[Biojava-l] Java Resource Management [a semi troll...]

Simon Brocklehurst simon.brocklehurst at cambridgeantibody.com
Mon Feb 10 13:44:34 EST 2003

Ewan Birney wrote:
> On Mon, 10 Feb 2003, Simon Brocklehurst wrote:
>>Ewan Birney wrote:
> True. Probably more of my reluctance is the relearning curve. But I often
> my algorithms try to use all the memory of the machine, and if I start
> running some extra overhead I wont be happy...
> ... but, yes, it is sheer laziness on my part with a shade of not wanting 
> to learn something which then wont work...

I'd be surprised(ish) if memory overhead caused you *too much* of a 
problem - it's more of a problem if you want to write programs with 
really small footprints.  However pushing the envelope, in terms of 
extracting the maximum from a given piece of hardware, clearly isn't one 
of Java's strengths.

Not sure how much memory you like to use in your software, so it might 
also be worth saying that writing Java programs that really use a *lot* 
of RAM (by a lot, I mean tens to hundreds of gigabytes) is at best going 
to be kinda cutting edge, and at worst might be completely impractical 
right now.

If you want to get up to speed with what current 64-bit JVMs are capable 
of in terms of performance with large heap sizes, there's a couple of 
articles at the URLs below to get started with:



There might be really significant productivity benefits to be had from 
at least *protoyping*/*designing* new algorithms in Java.  But to be 
convinced of this, you have to buy into the idea that Java really lets 
you focus more of your time on your problem (both design *and* 
implementation of solutions), and less on tracking down bugs and weird 
behaviours etc.  This is not an easy benefit to quantify.

Qualitatively people who have had success programming in Java, seem to 
feel it's a really productive language.  Personally, I can hardly bare 
to contemplate the idea of coding in C these days. To me, C feels 
restrictive compared to Java, in the way that FORTRAN felt restrictive 
after moving to C.

Dr Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics

Cambridge Antibody Technology
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Granta Park

Telephone: + 44 (0) 1763 263233
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