Hi Daniel, Why were the 7.2.1 & 7.2.0 builds configured with different options, as they not both being performed on the same OS, in which case I would expect the configure options to the same ?
Best Regards Hugh Williams Professional Services OpenLink Software, Inc. // http://www.openlinksw.com/ Weblog -- http://www.openlinksw.com/blogs/ LinkedIn -- http://www.linkedin.com/company/openlink-software/ Twitter -- http://twitter.com/OpenLink Google+ -- http://plus.google.com/100570109519069333827/ Facebook -- http://www.facebook.com/OpenLinkSoftware Universal Data Access, Integration, and Management Technology Providers > On 13 Aug 2015, at 20:39, Davis, Daniel (NIH/NLM) [C] <daniel.da...@nih.gov> > wrote: > > Hugh Williams wrote: >> Also, note the following 2 parameters: ThreadCleanupInterval, >> ResourcesCleanupInterval which can both be set to 1 in order to reduce >> memory leaking: >> >> >> http://docs.openlinksw.com/virtuoso/databaseadmsrv.html#ex_threadcleanupinterval >> >> although as this was not apparently occurring with 7.2.0 it may not help, >> but worth trying ... > > It does occur with 7.2.0 - I'd vainly hoped 7.2.1 would fix it. The XSLT > process produces the file ftp://ftp.nlm.nih.gov/online/mesh/mesh.nt, which > contains 11,917,672 triples. > I'm also using the ontology > ftp://ftp.nlm.nih.gov/online/mesh/vocabulary_0.9.ttl and the void file > ftp://ftp.nlm.nih.gov/online/mesh/void_0.9.ttl. > > I cannot actually say it is a "memory leak" because I haven't pulled out > those tools yet - VmRSS seems to grow linearly over time. > VmSize does the same, only the sloop is not as steep. > > I've built Virtuoso 7.2.1 on CentOS 6.6 as follows: > ./configure --prefix=<whatever> --with-readline > > Previously, with 7.2.0, my build was: > export CFLAGS="-O2 -m64" > ./configure --prefix=<whatever> --with-readline --with-iodbc=/usr > --without-internal-zlib --enable-shared --disable-static > > I've also configured it with ThreadCleanupInterval = 1 and > ResourcesCleanupInterval = 1. > > The reload I'm testing runs the following commands from an isql command-line: > > log_enable(2,1); > sparql clear graph <http://id.nlm.nih.gov/mesh>; > sparql clear graph <http://id.nlm.nih.gov/mesh/vocab>; > sparql clear graph <http://id.nlm.nih.gov/mesh/void>; > DB.DBA.ttlp(file_to_string_output('path-to-files/mesh.nt'), '', > 'http://id.nlm.nih.gov/mesh', 0); > DB.DBA.ttlp(file_to_string_output('path-to-files/vocabulary_0.9.ttl'), > '', 'http://id.nlm.nih.gov/mesh/vocab', 0); > rdfs_rule_set('http://id.nlm.nih.gov/mesh/vocab', > 'http://id.nlm.nih.gov/mesh/vocab'); > DB.DBA.ttlp(file_to_string_output('path-to-files/void_0.9.ttl'), '', > 'http://id.nlm.nih.gov/mesh/void', 0); > CHECKPOINT; > > I'm retrying with a shorter script, which only loads 100,000 triples: > > log_enable(2,1); > sparql clear graph <http://id.nlm.nih.gov/meshtest>; > DB.DBA.ttlp(file_to_string_output('path-to-files/small-mesh.nt', '', > 'http://id.nlm.nih.gov/meshtest', 0); > > If that proves stable, I'll do the following: > - stop clearing and reloading the vocabulary and void graphs and redefining > the ruleset > - let you guys know it worked. > > If that is not stable, I'll do one or several of the following: > - try virtuoso-opensource-6 > - open/comment on an issue on github.com/openlinksw/virtuoso-opensource/issues > - install valgrind and valgrind-devel and build with malloc debug > - evaluate switching to the directory scan option. > > Dan Davis, Systems/Applications Architect (Contractor), > Office of Computer and Communications Systems, > National Library of Medicine, NIH > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Virtuoso-users mailing list > Virtuoso-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/virtuoso-users
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