[gmx-users] strategy of clustering 10nodes ?
lindahl at stanford.edu
Thu May 22 20:01:01 CEST 2003
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
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
On Thursday, May 22, 2003, at 10:12 AM, Taeho Kim wrote:
> 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
> 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.
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