[ensembl-dev] problem installing ensembl_compara_61

[Andy Yates]

Can you check the number of available file handles on your machine Jeff. In the last load of a compara schema we managed to crash our machine because the partitioning used on these tables caused a lot of open file handles which would cause the error you've seen.

If this is the case then iterate through each file & load in its own mysqlimport process. That should help

Andy

On 14 Apr 2011, at 12:17, Fedor Gusev wrote:

> I've run into similar issues and solved them by splitting dumps into
> smaller files and importing them one by one.
> 
> On Wed, Apr 13, 2011 at 9:43 AM, Jeff Hussmann <jeff.hussmann at gmail.com> wrote:
>> Hello all -
>> 
>> I am trying to install a local mysql copy of ensembl_compara_61. Everything
>> goes fine until my script attempts to import the file
>> peptide_align_feature_mus_musculus_57.txt into mysql (as part of executing
>> the command "mysqlimport -u root --password=$password --fields_escaped_by=\\
>> $database -L $base_directory/$database/*.txt #>> $log_file_name") at which
>> point I get the error message
>> 
>> "mysqlimport: Error: 1016, Can't open file:
>> './ensembl_compara_61/peptide_align_feature_mus_musculus_57.frm' (errno:
>> 24), when using table: peptide_align_feature_mus_musculus_57".
>> 
>> Every peptide_align_feature_*.txt alphabetically before mus_musculus imports
>> without complaint (and installation of ensembl_compara_60 several months ago
>> on a different machine went smoothly).
>> 
>> Any idea what is going wrong?
>> 
>>  - Jeff
>> 
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>> 
>> 
> 
> 
> 
> -- 
> Kind regards,
> Fedor Gusev.
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/