AMBER Archive (2008)

Subject: Re: AMBER: Installing PMEMD with Amber10

From: Justin A. Lemkul (jalemkul_at_vt.edu)
Date: Fri May 30 2008 - 05:42:53 CDT

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

> Justin,
>
> > I am installing Amber10 on our cluster (Apple Xserve G5 nodes). The
> > OS on the nodes is Yellowdog Linux. The installation of AmberTools
> > and Amber10 proceeded with no problems, but I am having some difficulty
> > installing PMEMD. I have installed lam-7.1.3 that came with Amber10,
> > and am specifying the following:
> >
> > ./configure macosx_ppc gfortran lam pubfft nobintraj
>
> If the system you're talking about is this
>
> http://www.arc.vt.edu/arc/SystemX/
>
> you have access to MVAPICH that runs over InfiniBand and the IBM XL
> compilers... Am I missing something?

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.

-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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