Hi Michael, your heap is smaller than that: see the line from messages.log: Thu Aug 11 12:05:17 PDT 2011: Physical mem: 3006MB, Heap size: 668MB Please provide your JVM with a larger heap setting like -Xmx4G
Can you please upgrade your memory mapped config to take about 2G of that (in windows memory mapped memory is taken from the heap). If you start neo4j programmatically you can pass in a Map for that (see also http://wiki.neo4j.org/content/Configuration_Settings#Memory_mapped_I.2FO_settings) Current settings are in messages.log: > Thu Aug 11 12:05:17 PDT 2011: neostore.nodestore.db.mapped_memory=20M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.arrays.mapped_memory=130M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.index.keys.mapped_memory=1M > Thu Aug 11 12:05:17 PDT 2011: neostore.propertystore.db.index.mapped_memory=1M > Thu Aug 11 12:05:17 PDT 2011: neostore.propertystore.db.mapped_memory=90M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.strings.mapped_memory=130M > Thu Aug 11 12:05:17 PDT 2011: neostore.relationshipstore.db.mapped_memory=100M I also saw you're running Java7 on that one, right now we have no performance tests on Java7. Just to mention it. Btw. even on Kei's Macbook it shouldn't take a second to add 1000 vertices. Rather around a few milliseconds. Don't know what kind of overhead, the blueprints / cytoscape managers around the neo4j core add. I'm blueprints has a auto-tx mode where there is a new tx per each operation and you have to disable that (if you use external tx-managment). Cheers Michael Am 14.08.2011 um 05:00 schrieb Michael Kirby: > Hello, > > Here is my messages.log , I also recently got a new computer and it takes > about 3 seconds on that one. The heap for it 1809 MB. > > Thu Aug 11 12:05:17 PDT 2011: Opened [target\neo4jDB\nioneo_logical.log.1] > clean empty log, version=0 > Thu Aug 11 12:05:17 PDT 2011: Opened > [C:\Users\Michael\blueprints-graph-cytoscapeMaster\target\neo4jDB\index\lucene.log.1] > clean empty log, version=0 > Thu Aug 11 12:05:17 PDT 2011: TM opening log: target\neo4jDB\tm_tx_log.2 > Thu Aug 11 12:05:17 PDT 2011: --- CONFIGURATION START --- > Thu Aug 11 12:05:17 PDT 2011: Physical mem: 3006MB, Heap size: 668MB > Thu Aug 11 12:05:17 PDT 2011: Kernel version: Neo4j - Graph Database Kernel > 1.4.1 > Thu Aug 11 12:05:17 PDT 2011: Neo4j - Graph Database Kernel 1.4.1 > Thu Aug 11 12:05:17 PDT 2011: Operating System: Windows 7; version: 6.1; > arch: amd64; cpus: 2 > Thu Aug 11 12:05:17 PDT 2011: VM Name: Java HotSpot(TM) 64-Bit Server VM > Thu Aug 11 12:05:17 PDT 2011: VM Vendor: Sun Microsystems Inc. > Thu Aug 11 12:05:17 PDT 2011: VM Version: 17.0-b17 > Thu Aug 11 12:05:17 PDT 2011: Boot Class Path: > C:\Java\jdk1.6.0_21\jre\lib\resources.jar;C:\Java\jdk1.6.0_21\jre\lib\rt.jar;C:\Java\jdk1.6.0_21\jre\lib\sunrsasign.jar;C:\Java\jdk1.6.0_21\jre\lib\jsse.jar;C:\Java\jdk1.6.0_21\jre\lib\jce.jar;C:\Java\jdk1.6.0_21\jre\lib\charsets.jar;C:\Java\jdk1.6.0_21\jre\classes > Thu Aug 11 12:05:17 PDT 2011: Class Path: > C:\Users\Michael\blueprints-graph-cytoscapeMaster\target\test-classes;C:\Users\Michael\blueprints-graph-cytoscapeMaster\target\classes;C:\Users\Michael\workspace\api-parent\model-api\target\classes;C:\Users\Michael\.m2\repository\org\cytoscape\event-api\3.0.0-alpha6-SNAPSHOT\event-api-3.0.0-alpha6-SNAPSHOT.jar;C:\Users\Michael\.m2\repository\org\cytoscape\work-api\3.0.0-alpha6-SNAPSHOT\work-api-3.0.0-alpha6-SNAPSHOT.jar;C:\Users\Michael\.m2\repository\org\cytoscape\wrappers\tinkerpop-blueprints-core\0.9\tinkerpop-blueprints-core-0.9.jar;C:\Users\Michael\.m2\repository\org\cytoscape\wrappers\tinkerpop-blueprints-neo4j-graph\0.9\tinkerpop-blueprints-neo4j-graph-0.9.