dear Vijay,
> The message is as below:
>
> * NB pairs 160 259074 exceeds capacity (
> 259200) 15
> SIZE OF NONBOND LIST = 259200
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in locmem.f
> [15] MPI Abort by user Aborting program !
> [15] Aborting program!
> p15_14666: p4_error: : 1
This problem occurs because the estimate that sander makes of the required
memory to store the bond list is too small. It is possible to increase the
value of maxpr by editing locmem.f but this problem generally should not
occur and is likely a sign of deeper issues with your actual simulation
system.
Typically I have seen this problem occur when the system density is
unphysically high - then you get many more pairs within the cutoff than
would be expected. It can also occur when you have a very small periodic
system - say you build something like NMA in a periodic box with no water
around it - this would likely cause this problem as well.
It can also occur when the cutoff used for a PME simulation is either very
large or very small (I forget which way around).
So, if you want to edit the code and fix it find line 429 of
$AMBERHOME/src/sander/locmem.f and change it from
maxpr_float = natom * (cutoffnb + skinnb)**3 / 3.0d0
to
maxpr_float = max(natom * (cutoffnb + skinnb)**3 / 3.0d0,500000)
Then cd $AMBERHOME/src/
make clean
make (or make parallel)
However, I strongly recommend that you take a careful look at your system
and see if you can find anything unusual. Or alternatively post the full
details to the list and we can comment on it.
All the best
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
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Received on Sun Apr 22 2007 - 06:08:01 PDT
