AMBER Archive (2007)

Subject: Re: AMBER: pmend vs sander.MPI

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Dec 09 2007 - 11:35:48 CST

I tried in the light of the openmpi sander.MPI installation. In view of the
difficulties, and mostly in view of the difficulties encountered by other guys
with with unsupported installations, I had to recognize that I lack the time to
learn enough to come out. I can't disregard the lot chemical literature that
appears at no pace. A pity to be left at the slower sander.MPI right now with
heavy computations, though it is my fault.

With DOCK6.1 (mpich2) it was very simple: just pointing mpich2 to were openmpi
is installed.

Thanks
francesco

--- Robert Duke <rduke_at_email.unc.edu> wrote:

> Yes. The minimum number of processors is 1 (for which you must build the
> uniprocessor version in pmemd - the mpi version of pmemd requires a minimum
> of 2 processors, unlike sander). There currently is no OpenMPI
> configuration option, but you can probably look at the libraries and include
> files being used by sander.MPI, and will get it right.
> Regards - Bob Duke
> ----- Original Message -----
> From: "Francesco Pietra" <chiendarret_at_yahoo.com>
> To: "Amber" <amber_at_scripps.edu>
> Sent: Thursday, December 06, 2007 10:13 AM
> Subject: AMBER: pmend vs sander.MPI
>
>
> > Is pmend likely to improve performance with respect to sander.MPI for a
> > small
> > number of processors on dualopteron amd64 Linux/OpenMPI/intel compilers?
> > If
> > yes, which is the minimum number of processors to try if pmend defeats
> > sander.MPI in speed for a long MD (production)?
> >
> > Thanks
> > francesco pietra
> > Very likely the answer was already on the web, though I was unable to find
> > it.
> > I'll try to compile pmend according to the response.
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Never miss a thing. Make Yahoo your home page.
> > http://www.yahoo.com/r/hs
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

      ____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu