Hi Michael, I added a print statement to my code to output how many nodes have been inserted. The script zips along until it gets up around 18.6K nodes. Then the program halts when a Java exception is thrown, as shown below.
Inserting user 18629 Inserting user 18630 Inserting user 18631 Inserting user 18632 Inserting user 18633 Inserting user 18634 Inserting user 18635 Traceback (most recent call last): File "jive_app_db_graph_construction.py", line 53, in <module> node_idx['userid'][user_node['userid']] = user_node File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "<string>", line 11, in transaction RuntimeError: An unknown error occured while handling a Java Exception Strangely enough, the script returned a more explicit Out of Heap Memory error once when I reran the script. It's bizarre that the failure output is not consistent, given I start with a clean DB each time. Increasing the amount of available heap memory seems like the reasonable place to start. If you can let me know how to specify the amount of heap memory for the JVM instantiated by the bindings, that'd be great. I'm running on a MacBook Pro with 8 gigs of memory running OSX 10.6.8. Here's the contents of the messages.log file. 2011-10-14 10:34:17.336-0700: Creating new db @ /Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng/neostore 2011-10-14 10:34:17.419-0700: Opened [/Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng/nioneo_logical.log.1] clean empty log, version=0, lastTxId=1 2011-10-14 10:34:17.441-0700: Opened [/Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng/index/lucene.log.1] clean empty log, version=0, lastTxId=1 2011-10-14 10:34:17.443-0700: TM new log: tm_tx_log.1 2011-10-14 10:34:17.451-0700: --- CONFIGURATION START --- 2011-10-14 10:34:17.451-0700: Physical mem: 8192MB, Heap size: 123MB 2011-10-14 10:34:17.452-0700: Kernel version: Neo4j - Graph Database Kernel 1.5-SNAPSHOT (revision: 1.5.M02-4-g3d1e9d8) 2011-10-14 10:34:17.453-0700: Neo4j - Graph Database Kernel 1.5-SNAPSHOT (revision: 1.5.M02-4-g3d1e9d8) 2011-10-14 10:34:17.456-0700: Operating System: Mac OS X; version: 10.6.8; arch: x86_64; cpus: 8 2011-10-14 10:34:17.456-0700: VM Name: Java HotSpot(TM) 64-Bit Server VM 2011-10-14 10:34:17.456-0700: VM Vendor: Apple Inc. 2011-10-14 10:34:17.456-0700: VM Version: 20.1-b02-384 2011-10-14 10:34:17.456-0700: Boot Class Path: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsfd.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/laf.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/sunrsasign.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar 2011-10-14 10:34:17.457-0700: Class Path: /Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/antlr-2.7.7.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/asm-3.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/asm-analysis-3.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/asm-commons-3.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/asm-tree-3.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/asm-util-3.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/blueprints-core-0.9.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/geronimo-jta_1.1_spec-1.1.1.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages /neo4j/javalib/gremlin-1.2.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/groovy-1.8.1.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/jansi-1.5.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/jettison-1.3.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/lucene-core-3.1.0.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-cypher-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-graph-algo-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-graph-matching-1.5-SNAPSHOT.jar:/Users/chri s.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-jmx-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-kernel-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-lucene-index-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/neo4j-udc-1.5-SNAPSHOT.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/pipes-0.7.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/scala-library-2.9.0-1.jar:/Users/chris.diehl/.virtualenvs/py26-neo4j-embedded/lib/python2.6/site-packages/neo4j/javalib/stax-api-1.0.1.jar 2011-10-14 10:34:17.457-0700: Library Path: .:/Users/chris.diehl/Library/Java/Extensions:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java 2011-10-14 10:34:17.459-0700: Garbage Collector: ParNew: [Par Eden Space, Par Survivor Space] 2011-10-14 10:34:17.459-0700: Garbage Collector: ConcurrentMarkSweep: [Par Eden Space, Par Survivor Space, CMS Old Gen, CMS Perm Gen] 2011-10-14 10:34:17.459-0700: VM Arguments: [] 2011-10-14 10:34:17.459-0700: 2011-10-14 10:34:17.460-0700: create=true 2011-10-14 10:34:17.460-0700: logical_log=/Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng/nioneo_logical.log 2011-10-14 10:34:17.460-0700: neo_store=/Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng/neostore 2011-10-14 10:34:17.460-0700: neostore.nodestore.db.mapped_memory=20M 2011-10-14 10:34:17.460-0700: neostore.propertystore.db.arrays.mapped_memory=130M 2011-10-14 10:34:17.460-0700: neostore.propertystore.db.index.keys.mapped_memory=1M 2011-10-14 10:34:17.460-0700: neostore.propertystore.db.index.mapped_memory=1M 2011-10-14 10:34:17.460-0700: neostore.propertystore.db.mapped_memory=90M 2011-10-14 10:34:17.460-0700: neostore.propertystore.db.strings.mapped_memory=130M 2011-10-14 10:34:17.461-0700: neostore.relationshipstore.db.mapped_memory=100M 2011-10-14 10:34:17.461-0700: node_auto_indexing=false 2011-10-14 10:34:17.461-0700: rebuild_idgenerators_fast=true 2011-10-14 10:34:17.461-0700: relationship_auto_indexing=false 2011-10-14 10:34:17.461-0700: store_dir=/Users/chris.diehl/Graphs/ JiveCommunityV5.0.ng 2011-10-14 10:34:17.461-0700: use_memory_mapped_buffers=true 2011-10-14 10:34:17.461-0700: --- CONFIGURATION END --- 2011-10-14 10:34:17.518-0700: Extension org.neo4j.kernel.KernelExtension[kernel jmx] loaded ok 2011-10-14 10:34:17.520-0700: Extension org.neo4j.kernel.KernelExtension[kernel udc] loaded ok Chris On Thu, Oct 13, 2011 at 8:37 PM, Michael Hunger < michael.hun...@neotechnology.com> wrote: > Hi Chris, > > What do you mean by "ground to a halt" ? Is it using all available CPU or > heavy IO-waits (top, iostat, vmstat)? > > A thread dump (via jps + jstack ) would be great. > > You can probably pass in the config map into the Graph database call. > Current config is logged to messages.log, please share that too as well as > your system parameters (OS, CPU, RAM, Type of disk). > > Michael > > Am 13.10.2011 um 23:52 schrieb Chris Diehl: > > > Hey All, > > > > I just tested a Python script I've been working on to construct a > > multi-relational graph in Neo4j. I am using the new Python bindings for > > embedded Neo4j. After creating about 18K nodes, the database ground to a > > halt. > > > > In the past, when using Gremlin, I would up the heap size for the JVM > when > > encountering problems. I'm not sure how to tweak settings for the JVM now > > that I'm using the Python bindings to fire up the database. Can I do that > > from the GraphDatabase() call? Or do I need to look elsewhere to tweak > the > > JVM parameters? > > > > If you have any other suggestions about parameters I should change, I'm > all > > ears. > > > > Thanks! > > > > Chris > > > > -- > > View this message in context: > http://neo4j-community-discussions.438527.n3.nabble.com/Configuring-Neo4J-via-Python-bindings-tp3419961p3419961.html > > Sent from the Neo4j Community Discussions mailing list archive at > Nabble.com. > > _______________________________________________ > > 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 > _______________________________________________ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user