[Bioclusters] Stranger Time to serial BLAST

[Daniel Xavier de Sousa]

Hi for all,


 
For our work of parallel BLAST this is very important.


I’m executing the serial BLAST  program and have knew stranger (I guess) time
of execute with differences RAM memory.  Same with less memory, the difference of total
time between X memory and X/2 memory is little. 



Look:


 


PROGRAM NCBI BLAST == DATABASE NR (1.8 GB)


                        


Memory                    *TIME          * I/O               *SWAP


1 GB RAM              *0:03:01         *2610920        *9456


512 MB RAM         *0:03:10         *2670376        *18128


256 MB RAM         *0:03:35         *2713160        *21856


128 MB RAM         *0:04:22         *2751120         *30640


64 MB RAM           *0:05:30         *3050656         *64168


 


PROGRAM WUBLAST1.4 == DATABASE NR (1.8 GB)


Memory                     *TIME            *I/O                  *SWAP


1 GB RAM              *0:12:14         *2496144              *0


512 MB RAM         *0:13:37         *2500216              *0


256 MB RAM         *0:13:29         *2502376              *1720


128 MB RAM         *0:13:35         *2513432              *1760


64 MB RAM           *0:13:57         *2546192              *51048


 


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. 


 


So, I want help to two things:


1 – It results is normal, to WUBlast1.4 and NCBIBlast?


2 – What can I do to get more difference when I change my
RAM memory?


 


 


Thank very much, 


Daniel


 
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*        Daniel Xavier de Sousa                    *
*        Mestrando em Informática - PUC-Rio        *
*        E-MAIL : dsousaARROBAinf.puc-rio.br       *
*        Fone   : +55 21 35271500 - 4543           *
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