RE: AMBER: another sander bug?

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 25 Jan 2007 23:50:39 -0800

> --- src/sander/mdfil.f
> +++ src/sander/mdfil.f
> .@ -290,7 +290,7 @@ integer function iargc_wrap()
>
> if (numgroup > 1 .and. groups(1:1) /= ' ') then
> ia = 0
> - istart = 0
> + istart = 1
> iend = len(groupbuffer)
>
> do while (istart < iend)

I'll give you this one. It should only be an issue for Multisander MPI runs
with more than one group where this code is used in place of the iargc
intrinsic. However I think there may be more to it than this since this then
implies that the two loop indexes:

do while (istart < iend)
&
do while ( ie < iend .and. &
                  groupbuffer(ie:ie) /= ' ' )

should probably be <= rather than just <. Same is true for getarg_wrap.
Again these only affect multisander runs so I'll have dig up some test cases
and try it tomorrow.

> P.S. Although SANDER glorious module, it have a problem too:
> FORTRAN, FORTRAN and ... FORTRAN :-)

Not a problem, please feel free to re-write it in a language of your
choosing.

If it ends up running faster both in serial and in parallel than the current
code then I am sure that Dave will be happy for us to convert to your
version.

All the best
Ross

/\
\/
|\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.


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 28 2007 - 06:07:32 PST
Custom Search