[BioSQL-l] How fast to execute load_seqdatabase.pl parsing swiss-prot data into Oracle database?

[Hilmar Lapp]

On 10/9/03 1:00 AM, "Arthur Fen" <arthur.fen at vitagenomics.com> wrote:

> Dear sir:
> 
> I tried to load decompressed SWISSPROT data (Release 41.13 of
> 21-Jun-2003,"sprot.dat") into ORACLE database Server (ver 9.2.0.1.0 on
> Linux 9.0) by using the load_seqdatabase.pl script.
> 
> If I use following status to run the program, could you estimate the
> reasonable speed and time spanning for loading data?
> Environments:
> 2 AMD 2000+ CPU, 4 GB RAM, 80 GB HDD, Virtual swap 6G space.
> RedHat Linux 8.0,
> Perl v.5.8.1 (Compile on default setting by myself),
> BioPerl v.1.22, DBI v.1.37, DBD::Oracle v.1.14 and newest bioperl-db
> 
> 
> I got a relatively slow motion about 5,000 records/hr in comparing to
> mySQL.  Is it normal for using Oracle? Or I need to do some tuning for
> my system?

It should be able to go faster. Given your setup, if you want to use Oracle
for anything else than just toying around, you need more than one disk. Two
at minimum, three are better, most of the serious people have 4 or 5 mount
points. Ideally you can distribute archive & transaction logs, data
tablespace, and index tablespace each to separate disks.

Also, for the first upload don't supply --lookup to load_seqdatabase.pl.

    -hilmar

> 
> Thanks for your answer...
> 
> 
>                         Arthur
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
> 

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------