[Bioclusters] topbiocluster.org

Brodie, Kent brodie at mcw.edu
Thu Jun 23 12:34:00 EDT 2005

Hey- this is great.    I had done some similar work for a research
project here at MCW a few years back (mostly using performance tools
from NASA), but the work was lost when the sysadmin of the home I had
everything blew the server away without any backups.  Oooops.

Regardless, the stuff I had developed was a bit too narrow, and what I
just saw in your links appears to be good, and relatively portable,
stuff.   As soon as I have some time I'm going to give it a whirl.

How will we address issues such as differences between MPI
implementations, or other job schedulers (PBS PRO in our case) and such?

I look forward to a repository of results; I'd be more than happy to
submit them.   I see something along the lines of what can be found at
futuremark.com- a sort of gamers hardcore benchmarking submission
database deal......

--Kent C. Brodie
  Medical College of Wisconsin

> -----Original Message-----
> From: bioclusters-bounces+brodie=mcw.edu at bioinformatics.org
> [mailto:bioclusters-bounces+brodie=mcw.edu at bioinformatics.org] On
> Of James Cuff
> Sent: Thursday, June 23, 2005 11:08 AM
> To: bioclusters at bioinformatics.org
> Subject: [Bioclusters] topbiocluster.org
> Ok,
> So I put my money where my mouth is, (well 50 bucks anyway)
> http://topbiocluster.org is alive
> (well once the DNS gets pushed everywhere that is, I only set it last
> night, some of you may have to hang fire for a bit :-))
> We all talk a lot on this list about which cluster this, that and the
> other for application this that and the rest.  I also saw the last
> list yesterday, and to be frank I'm all done with linpak, we do other
> stuff, and it matters.
> There are two good benchmark tools I know of, both are currently
listed on
> the topbiocluster.org 'site', but I'm going to need a bit of help from
> folk to actually get this thing off the ground.
> My first thoughts are we build a list of what is actually out there in
> terms of bioclusters, bit like Glen's QA mail from the other day, then
> start to go about doing the benchmark gig.
> I'm also looking to the vendors a bit here (I know some of you folk
> out in here :-)).  Let me know off list if I'm opening up a can of
> or if you would like to help.  I want to keep this open, but there are
> often things best talked about off list...
> If we get this thing right it _will_ be a one stop shop for biocluster
> performance.
> I really want to capture NFS/SAN/storage figures in here, we all know
> not just about the number of CPUs.  We really need to see if we can
> capture the whole *cluster* performance, not just raw CPU
> So, let's open this up, and lets get talking...
> - How can we best start to fill in this web site?
> - Would people be happy to submit figures about their cluster?
> - What numbers shall we use for ranking?  What to run etc.
> - How do we capture storage aspects?
> I'm happy to do some of the grunt work here to collect information
> I guess it's best that we keep all the chat open on this list, and
> see what pops up.  As things come in, I'll start to flesh out the
> soem more.  Also, once we have a bit more of a scope as to what we
> actually rank, list and store, I'll be happpy to start on the mysql
> database, and get things rocking.
> submit at topbiocluster.org will work to send things in so I can get them
> into a database if we actually get going on it.
> Let's see what happens, this could be a bumpy ride, but it should be
> "Cabin crew, doors to automatic and cross check!"
> So I guess the floor is now open...
> Best,
> J.
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