[ensembl-dev] Biomart/martdb down?

[Rhoda Kinsella]

Hi Prem
When you are connecting to the marts it is advisable to use -A as the  
Ensembl marts are quite large. This option skips auto hashing and  
allows faster access to the tables.

mysql -uanonymous -hmartdb.ensembl.org -P5316 -A

If there are issues in future with the www.biomart.org servers, you  
can also access the Ensembl marts at http://www.ensembl.org/biomart/martview

I hope that helps,
Regards
Rhoda


On 22 Feb 2011, at 09:12, Premanand Achuthan wrote:

> Hi Steve
>
> Thanks for getting back. You are right, the biomart site is alright  
> now. But still have issues with mysql server.
>
> xxx at xxx-vm:~$ mysql -uanonymous -hmartdb.ensembl.org -P5316
> Welcome to the MySQL monitor.  Commands end with ; or \g.
> Your MySQL connection id is 85312
> Server version: 5.1.34 Source distribution
>
> Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
>
> mysql> use vega_mart_61;
> Reading table information for completion of table and column names
> You can turn off this feature to get a quicker startup with -A
>
> Database changed
> mysql> use ensembl_mart_61;
> Reading table information for completion of table and column names
> You can turn off this feature to get a quicker startup with -A
>
> ===
> I have waited here for more than 10 minutes, still it doesn't  
> switch. vega_mart_61 seems to be fine, but not able to use  
> ensembl_mart_61.
>
> Not sure if it has to do with my vms memory. Anyway, I can still go  
> ahead with the biomart service.
>
> Thanks
> Prem
>
>
>
>
>
>
>
> On 21/02/11 23:32, steve trevanion wrote:
>>
>> Hi Prem,
>>
>> Ensembl does not maintain the biomart website, please see http://www.biomart.org/contact.html 
>> . However their site does now appear to be OK
>>
>> We do maintain martdb.ensembl.org and that is responding fine for  
>> me. We have not had any other reports of problems, can you confirm  
>> you are using port 5316 ?
>>
>> Regards,
>>
>> Steve
>>
>> On 21/02/2011 17:35, Premanand Achuthan wrote:
>>>
>>> Hi All
>>>
>>> I have been trying to use biomart (http://www.biomart.org/biomart/martview/ 
>>> ) since afternoon, and I keep getting the following message
>>> 'Serious Error: Could not connect to mysql database  
>>> ensembl_mart_61: DBI connect('database=ensembl_mart_61;host=dcc-qa- 
>>> db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to  
>>> MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/ 
>>> biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/ 
>>> DBLocation.pm line 98'
>>>
>>> Also not able to connect to martdb.ensembl.org.ensembl_mart_61  
>>> through mysql client.
>>>
>>> Anybody having similar issues?
>>>
>>> Thanks
>>> Prem
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>
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>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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