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Re: [Bigdata-developers] Current Revision of Blazegraph: Journal consumes extremely much disk space
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From: Bryan T. <br...@sy...> - 2015-04-23 23:18:20
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I've updated the ticket. I've also copied my main conclusions inline below. I think that the issue here is the use of the small slot optimization without proper configuration of the indices in order to target small allocation slots for at least one of the indices. The small slot optimization changes the allocation policy in two ways. 1. It has a strong preference to use only empty 8k pages for small allocations (as configured, for allocations less than 1k). This allows us to coalesce writes by combining them onto the same page. 2. It has a preference to use allocation blocks that are relatively empty for small slots. As a consequence, the small slot optimization MAY recruit more allocators in order to have allocators for small slots that have good sparsity. The main goal of the small slot optimization is to optimize for indices that have very scattered IO patterns. The indices that exhibits this the most are the OSP and OCSP indices. In many cases even batched updates will modify no more than a single tuple per page on this index. However, in your configuration (and in mine when I enabled the small slot optimization without adjusting the branching factors), the O(C)SP indices were not created with a small branching factor, so the small slot allocation could not be put to any good effect. However it did have a negative effect -- by recruiting more allocators. If you want to use the small slot optimization, make sure that at least the O(C)SP index has a relatively small branching factor giving an effective slot size of 256 bytes or less on average. I suggest that you retest w/o the small slot optimization and with group commit still enabled. I've asked Martyn to look over the allocators from the small slot optimization run and think about whether we can make this policy a little more adaptive when the branching factors are not really tuned properly and too many allocators with too much wasted space are allocated as a result. Basically, how to avoid file bloat from misconfiguration. Thanks, Bryan ---- Bryan Thompson Chief Scientist & Founder SYSTAP, LLC 4501 Tower Road Greensboro, NC 27410 br...@sy... http://blazegraph.com http://blog.bigdata.com <http://bigdata.com> http://mapgraph.io Blazegraph™ <http://www.blazegraph.com/> is our ultra high-performance graph database that supports both RDF/SPARQL and Tinkerpop/Blueprints APIs. MapGraph™ <http://www.systap.com/mapgraph> is our disruptive new technology to use GPUs to accelerate data-parallel graph analytics. CONFIDENTIALITY NOTICE: This email and its contents and attachments are for the sole use of the intended recipient(s) and are confidential or proprietary to SYSTAP. Any unauthorized review, use, disclosure, dissemination or copying of this email or its contents or attachments is prohibited. If you have received this communication in error, please notify the sender by reply email and permanently delete all copies of the email and its contents and attachments. On Thu, Apr 23, 2015 at 9:36 AM, Andreas Kahl <ka...@bs...> wrote: > Ok, I can redo the test with smallSlots + groupCommit enabled, and run > http://localhost:8080/bigdata/status?dumpJournal&dumpPages after some > minutes. (I cannot run it on the fully loaded dataset because my disk is > not sufficient for the resulting Journal). > > By the way: Please find attached my custom Vocabulary classes. They are > just one of my many attempts to improve IO Perfomance on rotating disks. > > Best Regards > Andreas > > >>> Bryan Thompson <br...@sy...> 23.04.15 15.31 Uhr >>> > I just noticed that you have the full text index enabled as well. I have > not be enabling that. > > I would like to see the output from this command on the fully loaded data > sets. > > http://localhost:8080/bigdata/status?dumpJournal&dumpPages > > This will let us if any specific index is taking up a very large number of > pages. It will also tell us the distribution over the page sizes for each > index. > > Bryan > > ---- > Bryan Thompson > Chief Scientist & Founder > SYSTAP, LLC > 4501 Tower Road > Greensboro, NC 27410 > br...