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-kernel\1.4.1\neo4j-kernel-1.4.1.jar;C:\Users\Michael\.m2\repository\org\apache\geronimo\specs\geronimo-jta_1.1_spec\1.1.1\geronimo-jta_1.1_spec-1.1.1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-lucene-index\1.4.1\neo4j-lucene-index-1. > 4.1.jar;C:\Users\Michael\.m2\repository\org\apache\lucene\lucene-core\3.1.0\lucene-core-3.1.0.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-graph-algo\1.4.1\neo4j-graph-algo-1.4.1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-udc\1.4.1\neo4j-udc-1.4.1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-graph-matching\1.4.1\neo4j-graph-matching-1.4.1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-cypher\1.4.1\neo4j-cypher-1.4.1.jar;C:\Users\Michael\.m2\repository\org\scala-lang\scala-library\2.9.0-1\scala-library-2.9.0-1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-jmx\1.4.1\neo4j-jmx-1.4.1.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-kernel\1.4.1\neo4j-kernel-1.4.1-tests.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-ha\1.3\neo4j-ha-1.3.jar;C:\Users\Michael\.m2\repository\org\neo4j\neo4j-backup\1.3\neo4j-backup-1.3.jar;C:\Users\Michael\.m2\repository\org\apache\zookeeper\zookeeper\3.3.2\zookeeper-3.3.2.jar;C:\Users\Mi > chael\.m2\repository\org\neo4j\neo4j-com\1.3\neo4j-com-1.3.jar;C:\Users\Michael\.m2\repository\org\apache\servicemix\bundles\org.apache.servicemix.bundles.netty\3.2.3.Final_1\org.apache.servicemix.bundles.netty-3.2.3.Final_1.jar;C:\Users\Michael\.m2\repository\log4j\log4j\1.2.16\log4j-1.2.16.jar;C:\Users\Michael\workspace\api-parent\model-api\target\test-classes;C:\Users\Michael\.m2\repository\org\cytoscape\event-api\3.0.0-alpha6-SNAPSHOT\event-api-3.0.0-alpha6-SNAPSHOT-tests.jar;C:\Users\Michael\.m2\repository\junit\junit\4.8.2\junit-4.8.2.jar;C:\Users\Michael\.m2\repository\org\mockito\mockito-all\1.8.5\mockito-all-1.8.5.jar;C:\Users\Michael\.m2\repository\org\cytoscape\wrappers\tinkerpop-blueprints-sail-graph\0.9\tinkerpop-blueprints-sail-graph-0.9.jar;C:\Users\Michael\.m2\repository\org\slf4j\slf4j-log4j12\1.5.6\slf4j-log4j12-1.5.6.jar;C:\Users\Michael\.m2\repository\org\slf4j\slf4j-api\1.5.6\slf4j-api-1.5.6.jar;C:\Users\Michael\.m2\repository\org\o > penrdf\sesame\sesame-sail-api\2.4.0\sesame-sail-api-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-query\2.4.0\sesame-query-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-api\2.4.0\sesame-rio-api-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-queryalgebra-model\2.4.0\sesame-queryalgebra-model-2.4.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-collections\2.8.0\aduna-commons-collections-2.8.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-model\2.4.0\sesame-model-2.4.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-i18n\1.4.0\aduna-commons-i18n-1.4.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-iteration\2.10.0\aduna-commons-iteration-2.10.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-concurrent\2.7.0\aduna-commons-concurrent-2.7.0.jar;C:\Users\Michael\.m2\repository\info\aduna\co > mmons\aduna-commons-lang\2.9.0\aduna-commons-lang-2.9.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-queryparser-sparql\2.4.0\sesame-queryparser-sparql-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-queryparser-api\2.4.0\sesame-queryparser-api-2.4.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-net\2.7.0\aduna-commons-net-2.7.0.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-text\2.7.0\aduna-commons-text-2.7.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-sail-memory\2.4.0\sesame-sail-memory-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-sail-inferencer\2.4.0\sesame-sail-inferencer-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-queryparser-serql\2.4.0\sesame-queryparser-serql-2.4.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-queryalgebra-evaluation\2.4.0\sesame-queryalgebra-evaluation-2.4.0.jar;C:\ > Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-io\2.10.0\aduna-commons-io-2.10.