[Bioclusters] non linear scale-up issues?

[Rayson Ho]

UD: http://www.grid.org/stats/

325,033 years of CPU time collected


BOINC: http://boinc.berkeley.edu

Will be used by the next generation of SETI@home and other research
projects.

Rayson


--- David Gayler <dag_project@sbcglobal.net> wrote:
> however it doesn't seem like there is much in the
> way of
> cycle-stealing grid software solutions that are flexible, secure, and
> easy
> to use. I want to know what is missing currently to get these faster
> results
> reliably, despite hardware faults, etc.
> 
> I am aware of Condor (free), DataSynapse, Platform Computing, and
> others. I
> am interested in knowing what is, if anything, lacking in these
> solutions.
>  
> Thanks in advance.
> 
> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org
> [mailto:bioclusters-admin@bioinformatics.org] On Behalf Of
> bioclusters-request@bioinformatics.org
> Sent: Sunday, May 09, 2004 11:01 AM
> To: bioclusters@bioinformatics.org
> Subject: Bioclusters digest, Vol 1 #482 - 1 msg
> 
> When replying, PLEASE edit your Subject line so it is more specific
> than "Re: Bioclusters digest, Vol..."  And, PLEASE delete any
> unrelated text from the body.
> 
> 
> Today's Topics:
> 
>    1. Re: MPI clustalw (Guy Coates)
> 
> --__--__--
> 
> Message: 1
> Date: Sun, 9 May 2004 11:17:16 +0100 (BST)
> From: Guy Coates <gmpc@sanger.ac.uk>
> To: bioclusters@bioinformatics.org
> Subject: [Bioclusters] Re: MPI clustalw
> Reply-To: bioclusters@bioinformatics.org
> 
> > example web servers and services where you need rapid response for
> > single, or small numbers of jobs.
> 
> We (well, the ensembl-ites) do run a small amount of mpi-clustalw.
> The
> algorithm scales OK for small alignment (but they run quickly, so why
> bother?) but is horrible for large alignments.
> 
> These are figures for an alignment of a set of  9658 sequences,
> running on
> Dual 2.8GHz PIV  machines with gigabit.
> 
> Ncpus 	Runtime 	Efficiency
> ----  	------- 	-----------
> 2 	28:21:33	1
> 4   	19:49:05	0.72
> 8 	14:49:02	0.48
> 10  	14:09:41	0.4
> 16  	13:37:36	0.26
> 24  	13:00:30	0.18
> 32  	12:48:39	0.14
> 48  	12:48:39	0.09
> 64  	11:19:40	0.08
> 96  	11:30:09	0.05
> 128 	11:13:28	0.04
> 
> However, although the scaling is horrible, it does at least bring the
> runtime down to something more manageable. MPI clustalw only gets run
> for
> the alignments that the single CPU version chokes on. It may not be
> pretty, but at least you do get an answer, eventually. Horses for
> courses
> and all that.
> 
> 
> >
> > Guy/Tim - did you ever deploy that HMMer PVM cluster we talked
> about
> > for the Pfam web site?
> >
> 
> It's on the ever-expanding list of things to do. So, does anyone here
> have
> any opinions/experience  on the PVM verison of HMMer?
> 
> 
> Guy
> -- 
> Guy Coates,  Informatics System Group
> The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
> Tel: +44 (0)1223 834244 ex 7199
> 
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
> 
> 
> End of Bioclusters Digest
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters



	
		
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