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<body class='hmmessage'><div dir='ltr'>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?<BR>
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Anyone encounter/fix problems with a long running perl script using the ensembl api that generates too many file handles?<BR> <BR>
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From: Stuart.Watt@oicr.on.ca<BR>To: dev@ensembl.org<BR>Date: Tue, 27 May 2014 14:32:42 +0000<BR>Subject: Re: [ensembl-dev] './ensembl_compara_75/member.frm' (errno: 24)<BR><BR>
<DIV>I’ve hit that one before with MySQL running out of file handles. See: <A href="http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24" target=_blank>http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24</A>. You can usually set the server variable open-files-limit (IIRC, by default in many configs, it’s set low). </DIV>
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<DIV>All the best</DIV>
<DIV>Stuart</DIV>
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<DIV>On May 27, 2014, at 10:22 AM, Ed Gray <<A href="mailto:gray_ed@hotmail.com">gray_ed@hotmail.com</A>> wrote:</DIV><BR class=ecxApple-interchange-newline>
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<DIV dir=ltr> <BR>strange error:<BR> <BR>here is what I did:<BR> <BR>my @homs = @{$gene->get_all_homologous_Genes};<BR><BR>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.<BR>-------------------- EXCEPTION --------------------<BR>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.<BR>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<BR>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<BR>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<BR>STACK Bio::EnsEMBL::Compara::MemberSet::get_all_Members /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:443<BR>STACK Bio::EnsEMBL::Compara::MemberSet::get_all_GeneMembers /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:489<BR>STACK Bio::EnsEMBL::Gene::get_all_homologous_Genes /usr/local/share/perl/5.12.4/ensembl/modules/Bio/EnsEMBL/Gene.pm:857<BR>STACK main::process_homologs newget_gene_info.pl:423<BR>STACK toplevel newget_gene_info.pl:292<BR>Date (localtime) = Tue May 27 12:46:41 2014<BR>Ensembl API version = 75<BR>---------------------------------------------------<BR><BR></DIV></DIV></BLOCKQUOTE></DIV></DIV> </div></body>
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