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POUsing relationship index on gremlin is relatively slow
 

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  1. POUsing relationship index on gremlin is relatively slow
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    <p>In Neo4j, I have a relationship index 'index_e_ASSOC_sMETHdGEXP' containing about 180000 edges, all with an attribute 'property'. I want to do a simple query that lists 200 edges from the index, at this point regardless of the property value (later do a query like fetch the same attribute values for the 200 first edge out vertices where the edge property &lt;= 0.01), and fetch a few attribute values from the out node:</p> <pre><code>time = System.currentTimeMillis(); t = new Table(); g.idx('index_e_ASSOC_sMETHdGEXP')[[property: Neo4jTokens.QUERY_HEADER + "*"]][0..200].outV().id.as('nodeId').back(1).alias.as("alias").back(1).chr.as('chr').table(t,["nodeId","alias","chr"]).iterate(); System.currentTimeMillis() - time </code></pre> <p><strong>=713ms</strong></p> <p>Getting the 200 first edges from the index takes <strong>262ms</strong>:</p> <pre><code>time = System.currentTimeMillis(); g.idx('index_e_ASSOC_sMETHdGEXP')[[property: Neo4jTokens.QUERY_HEADER + "*"]][0..200]; System.currentTimeMillis() - time </code></pre> <p>Why is the first query completed so slowly? It shouldn't take this long to get 200 edges from a "predetermined list" and fetch a few attribute values from every output node. I'm a complete newbie when it comes to Cypher and Gremlin, so is there a faster way to do this query, either in Cypher or Gremlin? </p> <p>Edit: ran the query (1) 23 times:</p> <pre><code>==&gt; 1124 ==&gt; 983 ==&gt; 951 ==&gt; 864 ==&gt; 1175 ==&gt; 1189 ==&gt; 889 ==&gt; 917 ==&gt; 822 ==&gt; 872 ==&gt; 795 ==&gt; 736 ==&gt; 840 ==&gt; 1189 ==&gt; 723 ==&gt; 756 ==&gt; 691 ==&gt; 44609 ==&gt; 644 ==&gt; 640 ==&gt; 1110 ==&gt; 1007 ==&gt; 819 </code></pre> <p>Edit2: I have since re-imported the database with the following configuration:</p> <pre><code>dump_configuration=true cache_type=gcr neostore.nodestore.db.mapped_memory=100M neostore.relationshipstore.db.mapped_memory=4G neostore.propertystore.db.mapped_memory=200M neostore.propertystore.db.strings.mapped_memory=1G neostore.propertystore.db.arrays.mapped_memory=1G neostore.propertystore.db.index.keys.mapped_memory=1G neostore.propertystore.db.index.mapped_memory=1G relationship_cache_array_fraction=8 node_cache_array_fraction=8 node_cache_size=3G relationship_cache_size=6G </code></pre> <p>Now the query(1) actually takes longer: <strong>23849 ms</strong>. It's starting to look like a cache issue.