AMBER Archive (2008)

Subject: Re: AMBER: Installing PMEMD with Amber10

From: Justin A. Lemkul (jalemkul_at_vt.edu)
Date: Sat May 31 2008 - 07:24:30 CDT

Quoting Atro Tossavainen <atro.tossavainen+amber_at_helsinki.fi>:

> > That is true for the main (Mac OS X) partition. Things are slightly
> > different on the Linux partition. Since the compiler locations and
> > versions are somewhat different, and the IBM compilers gave me fits,
> > I decided to go for options that I thought would be easiest to use
> > right off - the lam that was packaged with Amber10, and gfortran,
> > which I was more used to working with.
>
> The biggest problem there is that using any other MPI but the packaged
> MVAPICH deal that supports the InfiniBand hardware is probably not going
> to give you access to the IB interconnect, and then scaling to multiple
> nodes will be really, really poor. gfortran might not be your biggest
> problem.
>
> Persist! Get the real compilers and, in particular, the interconnect,
> to work for you, and you will see excellent performance and very good
> scaling. You can get AMBER and PMEMD to work without, as a sort of
> "proof of concept", but if you're dreaming of actually doing real work
> with anything more than two nodes...

Thanks for the tip. I'll work with our admins to get it figured out.

-Justin

>
> --
> Atro Tossavainen (Mr.) / The Institute of Biotechnology at
> Systems Analyst, Techno-Amish & / the University of Helsinki, Finland,
> +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul_at_vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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