@sy... > http://blazegraph.com > http://blog.bigdata.com <http://bigdata.com> > http://mapgraph.io > > Blazegraph™ <http://www.blazegraph.com/> is our ultra high-performance > graph database that supports both RDF/SPARQL and Tinkerpop/Blueprints > APIs. MapGraph™ <http://www.systap.com/mapgraph> is our disruptive new > technology to use GPUs to accelerate data-parallel graph analytics. > > CONFIDENTIALITY NOTICE: This email and its contents and attachments are > for the sole use of the intended recipient(s) and are confidential or > proprietary to SYSTAP. Any unauthorized review, use, disclosure, > dissemination or copying of this email or its contents or attachments is > prohibited. If you have received this communication in error, please notify > the sender by reply email and permanently delete all copies of the email > and its contents and attachments. > > On Thu, Apr 23, 2015 at 8:54 AM, Andreas Kahl <ka...@bs...> > wrote: > > > Bryan, > > > > in the meantime, I could successfully load the file into a 18GB journal > > after disabling groupCommit (I simply commented out the line in > > RWStore.properties). > > I can try again with groupCommit enabled, but smallSlotOptimization > > disabled. > > > > Best Regards > > Andreas > > > > >>> Bryan Thompson <br...@sy...> 23.04.2015 13:24 >>> > > Andreas, > > > > I was not able to replicate your result. Unfortunately I navigated away > > from the browser page in which I had submitted the request, so it loaded > > all the data but failed to commit. However, the resulting file is only > > 16GB. > > > > I will redo this run and verify that the journal after the commit has > this > > same size on the disk. > > > > I was only assuming that this was related to group commit because of your > > original message. Perhaps I misinterpreted your message. This is simply > > about 1.5.1 (with group commit) vs 1.4.0. > > > > Perhaps the issue is related to the small slot optimization? Maybe in > > combination with group commit? > > > > *> com.bigdata.rwstore.RWStore.smallSlotType=1024* > > > > I could not replicate your properties exactly because you are using a > > non-standard vocabulary class. Therefore I simply deleted the default > > namespace (in quads mode) and recreated it with the defaults in triples > > mode. The small slot optimization and other parameters were not enabled > in > > my run. > > > > Perhaps you could try to replicate my experience and I will enable the > > small slots optimization? > > > > Thanks, > > Bryan > > > > ---- > > Bryan Thompson > > Chief Scientist & Founder > > SYSTAP, LLC > > 4501 Tower Road > > Greensboro, NC 27410 > > br...@sy... > > http://blazegraph.com > > http://blog.bigdata.com <http://bigdata.com> > > http://mapgraph.io > > > > Blazegraph™ <http://www.blazegraph.com/> is our ultra high-performance > > graph database that supports both RDF/SPARQL and Tinkerpop/Blueprints > > APIs. MapGraph™ <http://www.systap.com/mapgraph> is our disruptive new > > technology to use GPUs to accelerate data-parallel graph analytics. > > > > CONFIDENTIALITY NOTICE: This email and its contents and attacP. Any > unauthorized review, use, disclosure, > > dissemination or copying of this email or its contents or attachments is > > prohibited. If you have received this communication in error, please > notify > > the sender by reply email and permanently delete all copies of the email > > and its contents and attachments. > > > > On Thu, Apr 23, 2015 at 1:51 AM, Andreas Kahl <ka...@bs...> > > wrote: > > > > > Bryan & Martyn, > > > > > > Thank you very much for investigating the issue. I assume from the > > ticket > > > that the error will vanish if I disable groupCommit. I will do so for > the > > > meantime. > > > > > > Although there is already extensive information in Bryan's ticket, > please > > > find attached my logs and DumpJournal outputs: > > > - dumpJournal.html contains a dump from the 67GB journal after > Blazegraph > > > ran into "No space left on device" > > > - dumpJournalWithTraceEnabled.html is the same dump for a running query > > > when the journal was at about 14GB > > > - queryStatus.html is just the status page showing my query > > > - catalina.out.gz contains the trace outputs from starting Tomcat > until I > > > killed the curl running the SPARQL Update by Ctrl-C > > > - loadGnd.log.gz is Blazegraphs output when loading the data > > > > > > Best Regards > > > Andreas > > > > > > > > > > > > >>> Bryan Thompson <br...