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 >> https://bioinformatics.org/mailman/listinfo/bioclusters >> >> > > > -- > 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 > https://bioinformatics.org/mailman/listinfo/bioclusters >