[gmx-users] strategy of clustering 10nodes ?

[Jay Mashl]

I would agree with Erik to let the batch system take care of node allocation. I
can say that the OSCAR (oscar.sourceforge.net) clustering software for managing
jobs works;  I got it to work on an AMD cluster I have built recently.

There is one caution, though.  The version of LAM/MPI provided by OSCAR is
different than the default one that comes with gromacs, so you would have to
recompile gromacs.

Jay


On Thu, 22 May 2003, Erik Lindahl wrote:

> Hi Taeho,
>
> The best way to manage the nodes is to use a batch system like PBS -
> have a look at www.openpbs.org. That way you can keep them running
> 24/7, and there are also advanced features like fair-share scheduling
> avaliable.
>
> When it comes to interconnects there are two options: Either using
> something expensive (but fast) like myrinet, or use cheap ethernet with
> a central switch.
>
> Gigabit ethernet can provide slightly better performance if you find
> the price acceptable - Dell Computer sells pretty cheap switches
> nowadays...
>
> Cheers,
>
> Erik
>
>
>
>
> On Thursday, May 22, 2003, at 10:12  AM, Taeho Kim wrote:
>
> > Hi
> > We'd like to set up our own cluster, none commercial products, firstly
> > 10 nodes and go large later.  If you are in a situation with 2users
> > and 10nodes cluster, how could you split jobs / nodes?   i.e.
> > clustering nodes for multi-jobs like 2jobs (4nodes-6nodes, 8-2), 3jobs
> > (4-4-2), or 4jobs(3-3-2-2) ?  Is there anyone have similar
> > system/situation?
> >
> > And I wonder how important the network topology of cluster is to get
> > the best performance.  Do I need to optimize the hardware
> > interconnectivities of nodes? For example, one group of 4nodes need to
> > be connected each other, like ring topology.  If so, do I need to
> > compile Lam-mpi/fftw/Gromacs with a specific option to enable that
> > cluster group configuration ?
> >
> > Even though the size of simulation box will be another factor to
> > answer to this question, I'd be happy for any reference data.  I
> > appreciate any help or suggestions in advance.
> >
> > Taeho
> >
> >
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