Res: [Bioclusters] Stranger Time to serial BLAST

Daniel Xavier de Sousa danielucg at
Mon Mar 26 20:58:44 EDT 2007

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.

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                    *
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----- Mensagem original ----
De: Tim Cutts <tjrc at>
Para: HPC in Bioinformatics <bioclusters at>
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

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.


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