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-sail-nativerdf\2.4.0\sesame-sail-nativerdf-2.4.0.jar;C:\Users\Michael\.m2\repository\net\fortytwo\linked-data-sail\0.7\linked-data-sail-0.7.jar;C:\Users\Michael\.m2\repository\net\fortytwo\ripple\ripple-rdf\0.7\ripple-rdf-0.7.jar;C:\Users\Michael\.m2\repository\net\fortytwo\ripple\ripple-base\0.7\ripple-base-0.7.jar;C:\Users\Michael\.m2\repository\net\fortytwo\rdfflow\0.7\rdfflow-0.7.jar;C:\Users\Michael\.m2\repository\net\fortytwo\flow\0.7\flow-0.7.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-n3\2.4.2\sesame-rio-n3-2.4.2.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-rdfxml\2.4.2\sesame-rio-rdfxml-2.4.2.jar;C:\Users\Michael\.m2\repository\info\aduna\commons\aduna-commons-xml\2.7.0\aduna-commons-xml-2.7.0.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame > \sesame-rio-trig\2.4.2\sesame-rio-trig-2.4.2.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-trix\2.4.2\sesame-rio-trix-2.4.2.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-turtle\2.4.2\sesame-rio-turtle-2.4.2.jar;C:\Users\Michael\.m2\repository\commons-httpclient\commons-httpclient\3.1\commons-httpclient-3.1.jar;C:\Users\Michael\.m2\repository\commons-logging\commons-logging\1.0.4\commons-logging-1.0.4.jar;C:\Users\Michael\.m2\repository\commons-codec\commons-codec\1.2\commons-codec-1.2.jar;C:\Users\Michael\.m2\repository\org\restlet\org.restlet\1.0.5\org.restlet-1.0.5.jar;C:\Users\Michael\.m2\repository\net\fortytwo\sesametools\nquads\1.4\nquads-1.4.jar;C:\Users\Michael\.m2\repository\org\openrdf\sesame\sesame-rio-ntriples\2.4.2\sesame-rio-ntriples-2.4.2.jar;C:\Users\Michael\.m2\repository\net\fortytwo\sesametools\common\1.4\common-1.4.jar;/C:/Users/Michael/.eclipse/org.eclipse.platform_3.6.1_1709980481/configurati > on/org.eclipse.osgi/bundles/149/1/.cp/;/C:/Users/Michael/.eclipse/org.eclipse.platform_3.6.1_1709980481/configuration/org.eclipse.osgi/bundles/147/1/.cp/;/C:/Users/Michael/.eclipse/org.eclipse.platform_3.6.1_1709980481/configuration/org.eclipse.osgi/bundles/148/1/.cp/ > Thu Aug 11 12:05:17 PDT 2011: Library Path: > C:\Java\jdk1.6.0_21\bin;.;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program > Files > (x86)\PHP\;C:\Perl64\site\bin;C:\Perl64\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;c:\java\jdk1.6.0_21\bin\;C:\Program > Files\SlikSvn\bin\ > Thu Aug 11 12:05:17 PDT 2011: Garbage Collector: PS Scavenge: [PS Eden Space, > PS Survivor Space] > Thu Aug 11 12:05:17 PDT 2011: Garbage Collector: PS MarkSweep: [PS Eden > Space, PS Survivor Space, PS Old Gen, PS Perm Gen] > Thu Aug 11 12:05:17 PDT 2011: VM Arguments: [-Dfile.encoding=Cp1252] > Thu Aug 11 12:05:17 PDT 2011: > Thu Aug 11 12:05:17 PDT 2011: create=true > Thu Aug 11 12:05:17 PDT 2011: logical_log=target\neo4jDB\nioneo_logical.log > Thu Aug 11 12:05:17 PDT 2011: neo_store=target\neo4jDB\neostore > Thu Aug 11 12:05:17 PDT 2011: neostore.nodestore.db.mapped_memory=20M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.arrays.mapped_memory=130M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.index.keys.mapped_memory=1M > Thu Aug 11 12:05:17 PDT 2011: neostore.propertystore.db.index.mapped_memory=1M > Thu Aug 11 12:05:17 PDT 2011: neostore.propertystore.db.mapped_memory=90M > Thu Aug 11 12:05:17 PDT 2011: > neostore.propertystore.db.strings.mapped_memory=130M > Thu Aug 11 12:05:17 PDT 2011: neostore.relationshipstore.db.mapped_memory=100M > Thu Aug 11 12:05:17 PDT 2011: node_auto_indexing=false > Thu Aug 11 12:05:17 PDT 2011: rebuild_idgenerators_fast=true > Thu Aug 11 12:05:17 PDT 2011: relationship_auto_indexing=false > Thu Aug 11 12:05:17 PDT 2011: store_dir=target\neo4jDB > Thu Aug 11 12:05:17 PDT 2011: use_memory_mapped_buffers=false > Thu Aug 11 12:05:17 PDT 2011: --- CONFIGURATION END --- > Thu Aug 11 12:05:17 PDT 2011: Extension > org.neo4j.kernel.KernelExtension[kernel udc] loaded ok > Thu Aug 11 12:05:17 PDT 2011: Extension > org.neo4j.kernel.KernelExtension[kernel jmx] loaded ok > Thu Aug 11 12:05:17 PDT 2011: Extension > org.neo4j.kernel.KernelExtension[dummy] loaded ok > Thu Aug 11 12:05:17 PDT 2011: Extension > org.neo4j.kernel.KernelExtension[other dummy] loaded ok > Thu Aug 11 12:05:17 PDT 2011: Extension > org.neo4j.kernel.KernelExtension[online backup] loaded ok > Thu Aug 11 12:11:20 PDT 2011: Closed log target\neo4jDB\nioneo_logical.log > Thu Aug 11 12:11:22 PDT 2011: NeoStore closed > Thu Aug 11 12:11:22 PDT 2011: Closed log > C:\Users\Michael\blueprints-graph-cytoscapeMaster\target\neo4jDB\index\lucene.log > Thu Aug 11 12:11:22 PDT 2011: NeoStore closed > Thu Aug 11 12:11:22 PDT 2011: TM shutting down > > Thank you, > > Michael > > > > ---------- Forwarded message ---------- > From: Michael Hunger <michael.hun...@neotechnology.com> > Date: 2011/8/11 > Subject: Re: [Neo4j] Very Slow Transaction only on Windows > To: Neo4j user discussions <user@lists.neo4j.org> > > > Kei, > > How much heap does he use for the test? > > On windows memory mapped files are allocated within the java heap > space not outside as on *nix systems. > > There is a messages.log in the graphdb directory. > > Could you share its content with us? > > Thanks so much > > Michael > > Am 11.08.2011 um 21:58 schrieb Keiichiro Ono: > >> Hi. >> I have a summer student working on Cytoscape (graph >> visualization/analysis software)-Neo4j integration project using >> Blueprints framework. >> >> https://github.com/keiono/blueprints-graph-cytoscape/wiki >> >> Currently, I've got a question from him which I do not know the answer. >> >> Here is the very simple test code. It adds 1000 Vertices to Neo4j >> Graph using CommitManager: >> >> @Test >> public void testPerformance() { >> >> long start = System.currentTimeMillis(); >> final CommitManager manager = >> TransactionalGraphHelper.createCommitManager( >> (TransactionalGraph) graphImplementation, >> 1000); >> for (int i = 0; i < 1000; i++) { >> net.addNode(); >> manager.incrCounter(); >> } >> >> manager.close(); >> final long time = (System.currentTimeMillis() - start); >> System.out.println("Nodes added in " + time + " msec."); >> >> assertEquals(1000, net.getNodeCount()); >> >> // If we does not use transaction utility method, this can be >> minutes or hours... >> assertTrue(2000>time); >> } >> >> https://github.com/keiono/blueprints-graph-cytoscape/blob/master/src/test/java/org/cytoscape/blueprints/implementations/Neo4jTest.java >> >> where net is a wrapper object for Cytoscape graph model, and addNode() >> method simply calles graph.addVertex() method in Blueprints' Graph >> API. This test passes in less than a second on my MacBook, but on >> Windows PC, it takes 1+ minutes to finish. Seems transaction is not >> working correctly on Windows, but I do not understand why it happens >> only on Windows. >> >> Could you give me any suggestions to solve this Windows-dependent problem? >> >> Thanks, >> >> Kei >> Cytoscape Core Developer >> >> -- >> Keiichiro Ono http://www.keiono.net/ >> _______________________________________________ >> Neo4j mailing list >> User@lists.neo4j.org >> https://lists.neo4j.org/mailman/listinfo/user > > _______________________________________________ > Neo4j mailing list > User@lists.neo4j.org > https://lists.neo4j.org/mailman/listinfo/user > > > > -- > Keiichiro Ono http://www.keiono.net/ > _______________________________________________ > Neo4j mailing list > User@lists.neo4j.org > https://lists.neo4j.org/mailman/listinfo/user _______________________________________________ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
