Hi Tim Cutts, But as you can see in theses results using one database a quarter of NR or (NR/4) ~400 MB. Still there is a little difference. I'm using BLASTP But I will using BLASTN, can bee the difference to bee more bigger. Thanks Daniel Program Memory Time WUBLAT 1.4 1 GB Memory 0:02:49 WUBLAT 1.4 512 MB Memory 0:02:54 WUBLAT 1.4 256 MB Memory 0:02:41 WUBLAT 1.4 128 MB Memory 0:02:53 WUBLAT 1.4 64 MB Memory 0:02:56 Program Memory Time WUBLAT 2.0 1 GB Memory 0:04:20 WUBLAT 2.0 512 MB Memory 0:04:14 WUBLAT 2.0 256 MB Memory 0:04:10 WUBLAT 2.0 128 MB Memory 0:04:28 WUBLAT 2.0 64 MB Memory 0:04:50 Program Memory Time NCBI BLAST 1 GB Memory 00:02:49 NCBI BLAST 512 MB Memory 0:02:54 NCBI BLAST 256 MB Memory 0:02:41 NCBI BLAST 128 MB Memory 0:02:53 NCBI BLAST 64 MB Memory 0:02:56 ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Informática - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** ----- Mensagem original ---- De: Tim Cutts <tjrc at sanger.ac.uk> Para: HPC in Bioinformatics <bioclusters at bioinformatics.org> Enviadas: Segunda-feira, 26 de Março de 2007 2:14:16 Assunto: Re: [Bioclusters] Stranger Time to serial BLAST On 23 Mar 2007, at 6:35 pm, Daniel Xavier de Sousa wrote: > The difference using more memory, must be better. For > exempla, there is little difference using 1 GB and 512 MB for a > database of > 1.8GB (NR). The little difference is more accentuated to WUblast > 1.4 than NCIBI > BLAST. 1) You'd see a *much* more significant difference as soon as the machine has enough memory to cache the entire database in RAM. 2) Your test is also of BLASTP. I find that having sufficient RAM makes a lot more difference to BLASTN than to BLASTP - I suppose this is isn't surprising since nucleotide sequences are generally longer, so both the database and the DP matrix will be larger. > > 2 – What can I do to get more difference when I change my > RAM memory? Make sure you have enough memory that the entire database is resident in RAM, and you'll see a dramatic change in performance, especially when performing multiple queries one after another of the same database. We buy all our machines now with 2GB of RAM per core, which means on current dual-socket dual-core machines we always have at least 8GB RAM, and it makes an enormous difference (even the users noticed!) since it can cache an entire mammalian genome in RAM. Tim _______________________________________________ Bioclusters maillist - Bioclusters at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters __________________________________________________ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/