O(N) Garbage collection?

[Nick Sabalausky]

"retard" <re at tard.com.invalid> wrote in message 
news:ijp7pa$1d34$1 at digitalmars.com...
> Sat, 19 Feb 2011 14:32:27 -0500, dsimcha wrote:
>
>> On 2/19/2011 12:50 PM, Ulrik Mikaelsson wrote:
>>> Just a thought; I guess the references to the non-GC-scanned strings
>>> are held in GC-scanned memory, right? Are the number of such references
>>> also increased linearly?
>>
>> Well, first of all, the benchmark I posted seems to indicate otherwise.
>>   Second of all, I was running this program before on yeast DNA and it
>> was ridiculously fast.  Then I tried to do the same thing on human DNA
>> and it became slow as molasses.  Roughly speaking, w/o getting into the
>> biology much, I've got one string for each gene.  Yeast have about 1/3
>> as many genes as humans, but the genes are on average about 100 times
>> smaller.  Therefore, the difference should be at most a small constant
>> factor and in actuality it's a huge constant factor.
>>
>> Note:  I know I could make the program in question a lot more space
>> efficient, and that's what I ended up doing.  It works now.  It's just
>> that it was originally written for yeast, where space efficiency is
>> obviously not a concern, and I would have liked to just try a one-off
>> calculation on the human genome without having to rewrite portions of
>> it.
>
> Probably one reason for this behavior is the lack of testing. My desktop
> only has 24 GB of DDR3. I have another machine with 16 GB of DDR2, but
> don't know how to combine the address spaces via clustering. This would
> also horribly drag down GC performance. Even JVM is badly tuned for
> larger systems, they might use the Azul Java runtimes instead..

*Only* 24GB of DDR3, huh? :)

Makes me feel like a pauper: I recently upgraded from 1GB to 2GB of DDR1 ;) 
(It actually had been 2GB a few years ago, but I cannablized half of it to 
build my Linux box.)

Out of curiosity, what are you running on that? (Multiple instances of 
Crysis? High-definition voxels?)