AMBER Archive (2009)

Subject: Re: [AMBER] AMBER on a Mac Mini cluster PoC

From: Abdul Rehman Gani (amber_at_infostream.co.za)
Date: Mon Aug 17 2009 - 07:31:37 CDT

Alan wrote:
> Hi Abdul,

Hi Alan,

> Don't get confused. Amber is not ready for Xgrid directly as far as I
know.
> What used to happen is that Openmpi has a implementation suport for Xgrid
> and it used to work with openmpi 1.2.x but now it's broken with
1.3.x. See:
> https://svn.open-mpi.org/trac/ompi/ticket/1777

Okay, I think I am beginning to see how it all works. Or doesn't.

>
> Xgrid in openmpi is all about using your xgrid configuration to
submit your
> jobs from a openmpi application like e.g. pmemd as you'd do anyway. The
> advantage I see is that is quite simple and easy to setup a Xgrid cluster
> than go through lists os hosts, modifying file (e.g. /etc/hosts), ssh
> permission, etc.

I will be happy either way, but for now I am going to chase the OpenMPI
way. XGrid seems to have a few permission issues that I am having
trouble overcoming. I am going to take this problem over to the OpenMPI
list as Ross' suggestion of running make test.parallel on a single,
multi-cpu host did work. Maybe they can shed light on the problem I am
having.

Abdul

>
> Cheers,
> Alan
>

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