[BiO BB] open source ideas

Indraneel Majumdar indraneel at indialine.org
Thu Aug 23 11:49:22 EDT 2001

Hi Mark,

On Thu, Aug 23, 2001 at 08:07:23AM -0400, bioinfo wrote:
> 	Thanks as well Joel.  I wasn't trying to push anyone to code it.  It has
> been in the back of my mind for  awhile and I haven't had the time (and it

Yes, it happens to all of us all the time.
> 	Indraneel, what primary applications are you planning to use with the
> Beowulf?  I am in the process of setting up a HPC environment and have
> looked at Linux clusters.  I would be interested in hearing your thoughts
> about implementation and the applications you plan to use on it (if you can
> talk about it, that is...)

Thankfully, I can talk about what apps we are planning to run (the code
is open too but will be released only after papers are published, I wish
it could be made open now so people could point out the bugs). Actually
the primary aim is to use it as a cluster of workstations (COW) since
our multi processor (costly) servers running solaris are having a hard
time keeping up with the jobs. This probably shall be running code that
we develop inhouse, mainly protein structure analysis code. And since we
shall be making a beowulf anyway, it does not make sense not to use
MPICH and PVM, so hopefully we shall write our code to make best use of
the cluster as a parallel machine. And while we are at it, we shall also
be testing out the parallel implementations of different bioinformatics
software, when we require them.

The general plan is to use 8 diskless nodes using the AMD Athlon 1.4
GHz, Asus A7M266 motherboard, 512 MB DDR RAM, Netgear GA620 gigabit
ethernet provided we can get them. A 200 GB dual athlon (AMD 1.2 GHz,
Tyan thunder K7 S2462UNG, 2GB DDR RAM) file server per 8 nodes, and a
gateway (same as node with Ultra ATA disks). Currently I am trying to
search for maintainance and system software (like bwatch, schedulers
etc) to see what is available and which are easy to use, while
fulfilling our requirements.

I'll gladly accept any suggestions you have to offer.


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