[MonetDB-users] billions rows ?

eric Gtep eric.gtep at gmail.com
Sun Sep 28 12:38:59 CEST 2008


I'm testing for store large collections of genotypes on Monetdb.
In few words, a genotype is a little piece of information ( about 3 or
4 char ) related to an individual and a dna marker.
So a genotypes  looks like  contents of cell of sheet. Sometime we
need to access them by  individuals (cross marker), sometime by dna
marker (cross individual).
Today genotyping technologies provide  to get 600, 000,0000 genotypes by run.

Is MonetDB able to manage efficiently tables with several billions of rows ?

have you any example of application  with lot  ( > 1 billion) of rows
in only one table ?

I' ve compiled and installed monetDB/SQL on a Dell PE2950 with 2
quadcores intel xeon 2.66 Ghz and 4 GB RAM with success
I 've created a very basic table to store genotype :

Create table genotypes (

ind char(10),
mark char(10),

after I've populated this table with the "copy into table" statement
About 370 millions rows have been loaded after 7 minutes.
I haven't defined any index.

>From mclient I sent the query below :

select * from genotypes where alleles ="A A";

Immediatly the server became frozen and after about ten minutes a w
unix command showed : load average 16 !!!!
I stopped the query
Could you explain to me what has appended ?
Is this behaviour normal ?
Is it possible to restrict the cpu ressources allowed to monetDB ?

Thank you in advance for your advices and your help


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