[ensembl-dev] MySQL 5.1?

Jan-hinnerk Vogel jhv at sanger.ac.uk
Thu Sep 16 00:49:50 BST 2010

HI Kiran,

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
seq_region end.

Hth and let me know if you got more questions,

Kind regards,

                      Jan-Hinnerk Vogel

Ensembl Genebuild Team Project Leader

On 15 Sep 2010, at 22:30, Kiran Mukhyala wrote:

> Hello,
> 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  
> future.
> 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  
> 5.1?
> Thank you in advance,
> -Kiran
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 2063 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20100916/22d86d1b/attachment.p7s>

More information about the Dev mailing list