No, this is not what I describe. Only the tiny portion of the target genome is loaded and the tiny portion of the query genome is loaded. Nothing is duplicated between processes. We regularly do this with genomes here and can get perhaps 100,000 processes running on a 1,000 CPU core super computer and get the complete genome to genome alignment done in a few hours. This is much more simple and efficient than trying to write a complicated parallel functional program that would be difficult to operate in a variety of operating systems. The operating system itself is optimized to manage the separate threads of the individual processes that it manages. We don't have to duplicate that complication.
--Hiram ----- Original Message ----- From: "Peng Yu" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Tuesday, June 15, 2010 2:15:54 PM GMT -08:00 Tijuana / Baja California Subject: Re: [Genome] parallel blat I just realized that this is an option. But would this waste the memory as each process has to load its own genome? On Tue, Jun 15, 2010 at 11:28 AM, Hiram Clawson <[email protected]> wrote: > It isn't necessary to run parallel blat. Simply run thousands > of copies of it at the same time on different parts of your > target and query sequences. > > --Hiram > > ----- Original Message ----- > From: "Peng Yu" <[email protected]> > To: [email protected] > Sent: Monday, June 14, 2010 8:21:32 PM GMT -08:00 Tijuana / Baja California > Subject: [Genome] parallel blat > > A simple google search and the search in the output of blat command > help do not show up any information on if blat can be run using > multiple CPUs. If it support multi-threading or parallelism, would you > please let me know what option I should use? > > -- > Regards, > Peng > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