</p> <p>Interesting snippets of the db log:</p> <pre><code>2012-07-06 10:51:49,149 DEBUG [neo4j.diagnostics]: System memory information: 2012-07-06 10:51:49,152 DEBUG [neo4j.diagnostics]: Total Physical memory: 26,37 GB 2012-07-06 10:51:49,152 DEBUG [neo4j.diagnostics]: Free Physical memory: 11,99 GB 2012-07-06 10:51:49,153 DEBUG [neo4j.diagnostics]: Committed virtual memory: 16,43 GB 2012-07-06 10:51:49,153 DEBUG [neo4j.diagnostics]: Total swap space: 27,00 GB 2012-07-06 10:51:49,153 DEBUG [neo4j.diagnostics]: Free swap space: 26,96 GB 2012-07-06 10:51:49,154 DEBUG [neo4j.diagnostics]: JVM memory information: 2012-07-06 10:51:49,154 DEBUG [neo4j.diagnostics]: Free memory: 1,84 GB 2012-07-06 10:51:49,154 DEBUG [neo4j.diagnostics]: Total memory: 1,87 GB 2012-07-06 10:51:49,154 DEBUG [neo4j.diagnostics]: Max memory: 13,33 GB 2012-07-06 10:51:49,588 DEBUG [neo4j.diagnostics]: Storage files: 2012-07-06 10:51:49,589 DEBUG [neo4j.diagnostics]: messages.log: 304,72 kB 2012-07-06 10:51:49,589 DEBUG [neo4j.diagnostics]: neostore.propertystore.db.index: 1,02 kB 2012-07-06 10:51:49,589 DEBUG [neo4j.diagnostics]: neostore.propertystore.db: 401,18 MB 2012-07-06 10:51:49,590 DEBUG [neo4j.diagnostics]: neostore.relationshipstore.db.id: 9,00 B 2012-07-06 10:51:49,590 DEBUG [neo4j.diagnostics]: index.db: 1,42 kB 2012-07-06 10:51:49,590 DEBUG [neo4j.diagnostics]: tm_tx_log.1: 0,00 B 2012-07-06 10:51:49,590 DEBUG [neo4j.diagnostics]: neostore.relationshiptypestore.db.names.id: 9,00 B 2012-07-06 10:51:49,591 DEBUG [neo4j.diagnostics]: neostore.propertystore.db.id: 9,00 B 2012-07-06 10:51:49,591 DEBUG [neo4j.diagnostics]: neostore.nodestore.db: 478,88 kB 2012-07-06 10:51:49,591 DEBUG [neo4j.diagnostics]: nioneo_logical.log.active: 4,00 B 2012-07-06 10:51:49,591 DEBUG [neo4j.diagnostics]: neostore.nodestore.db.id: 9,00 B 2012-07-06 10:51:49,591 DEBUG [neo4j.diagnostics]: neostore.propertystore.db.strings.id: 9,00 B 2012-07-06 10:51:49,592 DEBUG [neo4j.diagnostics]: neostore.id: 9,00 B 2012-07-06 10:51:49,592 DEBUG [neo4j.diagnostics]: neostore.propertystore.db.strings: 34,15 MB 2012-07-06 10:51:49,592 DEBUG [neo4j.diagnostics]: neostore.relationshiptypestore.db.id: 9,00 B 2012-07-06 10:53:01,486 INFO [neo4j]: GC Monitor: Application threads blocked for an additional 14826ms [total block time: 14.826s] 2012-07-06 10:54:24,019 INFO [neo4j]: GC Monitor: Application threads blocked for an additional 875ms [total block time: 15.701s] 2012-07-06 10:55:25,441 INFO [neo4j]: GC Monitor: Application threads blocked for an additional 559ms [total block time: 16.26s] 2012-07-06 11:00:16,962 INFO [neo4j]: GC Monitor: Application threads blocked for an additional 775ms [total block time: 17.035s] </code></pre> <p>JVM parameters include </p> <pre><code>-XX:+DisableExplicitGC -Xms2000m, -Xmx15360m </code></pre> <p>It seems that the garbage collector interferes with the execution, why is that? With the JVM params I'm telling to the server instance to use max amount of ~15GB memory which should be plenty.</p> <p>Edit4: Doing query(1) adds the following to the log:</p> <pre><code>2012-07-06 11:40:31,973 INFO [neo4j]: GC Monitor: Application threads blocked for an additional 23745ms [total block time: 23.745s] 2012-07-06 11:40:33,961 INFO [neo4j]: RelationshipCache array size: 17895751 purge count: 0 size is: 0b, 100.0% misses, NaN% collisions (0). 2012-07-06 11:40:33,966 INFO [neo4j]: NodeCache array size: 17895751 purge count: 0 size is: 0b, 100.0% misses, NaN% collisions (0). </code></pre>
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