@sy...> 22.04.15 20.56 Uhr >>> > > > See http://trac.bigdata.com/ticket/1206. This is still in the > > > investigation stage. > > > > > > Thanks, > > > Bryan > > > > > > ---- > > > Bryan Thompson > > > Chief Scientist & Founder > > > SYSTAP, LLC > > > 4501 Tower Road > > > Greensboro, NC 27410 > > > br...@sy... > > > http://blazegraph.com > > > http://blog.bigdata.com <http://bigdata.com> > > > http://mapgraph.io > > > > > > Blazegraph™ <http://www.blazegraph.com/> is our ultra high-performance > > > graph database that supports both RDF/SPARQL and Tinkerpop/Blueprints > > > APIs. MapGraph™ <http://www.systap.com/mapgraph> is our disruptive > new > > > technology to use GPUs to accelerate data-parallel graph analytics. > > > > > > CONFIDENTIALITY NOTICE: This email and its contents and attachments > are > > > for the sole use of the intended recipient(s) and are confidential or > > > proprietary to SYSTAP. Any unauthorized review, use, disclosure, > > > dissemination or copying of this email or its contents or attachments > is > > > prohibited. If you have received this communication in error, please > > notify > > > the sender by reply email and permanently delete all copies of the > email > > > and its contents and attachments. > > > > > > On Wed, Apr 22, 2015 at 5:37 AM, Andreas Kahl <ka...@bs...> > > > wrote: > > > > > > > Hello everyone, > > > > > > > > I currently updated to the current Revision (f4c63e5) of Blazegraph > > from > > > > Git and tried to load a dataset into the updated Webapp. With Bigdata > > > 1.4.0 > > > > this resulted in a journal of ~18GB. Now the process was cancelled > > > because > > > > the disk was full - the journal was beyond 50GB for the same file > with > > > the > > > > same settings. > > > > The only exception was that I activated GroupCommit. > > > > > > > > The dataset can be downloaded here: > > > > > > > > > > http://datendienst.dnb.de/cgi-bin/mabit.pl?cmd=fetch&userID=opendata&pass=opendata&mabheft=GND.rdf.gz > > > > . > > > > Please find the settings used to load the file below. > > > > > > > > Do I have a misconfiguration, or is there a bug eating all disk > memory? > > > > > > > > Best regards > > > > Andreas > > > > > > > > Namespace-Properties: > > > > curl -H "Accept: text/plain" > > > > http://localhost:8080/bigdata/namespace/gnd/properties > > > > #Wed Apr 22 11:35:31 CEST 2015 > > > > > > com.bigdata.namespace.kb.spo.com.bigdata.btree.BTree.branchingFactor=700 > > > > com.bigdata.relation.container=gnd > > > > com.bigdata.rwstore.RWStore.smallSlotType=1024 > > > > com.bigdata.journal.AbstractJournal.bufferMode=DiskRW > > > > com.bigdata.journal.AbstractJournal.file=/var/lib/bigdata/bigdata.jnl > > > > > > > > > > > > > com.bigdata.rdf.store.AbstractTripleStore.vocabu.textIndex=true > > > > com.bigdata.btree.BTree.branchingFactor=700 > > > > > > > > > > > > > > com.bigdata.rdf.store.AbstractTripleStore.axiomsClass=com.bigdata.rdf.axioms.NoAxioms > > > > com.bigdata.rdf.sail.isolatableIndices=false > > > > com.bigdata.service.AbstractTransactionService.minReleaseAge=1 > > > > com.bigdata.rdf.sail.bufferCapacity=2000 > > > > com.bigdata.rdf.sail.truthMaintenance=false > > > > com.bigdata.rdf.sail.namespace=gnd > > > > com.bigdata.relation.class=com.bigdata.rdf.store.LocalTripleStore > > > > com.bigdata.rdf.store.AbstractTripleStore.quads=false > > > > com.bigdata.journal.AbstractJournal.writeCacheBufferCount=500 > > > > com.bigdata.search.FullTextIndex.fieldsEnabled=false > > > > com.bigdata.relation.namespace=gndity=10000 > > > > com.bigdata.rdf.sail.BigdataSail.bufferCapacity=2000 > > > > com.bigdata.rdf.store.AbstractTripleStore.statementIdentifiers=false > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > > > > Develop your own process in accordance with the BPMN 2 standard > > > > Learn Process modeling best practices with Bonita BPM through live > > > > exercises > > > > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- > > > > event?utm_ > > > > > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > > > > _______________________________________________ > > > > Bigdata-developers mailing list > > > > Big...@li... > > > > https://lists.sourceforge.net/lists/listinfo/bigdata-developers > > > > > > > > > > > > > > > > > > |
