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Re: [ccp4bb]: Parallelization of ccp4 programs on linux cluster ?



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Hej Martin!!

> I have a small cluster of Linux Redhat7.3 openMosix machines and would
> like to take advantage of program parallelization. Has anyone had
> success on parallelizing parts of the ccp4 suite under linux ?

PVM (Parallel Virtual Machine) is one example of a program system that is
commonly used in Linux clusters. However, no crystallographic program that
I know of has been programmed to make use of such a system. Strangly
enough, because many computational problems in crystallography are well
suited for parallelization. For example, it is possible to compute an
electron density map in different slices at the same time. Images can been
processed in parallel, and different models can be refined in parallel.  
But most CCP4 programs are so fast that it is probably not worth the
effort to parallelize them.

Ah, I just remembered that Arp/wARP has incorporated an rsh-based scheme
that enables you to use different processors.

PVM will give you a "virtual machine" consisting of your available CPUs,
and if you submit programs that are not parallelized, it will perform some
kind of load-balancing on those machines. It's kinda fun to play with, so
go look at http://www.epm.ornl.gov/pvm . There are RPMs in the standard
RH7.3 distribution, so it is easy!

Hygge-hejsa ;-)
/Morten

-- 
Morten Kjeldgaard <mok@imsb.au.dk>
Department of Molecular Biology, Aarhus University
Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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