Hi Peng,
yes, I digged into the BLAT-suite years ago and found, what you describe. The authors (Jim Kent) stated that the Blat-tools (gfServer/gfClient/blat) do make heavy use of the computer memory (RAM), which would result in inefficient multithreading, because the more CPUs (on a single machine) the lessmemorybandwidth would remain per CPU, such that increasing the number of threads would cause the CPUs to wait for memory inquiries longer and longer. However,due to the upcoming multi-core technologies,available memory bandwidth per CPU has beensignificantlyimproved, such that this exlaination is sort of obsolete. So to overcome this single-threading-limitation you could do two things: 1) on a single machine running gfServer and gfClient concurrently: either use the blat executable (insead of gfClient/gfServer) or runmultiple gfClients against a single gfServer. To my experience four gfClients exhaust one gfServer. So on a two-core machine, run one gfServer and up to four gfClients. 2) on a bunch of machines, where one multi-core is running gfServer exclusively: unless available amount of RAM is a concern in your server, set up multiple gfServers on the same machine but on different tcp-ports and distribute your gfClients to connect to these ports manually. And a short comment on the support of multiple clients: gfServer *DOES* support multiple clients. It cues incoming client connections and processes alignments in fifo-fashion. But, and here you are right, gfServer does this sequentially and *NOT* parallelly. To have gfServer operate parallelly you need to follow one of the above workarounds. Hope, this helps. Cheers, Uwe Peng Yu <[email protected]> hat am 3. November 2011 um 04:26 geschrieben: > Hi, > > If I have one gfServer and multiple gfClient access the gfServer, the > gfServer will use 1 single cpu for 100%, the client will use only a > few percent of CPU. Also, according to the following discussion, it > seems that gfServer is single threaded. I want to confirm whether it > is so. Is there any update on gfServer to support multiple clients? > > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2007-July/000543.html > > -- > Regards, > Peng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
