AMBER Archive (2002)

Subject: Re: Please give me a hand on understanding AMBER/MPI and locmem.

From: Margaret Cheung (cheung_at_physics.ucsd.edu)
Date: Sat Aug 03 2002 - 17:23:50 CDT

Dear Dr. Case,

Yes. it fixed the problem! Thanks a bunch! ^_^

Sincerely,
Margaret S. Cheung
Physics Department 0319
University of California, San Diego
9500 Gilman Drive,
La Jolla, CA 92093-0319
http://www-physics.ucsd.edu/~cheung

On Sat, 3 Aug 2002, David Case wrote:

> On Fri, Aug 02, 2002, Margaret Cheung wrote:
> >
> > I'm still using sander_classic and lately I've been trying
> > to increase the array size of CN1, CN2, ASOL, BSOL listed in parms.h, due
> > to
> > having a large number of NTTYPE (larger than default 60) in the system.
> > The forces and energies were calculated correctly if the executable
> > is not compiled for parallel tasks. However, when executables were
> > compiled with MPI libraries, all my outputs were wrong. (note that: if I
> > don't touch parms.h, everything works fine for sander_classic).
>
> If you change the size of the common blocks in parms.h, you also have to
> edit the lines in parallel.f that broadcast this info to all nodes:
>
> call mpi_bcast(RK,23320,MPI_DOUBLE_PRECISION,
> + 0,MPI_COMM_WORLD,ierr)
> call mpi_bcast(IPN,1200,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
>
> That is, the "23320" and "1200" are hardwired to the original sizes, and
> need to be changed when parms.h is changed. That is, 23320 has to be set to
> the total number of double precision variables in the parms common
> block....
>
> Yes, I know this is horrible progamming...it has been mostly fixed in the
> current releases (but not completely....) *Surely* by release 8 it will be
> completely fixed :-)
>
> There may be some other change I'm not remembering, but I think changing
> the lines above will fix your problem.
>
> ...regards...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
> ==================================================================
>
>