Hi Andrew, I don't see anything running in that thread dump. No threads are processing requests. Are you sure it's taking a long time, or is it maybe finished? Try capturing the thread dump exactly when you experience slowness. I'd also suggest bumping the initial heap to at least 512MB or something like that. How much RAM do you have? How much data are you inserting?
Thanks, David On Thu, Nov 10, 2011 at 2:56 PM, andrew ton <andrewt...@yahoo.com> wrote: > > > Hi David, > > I increased the memory settings in neo4j-wrapper.conf as below > # Initial Java Heap Size (in MB) > wrapper.java.initmemory=30 > > # Maximum Java Heap Size (in MB) > wrapper.java.maxmemory=1024 > > However the same problem is still happening. I attach the thread dump to > this mail. I appreciate it if you tell me what's wrong based on the thread > dump. > > Thank you! > > > ________________________________ > From: David Montag <david.mon...@neotechnology.com> > To: Neo4j user discussions <user@lists.neo4j.org> > Sent: Thursday, November 10, 2011 11:39 AM > Subject: Re: [Neo4j] Neo4j REST server's log files > > Hi Andrew, > > Good to hear that you got the logging sorted out. > > Regarding the actual issues, it sounds like you're describing two different > things. One is that you index ontology nodes in one global index and > therefore run into conflicts. The other is that the upload appears to stall > for some reason. > > Regarding the global index, did you intend to design the system that way, > or do you really want a separate index for each ontology? It sounds like > that would be reasonable. > > As for the stalled upload, a thread dump during the slow processing would > be most helpful. On a Linux system, you can capture that by doing kill -3 > <pid> on the Java process. It should then go to console.log. > > Thanks, > David > > On Thu, Nov 10, 2011 at 8:21 AM, andrew ton <andrewt...@yahoo.com> wrote: > > > > > > > Hi David, > > > > Thank you for getting back to me! > > Finally I can make it work by changing the log level from INFO (by > > default) to FINEST in the logging.property. > > > > I have a question for you though. Currently my project have a problem > with > > uploading data to the store. I created only 1 index for the whole > > application and the node name as the key. Several nodes in different > > ontologies have the same names. So when an ontology is uploaded to the > > store and has a node that its name has been already in the index (by > > previous ontologies) this node is not created in the graph of this > > ontology. My app can upload a number of ontologies and graphs are created > > successfully for each ontology in the store. However when the process > > uploads the 9th ontology the store does not respond and it seems busy > with > > some internal process like looking up the node in the index or something > > else. I'm stuck and don't know the cause of the problem. Do you have any > > clue or suggestions? > > > > Appreciate your help! > > > > Regards, > > > > > > ________________________________ > > From: David Montag <david.mon...@neotechnology.com> > > To: Peter Neubauer <peter.neuba...@neotechnology.com> > > Cc: Neo4j user discussions <user@lists.neo4j.org> > > Sent: Wednesday, November 9, 2011 10:07 PM > > Subject: Re: [Neo4j] Neo4j REST server's log files > > > > Hi Andrew, > > > > Let's connect during the day tomorrow for a higher-bandwidth discussion. > Do > > you have Skype? > > > > Thanks, > > David > > > > On Wed, Nov 9, 2011 at 1:23 PM, Peter Neubauer < > > peter.neuba...@neotechnology.com> wrote: > > > > > Andrew, > > > this sounds like the RRD database in the server got broken. Could you > > > delete data/rrd and start up again? Also, David is in your timezone > > > and maybe can connect with you directly to look into this? > > > > > > Cheers, > > > > > > /peter neubauer > > > > > > GTalk: neubauer.peter > > > Skype peter.neubauer > > > Phone +46 704 106975 > > > LinkedIn http://www.linkedin.com/in/neubauer > > > Twitter http://twitter.com/peterneubauer > > > > > > http://www.neo4j.org - NOSQL for the Enterprise. > > > http://startupbootcamp.org/ - Öresund - Innovation happens HERE. > > > > > > > > > > > > On Wed, Nov 9, 2011 at 10:07 PM, andrew ton <andrewt...@yahoo.com> > > wrote: > > > > > > > > > > > > Hi Peter, > > > > > > > > I don't understand much your question. However, in my Restlet > > > application I have a logging service using Java log to record all > > processes > > > in my app. My problem is that I upload 20 ontologies and after serveral > > > ontologies the Neo4J stops responding my REST request. It seems busy > with > > > some index lookup process. Consequently my app throws > > > a NoHttpResponseException: The target server failed to respond. > > > > I'd like to see what causes the problem inside Neo4J. Unfortunately > > both > > > messages.log and neo4j.x.x.log do not show run time processes. > > > > BTW, when I start up the server the neo4j.x.x.log shows > > > > > > > > INFO: Server started on [http://localhost:7474/] > > > > Nov 9, 2011 10:22:22 AM org.neo4j.server.logging.Logger log > > > > WARNING: > > > > java.lang.IllegalArgumentException: Bad sample time: 1320862942. Last > > > update time was 1320862942, at least one