[Bioclusters] parallel blast???

Chris Dagdigian bioclusters@bioinformatics.org
Sat, 21 Sep 2002 19:10:12 -0400

On Tuesday, September 17, 2002, at 10:41  AM, Romualdo Zayas Lagunas 

> On Mon, 16 Sep 2002, Chris Dagdigian wrote:
>> an bring a $300,000 NFS/NAS system
>> to its knees. Storage does matter.
>> Blast performance also depends on you tune your DRM (gridengine or LSF
>> etc. etc.) and how  you adjust your workflow with respect to splitting
>> large databases, locally caching data on compute nodes etc. etc.
> I'm sorry, I didn't understand DRM, what does that mean???

Sorry for the acronym. DRM == "Distributed Resource Management". This 
is a generic term that is used to describe software systems such as 
PBS, Condor, Sun GridEngine, Platform LSF etc. etc.

DRM software is what allows you push work across a cluster or compute 
farm. At the most simple/basic level a DRM will give you the ability to 
bulk submit many jobs or tasks to the system which will then be 
executed and load-balanced across all the machines in your cluster or 

>> What are you trying to benchmark for? Picking the right CPU?
> Yes we want to buy a cluster and we want the "right" CPU.
>> Some people on this list may have already done this. My personal
> preference
>> is Intel Pentium III's right now because:
>> o P IV's are way too expensive
>> o P III's are dirt cheap
>> o There are a ton of dual-CPU motherboard options for the PIII 
>> allowing
>> me flexible choices of system packaging and vendor
>> o Athalon / AMDs are super fast but your motherboard choices are
>> limited and you need to be really  careful about cooling and 
>> ventilation
> But, PTM III is an "old" processor, it isn't????
> PTM IV, I agree with you...
> Athlon....I don't know enough about that...

Pentium IIIs are "old" if you listen to Intel :) They have a vested 
interest in moving people to the more expensive Pentium IV platform. 
While it is true that Intel will probably end-of-life them sometime 
soon they are still really good when it comes to price/performance 

Many of the large, production-grade and 'conservative' clusters and 
farms I've seen are built around PIII CPUs in the compute elements. 
They are rock solid stable and your choice of motherboards and products 
is still huge.  I've never heard of a PIII cluster falling over because 
of heat or flaky hardware or mainboard reliability problems. Your 
particular needs or benchmark results may point you towards a Pentium 
IV or AMD chip though so do your own testing...