[Bioclusters] parallel blast???

[Hunter Matthews]

I looked at using it here, but frankly if it can't survive even a simple
reboot of one node in 6, its useless.


On Mon, 2002-09-30 at 18:30, David Thomas wrote:
> I just came from IEEE Cluster 2002 where there was a talk from the PVFS -- 
> parallel virtual file system.
> 
> I understand that the performance of this software is outstanding.
> It's not stable enough and fault-tolerant enough for the enterprise but it 
> might be interesting to test it out for ourselves on BLAST.  Has anyone
> played with it?
> 
> Dave
> 
> On Sat, Sep 21, 2002 at 07:01:34PM -0400, Chris Dagdigian (dag@sonsorol.org) wrote:
> Subject: Re: [Bioclusters] parallel blast???
> Message ID: <13526FA8-CDB6-11D6-8DCD-00039397F4C8@sonsorol.org>
> 
> > 
> > Last time I looked at them solid state disks were amazingly expensive. 
> > I was thinking about trying them out as swap devices on a big 
> > alphaserver but ended  up deciding to spend the $$ on more physical 
> > memory for the system.
> > 
> > In a blast or blast-farm context I'd probably just skip the solid state 
> > disks and instead put the databases into a ramdisk. That would be a 
> > cheaper approach since you don't really need the 
> > data-is-kept-when-power-goes-away or the backup hard disk that solid 
> > state systems give you. You also are limited by whatever pipe connects 
> > the SSD to the system (SCSI?).
> > 
> > Even ramdisks are of limited utility given the size and growth rate of 
> > some of the more common sequence databases -- you'd fall behind 
> > eventually.
> > 
> > Although -- if you put 1 or 2 GB ramdisks in each of your cluster nodes 
> > and then set up a system for chunking blast databases into 
> > ramdisk-friendly sizes you could build a really fast blast farm. In 
> > that context the performance bottleneck would then become the time and 
> > resources needed to merge the XML output from N queries against split 
> > databases into a single result file. I've seen such systems in the past 
> > and merging the results could in some cases take longer than the actual 
> > search did.
> > 
> > -Chris
> > 
> > 
> > 
> > On Tuesday, September 17, 2002, at 08:38  AM, Steve Gaudet wrote:
> > 
> > > Hello Chris,
> > >
> > >> <snip>
> > >>
> > >> You can have the fastest server on earth but if you searching with
> > >> blast against an NFS mounted database and your network or
> > >> fileserver is
> > >> slow then your blast searching speeds will be horrible. Give
> > >> me a small
> > >> number of speedy linux boxes and I can bring a $300,000
> > >> NFS/NAS system
> > >> to its knees. Storage does matter.
> > >
> > > Anyone ever look or try solid state disks?
> > >
> > >
> > >> <snip>
> > 
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
> 
> 
-- 
Hunter Matthews                          Unix / Network Administrator
Office: BioScience 145/244               Duke Univ. Biology Department
Key: F0F88438 / FFB5 34C0 B350 99A4 BB02  9779 A5DB 8B09 F0F8 8438
Never take candy from strangers. Especially on the internet.