Query: Blast on Scyld beowulf

[Ron Chen]

For batch jobs, you should use a batch system to queue
up the jobs.

PBS is always opensource:
http://www.openpbs.com

Sun recently opensourced Gridware:
http://gridengine.sunsource.net
http://www.sun.com/gridware

See RiboTargets
http://www.sun.com/software/gridware/quotes.html#ribotargets

"As a drug discovery company pioneering the use of
high throughput molecular docking software and
bioinformatics applications for antibiotic lead
development, we require a very high performance
system..."

The idea of having a batch system is that you submit
the jobs and leave the cluster does the work for you.
The batch system will start the jobs when the
resources are available, nights, weekends, etc.

The software can use the unused desktops at night
while returning the processor back to their owners
during daytime.


-Ron



--- Tim Chipman <timchipman at MailAndNews.com> wrote:
> I apologize if this topic has been hashed over a
> million times ; I've just 
> joined the list, and read through the last year
> worth of archived postings. No 
> clear success so though I should ask.
> 
> 
> 
> 
> 
> I'm curious about the feasibility of running
> sequence analysis apps (blast, 
> hmmer, fasta) on a scyld-beowulf setup.
> 
> 
> 
> 
> 
> I have seen some mention of "demos done by tigr at
> recent conferences of blast 
> on beowulf" ; other mention that "no free
> parallelized blast is yet available, 
> use fasta instead" ; and a great archive of
> discussion on the topic at the 
> URL,
> 
>  http://sapiens.wustl.edu/~ikorf/beowulf.html ,
> which highlights the 
> differences / possible more appropriate arrangements
> of batch job queues vs. 
> parallelized jobs.
> 
> Additionally, most discussions I've found on the
> 'net (via google searches) 
> pre-date scyld beowulf and typically take the
> approach of earlier more 
> traditional beowulf clusters where each node had a
> full OS install, apps & 
> data maintained locally (or via NFS shares) & the
> like.
> 
> Ideally, what I'm looking for is comments on how one
> can setup things to work 
> with a scyld beowulf (hence more straightforward to
> setup / maintain) and what 
> (if any) tweaks are required to encourage relatively
> efficient use of 
> resources.
> 
> I also suspect that the soon-to-be-available new
> scyld beowulf (which includes 
> PVM out of the box, not present previously?) will be
> a significant help.. but 
> of course I'm still a tad unclear. Sigh.
> 
> All this to say: If anyone has any pointers or
> comments relating to this topic 
> of (dna,protein) sequence analysis / comparison on
> scyld beowulf (even if it 
> is to say, "blargh! you must you *this* 'other'
> implementation..") ... then I 
> will certainly very much appreciate if people can
> e-mail me such info.
> 
> If I get a significant number of replies, I'll
> probably post a summary to the 
> list of the salient points, just to create a
> reference which will help prevent 
> other newbies like myself from asking the same
> questions in the near future.
> 
> Thanks very much,
> 
> 
> Tim Chipman 
> 
> 
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