[Bioclusters] BLAT users?

Ran Rubinstein bioclusters@bioinformatics.org
Mon, 01 Nov 2004 18:18:05 +0200

Hi David

Please elaborate on what does 'stop working' mean. The leaks program can 
find a lot more memory leaks and the program can still be correct - try 
looking at the process memory usage, and see if it grows over time, and 
whether it reaches the size of the physical RAM.


David Adelson wrote:

> This may be the wrong forum to look for an answer, but I thought I 
> would start here.
> We have been using BLAT on G4 Xserves (2GB RAM) for some time now.  
> Given the memory limitations, we carve up the database into chunks so 
> that we don't get a malloc error message telling us we have run out of 
> huge memory.  We then parallelize the job and run the chunks in 
> parallel on our cluster.  This works for modest query sizes (15,000 
> ESTs vs 1.2GB database-hs_chroms1-6).  However, when we scaled up to 
> larger queries (493365 ESTs vs 1.3GB database-bovine genome 
> 200,000scaffolds) we see blat just sort of stop working after a 
> while.  I ran the leaks program and found 91832 memory leaks, so the 
> problem seems to be memory related.  I would be curious to know if 
> anyone else has seen this type of behavior with BLAT.  I am in the 
> process of contacting Jim Kent about this, but thought it would not 
> hurt to ask some other knowledgeable computational biologists about this.
> thanks in advance,
> Dave Adelson
> Texas A&M University
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Ran Rubinstein
Dept. of Molecular Biology
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992