Hi John, I suppose you did not set -XX:MaxDirectMemorySize=512g parameter.
On Wed, May 17, 2017 at 7:07 PM John J. Szucs <[email protected]> wrote: > After 70 hours on a 32GB VM, ODB 2.2.20, JRE 8u131, the job failed with a > direct buffer memory exception. Given the complications I mentioned above, > my next step is going to be to get a high-RAM AWS EC2 instance and run this > there. However, as I mentioned above, my leadership is getting frustrated > with this situation. > > -- John > > 'Battle of banja luka'. > com.orientechnologies.orient.core.exception.ODatabaseException: Error on > retrieving record #63:19090001 (cluster: xlink_simple_2) > > DB name="kb" > at > com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.executeReadRecord(ODatabaseDocumentTx.java:2050) > at > com.orientechnologies.orient.core.tx.OTransactionOptimistic.loadRecord(OTransactionOptimistic.java:187) > at > com.orientechnologies.orient.core.tx.OTransactionOptimistic.loadRecord(OTransactionOptimistic.java:162) > at > com.orientechnologies.orient.core.tx.OTransactionOptimistic.loadRecord(OTransactionOptimistic.java:291) > at > com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.load(ODatabaseDocumentTx.java:1729) > at > com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.load(ODatabaseDocumentTx.java:102) > at > com.orientechnologies.orient.core.id.ORecordId.getRecord(ORecordId.java:329) > at > com.tinkerpop.blueprints.impls.orient.OrientEdgeIterator.createGraphElement(OrientEdgeIterator.java:72) > at > com.tinkerpop.blueprints.impls.orient.OrientEdgeIterator.createGraphElement(OrientEdgeIterator.java:44) > at > com.orientechnologies.orient.core.iterator.OLazyWrapperIterator.hasNext(OLazyWrapperIterator.java:93) > at > com.orientechnologies.common.collection.OMultiCollectionIterator.hasNextInternal(OMultiCollectionIterator.java:97) > at > com.orientechnologies.common.collection.OMultiCollectionIterator.hasNext(OMultiCollectionIterator.java:78) > at com.lusidity.mind.model.Node.getLinks(Node.java:308) > at com.lusidity.mind.model.Node.hasLink(Node.java:435) > at > com.lusidity.mind.etl.providers.mediawiki.BaseMediaWikiPage.loadHyperlinks(BaseMediaWikiPage.java:401) > at > com.lusidity.mind.etl.providers.mediawiki.BaseMediaWikiPage.link(BaseMediaWikiPage.java:260) > at > com.lusidity.mind.etl.providers.mediawiki.BaseMediaWikiPage.load(BaseMediaWikiPage.java:240) > at > com.lusidity.mind.etl.providers.mediawiki.BaseMediaWikiPage.process(BaseMediaWikiPage.java:98) > at > com.lusidity.mind.etl.providers.mediawiki.ArticleHandler.process(ArticleHandler.java:113) > at > com.lusidity.mind.etl.providers.mediawiki.ArticleHandler.process(ArticleHandler.java:75) > at info.bliki.wiki.dump.WikiXMLParser.endElement(WikiXMLParser.java:155) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:609) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2967) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602) > at > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770) > at > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) > at info.bliki.wiki.dump.WikiXMLParser.parse(WikiXMLParser.java:194) > at > com.lusidity.mind.etl.providers.mediawiki.MediaWiki.run(MediaWiki.java:133) > at > com.lusidity.mind.etl.providers.mediawiki.MediaWiki.run(MediaWiki.java:110) > at > com.lusidity.mind.shell.commands.ImportCommand.execute(ImportCommand.java:105) > at com.lusidity.mind.shell.Shell.execute(Shell.java:265) > at com.lusidity.mind.shell.Shell.execute(Shell.java:214) > at > com.lusidity.mind.shell.commands.ExecCommand.lambda$execute$0(ExecCommand.java:82) > at java.util.Iterator.forEachRemaining(Iterator.java:116) > at > java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) > at > java.util.stream.ReferencePipeline$Head.forEachOrdered(ReferencePipeline.java:590) > at > com.lusidity.mind.shell.commands.ExecCommand.execute(ExecCommand.java:78) > at com.lusidity.mind.shell.Shell.execute(Shell.java:265) > at com.lusidity.mind.shell.Shell.execute(Shell.java:214) > at com.lusidity.mind.shell.Shell.run(Shell.java:173) > at com.lusidity.mind.Program.runInteractive(Program.java:209) > at com.lusidity.mind.Program.run(Program.java:170) > at com.lusidity.mind.Program.main(Program.java:102) > Caused by: java.lang.OutOfMemoryError: Direct buffer memory > at java.nio.Bits.reserveMemory(Bits.java:694) > at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:123) > at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:311) > at > com.orientechnologies.common.directmemory.OByteBufferPool.allocateBuffer(OByteBufferPool.java:328) > at > com.orientechnologies.common.directmemory.OByteBufferPool.acquireDirect(OByteBufferPool.java:279) > at > com.orientechnologies.orient.core.storage.cache.local.OWOWCache.cacheFileContent(OWOWCache.java:1280) > at > com.orientechnologies.orient.core.storage.cache.local.OWOWCache.load(OWOWCache.java:656) > at > com.orientechnologies.orient.core.storage.cache.local.twoq.O2QCache.updateCache(O2QCache.java:1102) > at > com.orientechnologies.orient.core.storage.cache.local.twoq.O2QCache.doLoad(O2QCache.java:353) > at > com.orientechnologies.orient.core.storage.cache.local.twoq.O2QCache.load(O2QCache.java:298) > at > com.orientechnologies.orient.core.storage.impl.local.paginated.base.ODurableComponent.loadPage(ODurableComponent.java:148) > at > com.orientechnologies.orient.core.storage.impl.local.paginated.OPaginatedCluster.readRecordBuffer(OPaginatedCluster.java:691) > at > com.orientechnologies.orient.core.storage.impl.local.paginated.OPaginatedCluster.readRecord(OPaginatedCluster.java:667) > at > com.orientechnologies.orient.core.storage.impl.local.paginated.OPaginatedCluster.readRecord(OPaginatedCluster.java:646) > at > com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.doReadRecord(OAbstractPaginatedStorage.java:3260) > at > com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.readRecord(OAbstractPaginatedStorage.java:2879) > at > com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.readRecord(OAbstractPaginatedStorage.java:1064) > at > com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx$SimpleRecordReader.readRecord(ODatabaseDocumentTx.java:3436) > at > com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.executeReadRecord(ODatabaseDocumentTx.java:2012) > ... 47 common frames omitted > > > On Tue, May 16, 2017 at 11:42 AM, John J. Szucs <[email protected]> > wrote: > >> I've had some "complications" (namely, being hospitalized for a medical >> issue), but I am running the job right now with OrientDB 2.2.20 and JRE >> 8u131. It's only a 32GB VM for now, but it's almost 50% complete and the >> results are good so far. >> >> On Mon, May 15, 2017 at 10:29 AM, Claudio Massi <[email protected]> >> wrote: >> >>> Hi John, >>> if you have 64gb ram, to avoid swapping jvm, try to keep process size >>> below 64gb, so use Xmx + MaxDirectMemorySize below the available ram >>> >>> Try orientdb 2.2.20 with java 8u131-b11 , if using G1GC >>> >>> Monitor heap usage with: jstat -gc pid 120s 9999999 >>> >>> Monitor direct memory usage with any jmx tool (see >>> http://andreylomakin.blogspot.it/2016/05/how-to-calculate-maximum-amount-of.html >>> ) >>> - use jconsole, section MBeans, choose >>> com.orientechnologies.common.directmemory -> OByteBufferPoolMXBean -> >>> Attribute >>> - use MonBuffers.java (Source from Alan B. in >>> https://gist.github.com/t3rmin4t0r/1a753ccdcfa8d111f07c then increment >>> Thread.sleep(2000), and run adding tools.jar in classpath ) >>> - use jmxterm (http://wiki.cyclopsgroup.org/jmxterm/) >>> ... >>> >>> Claudio >>> >>> Il giorno venerdì 5 maggio 2017 18:57:26 UTC+2, John J. Szucs ha scritto: >>>> >>>> Andrey, >>>> >>>> THANK YOU! I will give this a try as soon as I can. >>>> >>>> I will also do some JVM profi >>>> >>>> — John >>>> >>>> On May 5, 2017, at 05:05, Andrey Lomakin <[email protected]> wrote: >>>> >>>> Hi John, >>>> If you wish you could use this build till we will do official release >>>> https://drive.google.com/file/d/0B2oZq2xVp841T2diVGtTcmZ5OTQ/view?usp=sharing >>>> >>>> >>>> On Fri, May 5, 2017 at 11:58 AM Andrey Lomakin <[email protected]> >>>> wrote: >>>> >>>>> HI John, >>>>> >>>>> I suppose you encountered issue >>>>> https://github.com/orientechnologies/orientdb/issues/7390 >>>>> We will provide release soon. >>>>> >>>>> Also please do not use such huge heap size we use heap only to keep >>>>> temporary data, so I suggest you lower heap size to get ODB the chance to >>>>> use more direct memory. >>>>> >>>>> On Fri, May 5, 2017 at 10:51 AM Luigi Dell'Aquila < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi John, >>>>>> >>>>>> How are you doing the import? Are you working in transaction? Some >>>>>> code will help us understand where the problem is >>>>>> >>>>>> Thanks >>>>>> >>>>>> Luigi >>>>>> >>>>>> >>>>>> 2017-05-05 3:53 GMT+02:00 John J. Szucs <[email protected]>: >>>>>> >>>>>>> Hello, OrientDB community! It's me again with another question. >>>>>>> >>>>>>> I am still working on my project and have encountered another >>>>>>> serious challenge: it seems that writing to indices (especially edge >>>>>>> indices?) can cause OrientDB's direct (non-JVM) memory usage to grow >>>>>>> without bounds until the system effectively grinds to a halt due to >>>>>>> swap. >>>>>>> >>>>>>> The specific use case is building a graph based on (English) >>>>>>> Wikipedia. There are