It was not OSX specific and would probably only have affected you if you were using the blast8 output option. It looks like the problems were solved as determined from a sample job I am still running on one node. I need to check the cluster version next, but do not anticipate problems if the single node job completes without problems. Dave On Nov 2, 2004, at 3:23 AM, Ran Rubinstein wrote: > I was asking because I am using BLAT with bigger databases (but > smaller query load) on IRIX, with great success - but this could still > affect me when the system goes into production. Is it an OSX specific > issue? Were your problems solved? > > Thanks, > > David Adelson wrote: > >> 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 >>> >> >> _______________________________________________ >> 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 >