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<body class='hmmessage'><div dir='ltr'>Hi Andy,<BR>
<BR>
Thanks for the info. Setting our open-files-limit seems to have resolved the earlier error.<BR>
<BR>
I am running into another curious error its a DBD::mysql::st execute failed: MySQL server has gone away. <BR>
I do a "$registry->set_reconnect_when_lost();" but oddly that doesn't seem to help.<BR>
<BR>
questions:<BR>
<BR>
1) When is the correct time to do a "$registry->set_reconnect_when_lost();", just after the $registry->load_registry_from_db( ....)? or after the $registry->get_adaptor( ...) call?<BR>
<BR>
2) I am using gene->get_all_homologous_Genes() method of Gene.pm which hands me back a Homology Object. The Gene is from a Slice Object in a "core" database adapter. The Homology really isnt a "Core" thing but instead a "Compara" thing. From the Gene in the Homology obect <BR>
<BR>
here is an example sort of code:<BR>
<BR>
foreach my $slice (@{ $slices_ref }) {<BR>
my $all_genes_ref = $slice->get_all_Genes();<BR>
foreach my $gene ( @{ $all_genes_ref } ) { #all of the above code worked before<BR>
my @homs = @{$gene->get_all_homologous_Genes}; #may be erroring here<BR>
foreach my $all_homs (@homs){ #may be erroring here<BR>
my ($hgene, $compara, $homspecies) = @{$all_homs};<BR>
$myexternalname = $hgene->external_name;<BR> $mydescription = $hgene->description; <BR>
$myassemblyversion = $hgene->feature_Slice->coord_system->version; #may be erroring here<BR>
<BR>
....<BR>
Anyhow, after I've connected, gotten the core adapter set_reconnect_when_lost etc. The code runs for about 20 minutes cycling therough genes and getting homologs then starts intermittently spitting out these: DBD::mysql::st execute failed: MySQL server has gone away at /...../EnsEMBL/DBSQL/BaseAdaptor.pm line 482. These seem to come a couple at a time then a wait then then later the script just seems to abruptly stop abnormally without any real error.<BR>
<BR>
So I think I may be confusing the system perhaps by starting with a "core" connection, jumping to a "compara" connection and then back to another "core" in another species.<BR>
<BR>
Yikes! Does any of this make sense?<BR>
<BR>
Ed<BR>
<BR>
<BR>
<DIV>> From: ayates@ebi.ac.uk<BR>> Date: Wed, 28 May 2014 09:23:33 +0100<BR>> To: dev@ensembl.org<BR>> Subject: Re: [ensembl-dev] './ensembl_compara_75/member.frm' (errno: 24)<BR>> <BR>> Hi,<BR>> <BR>> In the past we've seen this kind of behaviour linked to code which connects & disconnects from a database too often. MySQL traditionally assigns a connection to a linux process. Later versions of MySQL (5.6 enterprise), MariaDB & Percona Server have switched to using a pool of threads IIRC which does alleviate the problem.<BR>> <BR>> Anyway going back to Ensembl. I've seen the issue appear because the disconnect_if_idle flag is turned on in a DBConnection object. Of course this maybe your intended behaviour as otherwise you are responsible for cleaning up the connections you create and filling up a MySQL server with idle connections. At any rate raising open-files-limit is a good way to alleviate this. To give you an idea our servers are normally set to 132,106.<BR>> <BR>> Andy<BR>> <BR>> ------------<BR>> Andrew Yates - Ensembl Support Coordinator<BR>> European Bioinformatics Institute (EMBL-EBI)<BR>> European Molecular Biology Laboratory<BR>> Wellcome Trust Genome Campus<BR>> Hinxton<BR>> Cambridge CB10 1SD<BR>> Tel: +44-(0)1223-492538<BR>> Fax: +44-(0)1223-494468<BR>> http://www.ensembl.org/<BR>> <BR>> On 27 May 2014, at 16:02, Ed Gray <gray_ed@hotmail.com> wrote:<BR>> <BR>> > 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>> > <BR>> > Anyone encounter/fix problems with a long running perl script using the ensembl api that generates too many file handles?<BR>> > <BR>> > 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>> > 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). <BR>> > <BR>> > All the best<BR>> > Stuart<BR>> > <BR>> > <BR>> > On May 27, 2014, at 10:22 AM, Ed Gray <gray_ed@hotmail.com> wrote:<BR>> > <BR>> > <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></DIV> </div></body>
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