approximately 17.4M vertices representing pages >>>>>>> (including articles, categories, and various meta pages). These vertices >>>>>>> are connected by approximately 65M (at last count) edges. There are a >>>>>>> few >>>>>>> super-nodes. For example, the vertex representing >>>>>>> https://en.wikipedia.org/wiki/United_States has (at last count) >>>>>>> 306K incoming edges and 822 outgoing edges. However, the degree of the >>>>>>> vertices roughly follows a Zipf distribution and the vast majority of >>>>>>> vertices have only a few (<10) total (in and out) edges. There are also >>>>>>> some other vertex and edge types for lexical data, but I think those are >>>>>>> secondary to the issue. >>>>>>> >>>>>>> Per previous discussion here and on StackOverflow, I have added >>>>>>> automatic edge indices on in, out, or the composite of the two to >>>>>>> optimize >>>>>>> edge queries. When I run the process to extract, transform, and load the >>>>>>> data from Wikipedia's XML dumps (using my own ETL code, not OrientDB's), >>>>>>> after 24-48 hours, the Linux System Monitor shows that physical memory >>>>>>> usage has reached 99.9% and then swap usage begins to grow. At this >>>>>>> point, >>>>>>> the process is effectively halted by swap thrashing. >>>>>>> >>>>>>> I am running this on a Fedora 25 Linux VM with 64GB RAM and 16 CPU >>>>>>> cores allocated. The JVM settings are as follows: >>>>>>> >>>>>>> -Xmx32g -Xms32g -server -XX:+PerfDisableSharedMem -XX:+UseG1GC >>>>>>> -XX:MaxDirectMemorySize=64413m -Dstorage.wal.syncOnPageFlush=false >>>>>>> >>>>>>> The MaxDirectMemorySize parameter is recommended by OrientDB itself, >>>>>>> during start-up with the "out-of-memory errors" warning. It does seem >>>>>>> odd >>>>>>> to me that Xmx+MaxDirectMemorySize>available RAM, but I'm more of a deep >>>>>>> R&D (not DevOps) guy, so I'm just accepting that unless someone advises >>>>>>> me >>>>>>> otherwise. >>>>>>> >>>>>>> If I disable the edge indices, then the process runs fine and >>>>>>> completes in a "reasonable" (for it) amount of time: 2-3 days. Of >>>>>>> course, >>>>>>> if I do this, my run-time performance suffers intolerably. >>>>>>> >>>>>>> I am running this with OrientDB 2.2.19. I was able to quickly get my >>>>>>> code to build with 3.0 M1, but some of the unit tests fail and I am >>>>>>> under >>>>>>> far too much pressure about this issue from my leadership to try to >>>>>>> troubleshoot them right now. >>>>>>> >>>>>>> What can I do to solve this issue? Thanks in advance for your help! >>>>>>> >>>>>>> -- John >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> --- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "OrientDB" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to [email protected]. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> --- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "OrientDB" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> -- >>>>> Best regards, >>>>> Andrey Lomakin, R&D lead. >>>>> OrientDB Ltd >>>>> >>>>> twitter: @Andrey_Lomakin >>>>> linkedin: https://ua.linkedin.com/in/andreylomakin >>>>> blogger: http://andreylomakin.blogspot.com/ >>>>> >>>> -- >>>> Best regards, >>>> Andrey Lomakin, R&D lead. >>>> OrientDB Ltd >>>> >>>> twitter: @Andrey_Lomakin >>>> linkedin: https://ua.linkedin.com/in/andreylomakin >>>> blogger: http://andreylomakin.blogspot.com/ >>>> >>>> -- >>>> >>>> --- >>>> You received this message because you are subscribed to a topic in the >>>> Google Groups "OrientDB" group. >>>> To unsubscribe from this topic, visit >>>> https://groups.google.com/d/topic/orient-database/p0JF5IGsqcs/unsubscribe >>>> . >>>> To unsubscribe from this group and all its topics, send an email to >>>> [email protected]. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>>> >>>> -- >>> >>> --- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "OrientDB" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/orient-database/p0JF5IGsqcs/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, send an email to >>> [email protected]. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> > -- > > --- > You received this message because you are subscribed to the Google Groups > "OrientDB" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > For more options, visit https://groups.google.com/d/optout. > -- Best regards, Andrey Lomakin, R&D lead. OrientDB Ltd twitter: @Andrey_Lomakin linkedin: https://ua.linkedin.com/in/andreylomakin blogger: http://andreylomakin.blogspot.com/ -- --- You received this message because you are subscribed to the Google Groups "OrientDB" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. For more options, visit https://groups.google.com/d/optout.
