[ensembl-dev] MySQL 5.1?
jhv at sanger.ac.uk
Thu Sep 16 00:49:50 BST 2010
we're currently running Mysql version: 5.1.39 on the instances we're
using for production.
The code works with InnoDB too - however we're using mainly MyISAM ,
only under very heavy
load I convert a table to InnoDB, ie mostly tables which have a lot of
reads/inserts and deletions
from multiple hosts, ie job + input_id_analysis. You will get better
read performance with MyISAM.
I would not go below 5.1.39 as there where some mysql performance
issues with left joins over empty tables
( ie the api does that with gene + gene-stable_id, transcript +
transcript_stable_id etc ). Also, there was a
mysql bug in one earlier 5.1 version which ignored an 'ordered by'
clause which caused trouble ( Exons did
not get returned ordered by their rank, which caused trouble for the
If you have big tables new partition feature is quite nice - we've
also seen that mysql queries on huge tables
speed up if you sort the entries in the table, ie sort the
dna_align_feature table by seq_region_id, seq_region_start and
Hth and let me know if you got more questions,
Ensembl Genebuild Team Project Leader
On 15 Sep 2010, at 22:30, Kiran Mukhyala wrote:
> A few of my local Ensembl database tables crashed recently and I am
> looking into the possible causes and options to avoid this in the
> Does the Ensembl API work with the InnoDB storage engine? My current
> server version is 5.0.83. Do you recommend upgrading the server to
> Thank you in advance,
> Dev mailing list
> Dev at ensembl.org
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