[ensembl-dev] './ensembl_compara_75/member.frm' (errno: 24)

[Ed Gray]

Good info Stuart.  We have very few users and connections.  It would seem to me though that the root problem might be not destroying an object properly eh?

 

Anyone encounter/fix problems with a long running perl script using the ensembl api that generates too many file handles?
 



From: Stuart.Watt at oicr.on.ca
To: dev at ensembl.org
Date: Tue, 27 May 2014 14:32:42 +0000
Subject: Re: [ensembl-dev] './ensembl_compara_75/member.frm' (errno: 24)


I’ve hit that one before with MySQL running out of file handles. See: http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24. You can usually set the server variable open-files-limit (IIRC, by default in many configs, it’s set low). 


All the best
Stuart




On May 27, 2014, at 10:22 AM, Ed Gray <gray_ed at hotmail.com> wrote:


 
strange error:
 
here is what I did:
 
my @homs = @{$gene->get_all_homologous_Genes};

DBD::mysql::st execute failed: Can't open file: './ensembl_compara_75/member.frm' (errno: 24) at /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 168.
-------------------- EXCEPTION --------------------
MSG: Detected an error whilst executing SQL 'SELECT m.member_id, m.source_name, m.stable_id, m.version, m.taxon_id, m.genome_db_id, m.description, m.chr_name, m.chr_start, m.chr_end, m.chr_strand, m.sequence_id, m.gene_member_id, m.canonical_member_id, m.display_label, hm.cigar_line, hm.perc_cov, hm.perc_id, hm.perc_pos FROM  (member m, homology_member hm)  WHERE hm.homology_id = ? AND m.member_id = hm.peptide_member_id ': DBD::mysql::st execute failed: Can't open file: './ensembl_compara_75/member.frm' (errno: 24) at /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 168.
STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:169
STACK Bio::EnsEMBL::Compara::DBSQL::AlignedMemberAdaptor::fetch_all_by_Homology /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignedMemberAdaptor.pm:120
STACK Bio::EnsEMBL::Compara::DBSQL::AlignedMemberAdaptor::fetch_all_by_AlignedMemberSet /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignedMemberAdaptor.pm:88
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_Members /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:443
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_GeneMembers /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:489
STACK Bio::EnsEMBL::Gene::get_all_homologous_Genes /usr/local/share/perl/5.12.4/ensembl/modules/Bio/EnsEMBL/Gene.pm:857
STACK main::process_homologs newget_gene_info.pl:423
STACK toplevel newget_gene_info.pl:292
Date (localtime)    = Tue May 27 12:46:41 2014
Ensembl API version = 75
---------------------------------------------------

 		 	   		  
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