[Beowulf] Re: building a new cluster

SC Huang schuang21 at yahoo.com
Wed Sep 1 21:29:38 PDT 2004

Yes, the "serial" FFTW seems to run faster than the one (downloaded from netlib.org) that I used in my MPI code. Since I need to do a few things between FFT's, so I just wrote my own "MPI"  version (by taking advantage of my particular data structure) without figuring out how to do it, perhaps more neatly :-), using FFTW. I did not use FFT provided by commercial vendors because I need to port the code across various platforms. Having source codes and being able to recompile is very important to me.
Thanks for the hints of Warewulf; that's something I did not know of. Will have to some homework. :-)

Tim Mattox <tmattox at gmail.com> wrote:
On Wed, 01 Sep 2004 21:46:25 -0400, Joe Landman
> SC Huang wrote:
> > Thanks, Jeff.
> >
> > 1. It is not frequency domain modeling. The FFT's, together with a
> > multigrid method, are used in solving a Poisson equation (for each
> > time step) in the solution procedure.

You should also take a look at FFTW http://www.fftw.org/ but unfortunately
their version 3.0 doesn't yet do MPI. The older 2.1.5 version does MPI.

> > 4. Thanks for the suggestions on the diskless or other file systems. I
> > will discuss that with my group members.
> This is an interesting way to go if your IO can be non-local, or if you
> just need local scratch space. It makes building clusters quite
> fast/easy.

You can use Warewulf to boot the nodes from ramdisks (via PXE or
Etherboot), and then use local disks for swap and scratch storage
(possibly as part of a PVFS/GFS/Luster/"did I forget one?"/GPFS file system).
See http://warewulf-cluster.org/ for more details. Disclaimer: Warewulf
was such a great system I became one of it's developers.

> > Also, I heard of the name "channel bonding" here and there. Is that
> > some kind of network connection method for cluster (to use standard
> > switches to achieve faster data transfer rate)? Can someone briefly
> > talk about it, or point me to some website that I can read about it? I
> > did some google search about it but the materials are too technical to
> > me. :( Is it useful for a cluster of about 30-40 nodes?
> There are plusses and minuses to channel bonding. Search back through
> the archives for details. I am not sure if the issues with latency and
> out of order packet send/receive have been addressed in 2.6.

I'm sure others can comment from experience, but my impression
has been that, at least for the time being, channel bonding with GigE
isn't particularly helpful, and can slow things down in some situations.
I'd hoped to have tested this myself already, but other research priorities
have been higher.

Good luck on your cluster design choices.
Tim Mattox - tmattox at gmail.com - http://homepage.mac.com/tmattox/

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