[Bioclusters] BLAT users?

David Adelson bioclusters@bioinformatics.org
Mon, 1 Nov 2004 10:48:05 -0600

Thanks.  Stops working means no output generated for a considerable 
time and 0%cpu usage for the process for some time.

Jim Kent worked on this over the weekend and actually found 3 memory 
leaks that he fixed.  The new source and binaries are available for 
download from his website/ftpsite as v31.

Dave Adelson

On Nov 1, 2004, at 10:18 AM, Ran Rubinstein wrote:

> 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.
> Regards,
> 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
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
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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
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
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