[Beowulf] Can Beowulf with Linux run all the desktop applications

Tony Travis a.travis at abdn.ac.uk
Wed Feb 25 04:35:55 PST 2009

Tim Cutts wrote:
 > > On 24 Feb 2009, at 6:10 am, Rajib Bandopadhyay wrote:
 > >
 >> >> Dear friends,
 >> >> Can Beowulf with Linux run all the desktop applications? Will 
they run
 >> >> faster?
 > >
 > > Beowulf is Linux, so yes, it can run them.  Will it be faster?  No.
 > > Virtually nothing in the desktop application space can handle parallel
 > > running, and the additional network overhead of having the
 > > applications running on a server and displaying to your local display
 > > will most likely actually make things feel slower.

Hello, Tim.

I use our openMosix Beowulf as an NX terminal server and it works quite
well running 'desktop' applications. Where it scores most, of course, is
in automatically migrating computationally intensive bioinformatics or
statistics tasks running in e.g. R onto compute nodes.

A common problem that I encounter is that many biologists attempt to do
'everything' on their own desktop/laptop PC. As a consequence, their
underpowered PC's go catatonic while they try to run bioinformatics
programs that render them useless for normal 'office' applications...

My strategy is to provide a graphical desktop interface on the Beowulf
and encourage biologists to run their computationally demanding programs
there, in a familiar environment, but use their desktop/laptop PC for
'office' applications. This relieves them (and me) from the burden of
updating and supporting bioinformatics programs and databases on PC's.

I think there needs to be a reasonable balance between providing a
'familiar' Micro$oft Windows-like GUI on a Beowulf, so that biologists
can use it without an excessively steep learning curve, and some common
sense that divides the work they want to do appropriately between the
resources available. Much of what we do can be accomplished using a web
browser, with a Beowulf as a 'back-end' server, but there are also some
bioinformatics applications that are much easier to use in a native GUI.

Quite a lot of bioinformatics, as you know, is 'embarrasingly' parallel.
The fact that a lot of 'desktop' bioinformatics software doesn't use MPI
etc. to exploit the aggregate resources of a Beowulf doesn't mean that
it is pointless running it on a Beowulf. In fact, a Beowulf makes a good
terminal server and you can still use it to run parallel programs  ;-)


Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt

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