[Bioclusters] Journalist request: linux cluster user feedback

Alan Hart bioclusters@bioinformatics.org
Fri, 20 Sep 2002 08:43:18 +0100

As below ...
Let me know if you want any more detail.
Alan Hart 
UNIX Manager 
Oxford GlycoSciences

> -----Original Message-----
> From:	Bernadette Toner [SMTP:btoner@genomeweb.com]
> Sent:	19 September 2002 17:44
> To:	bioclusters@bioinformatics.org
> Subject:	[Bioclusters] Journalist request: linux cluster user
> feedback
> Hi everybody -
> I'm conducting an informal survey on user trends for bioinformatics Linux
> clusters for BioInform newsletter and I'm looking for as much input as
> possible.
> The set of questions below has already been sent out to around 40 people
> who
> use Linux clusters for bioinformatics. If anyone on this list has a few
> minutes to add their two cents, that would be really helpful. Feel free to
> forward this e-mail to anyone else you know of who may be interested in
> participating.
> I'll post the results to this list once the article comes out - probably
> in
> about two weeks.
> Here's the questions (please respond directly to btoner@genomeweb.com):
> - How long have you had your Linux cluster running?
	1 year

> - How many nodes was your cluster originally? How many nodes is it now? Do
> you have plans to add more in the future?
	10 now 20 expect to go 100+ in 2003

> - Did you build your cluster yourself or use an independent consultant or
> hardware vendor (If so, please specify who)?
	Total self build (based on previous experience in the Oil Industry)

> - What type of processors make up your cluster?
	Intel 1.2 GHz's

> - What type of distributed resource management software (ie, LSF, PBS, Sun
> Grid Engine) do you use?
	Mosix Kernel level load sharing with Sun Grid queuing resource on

> - What bioinformatics/life science applications do you run on the cluster?
> Has this changed at all in the time you've had it running?
	Sometimes daily changes !  Blast, fgenes, clustalw, emboss, fasta,
iprscan and lots more ...

> - Do you use a parallel Blast application? If so, which one (ie, BeoBlast,
> NBlast, Blackstone PowerBlast, TurboBlast, Paracel Blast)?

> - Is the price/performance of your Linux cluster better or worse than you
> expected it to be? Please elaborate, if possible.
	Good although my opinion is take more man hours to support than an
equivalent UNIX (e.g. solaris) cluster

> - Is the total cost of ownership of your Linux cluster (including air
> conditioning/cooling, sys-admin costs, downtime, footprint, etc.) better
> or
> worse than you expected it to be? Please elaborate, if possible.

> - Overall, what are the biggest advantages to using a Linux cluster in
> bioinformatics? What are the biggest drawbacks?
	Opensource flexible build, low cost, easy to modify, good price
performance, lots of open source BioInf. code, dual boot NT & linux for more
flexibility, there is nothing else out there like "mosix" !

> - What future improvements would be on your wish list for Linux cluster
> technology for bioinformatics applications?
	More snmp c.f. mosix does CPU level load sharing, often apps. are
memory bound.
	More processors per nodes or kernel level snmp

> All responses will be treated as confidential. If you're willing and have
> the time to discuss any of these questions further, please let me know
> what
> day and time would be most convenient for a follow-up discussion.
	Not willing to discuss but interested in other responses.
	OGS config is confidential please.

> Thanks in advance to all -
> Bernadette Toner
> ......................................
> Bernadette Toner
> Editor, BioInform
> GenomeWeb LLC
> 212-651-5636
> btoner@genomeweb.com
> www.bioinform.com
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

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