second step is required > > > > at org.rrd4j.core.RrdDb.store(RrdDb.java:553) > > > > at org.rrd4j.core.Sample.update(Sample.java:197) > > > > at > > > > org.neo4j.server.rrd.RrdSamplerImpl.updateSample(RrdSamplerImpl.java:62) > > > > at > org.neo4j.server.rrd.RrdFactory$1.updateSample(RrdFactory.java:109) > > > > at org.neo4j.server.rrd.RrdJob.run(RrdJob.java:43) > > > > at org.neo4j.server.rrd.ScheduledJob$1.run(ScheduledJob.java:41) > > > > at java.util.TimerThread.mainLoop(Timer.java:512) > > > > at java.util.TimerThread.run(Timer.java:462) > > > > > > > > .... > > > > > > > > Nov 9, 2011 12:43:44 PM > com.sun.jersey.api.core.PackagesResourceConfig > > > init > > > > INFO: Scanning for root resource and provider classes in the > packages: > > > > org.neo4j.server.webadmin.rest > > > > Nov 9, 2011 12:43:44 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > logClasses > > > > INFO: Root resource classes found: > > > > class org.neo4j.server.webadmin.rest.MonitorService > > > > class org.neo4j.server.webadmin.rest.RootService > > > > class org.neo4j.server.webadmin.rest.JmxService > > > > class org.neo4j.server.webadmin.rest.ConsoleService > > > > Nov 9, 2011 12:43:44 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > init > > > > INFO: No provider classes found. > > > > Nov 9, 2011 12:43:44 PM > > > com.sun.jersey.server.impl.application.WebApplicationImpl _initiate > > > > INFO: Initiating Jersey application, version 'Jersey: 1.9 09/02/2011 > > > 11:17 AM' > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.PackagesResourceConfig > > > init > > > > INFO: Scanning for root resource and provider classes in the > packages: > > > > org.neo4j.server.rest.web > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > logClasses > > > > INFO: Root resource classes found: > > > > class org.neo4j.server.rest.web.ResourcesService > > > > class org.neo4j.server.rest.web.BatchOperationService > > > > class org.neo4j.server.rest.web.RestfulGraphDatabase > > > > class org.neo4j.server.rest.web.DatabaseMetadataService > > > > class org.neo4j.server.rest.web.ExtensionService > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > logClasses > > > > INFO: Provider classes found: > > > > class org.neo4j.server.rest.web.DatabaseBlockedExceptionMapper > > > > Nov 9, 2011 12:43:45 PM > > > com.sun.jersey.server.impl.application.WebApplicationImpl _initiate > > > > INFO: Initiating Jersey application, version 'Jersey: 1.9 09/02/2011 > > > 11:17 AM' > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.PackagesResourceConfig > > > init > > > > INFO: Scanning for root resource and provider classes in the > packages: > > > > org.neo4j.server.rest.discovery > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > logClasses > > > > INFO: Root resource classes found: > > > > class org.neo4j.server.rest.discovery.DiscoveryService > > > > Nov 9, 2011 12:43:45 PM > com.sun.jersey.api.core.ScanningResourceConfig > > > init > > > > INFO: No provider classes found. > > > > Nov 9, 2011 12:43:45 PM > > > com.sun.jersey.server.impl.application.WebApplicationImpl _initiate > > > > INFO: Initiating Jersey application, version 'Jersey: 1.9 09/02/2011 > > > 11:17 AM' > > > > > > > > Sorry for this long mail. > > > > > > > > Thanks, > > > > > > > > > > > > ________________________________ > > > > From: Peter Neubauer <peter.neuba...@neotechnology.com> > > > > To: Neo4j user discussions <user@lists.neo4j.org> > > > > Sent: Wednesday, November 9, 2011 10:29 AM > > > > Subject: Re: [Neo4j] Neo4j REST server's log files > > > > > > > > Andrew, > > > > Go you have the generating code somewhere you check and reproduce? > > > > On Nov 9, 2011 6:26 PM, "andrew ton" <andrewt...@yahoo.com> wrote: > > > > > > > >> > > > >> > > > >> Hi Peter, > > > >> > > > >> I tried the messages.log but it only showed processes up to the time > > > when > > > >> the server is up > > > >> > > > >> 2011-11-09 08:59:19.669-0800: --- CONFIGURATION END --- > > > >> 2011-11-09 08:59:19.733-0800: Extension > > > >> org.neo4j.kernel.KernelExtension[kernel jmx] loaded ok > > > >> 2011-11-09 08:59:19.857-0800: Extension > > > >> org.neo4j.kernel.KernelExtension[shell] loaded ok > > > >> 2011-11-09 08:59:19.858-0800: Extension > > > >> org.neo4j.kernel.KernelExtension[kernel udc] loaded ok > > > >> > > > >> The manual shows that the logging is configured in > > > conf/logging.properties > > > >> (java.util.logging.FileHandler.pattern=data/log/neo4j.%u.%g.log). > I'm > > > using > > > >> the default settings but the log file was not updated in the run > time. > > > >> My purpose is that I want to see what is wrong when I failed to > store > > an > > > >> ontology into Neo4J. > > > >> Please help me out! > > > >> > > > >> Thanks and regards, > > > >> > > > >> > > > >> > > > >> ________________________________ > > > >> From: Peter Neubauer <peter.neuba...@neotechnology.com> > > > >> To: Neo4j user discussions <user@lists.neo4j.org> > > > >> Sent: Wednesday, November 9, 2011 8:46 AM > > > >> Subject: Re: [Neo4j] Neo4j REST server's log files > > > >> > > > >> Andrew, > > > >> The database logs are in data/graphdb / messages.log > > > >> On Nov 9, 2011 5:39 PM, "andrew ton" <andrewt...@yahoo.com> wrote: > > > >> > > > >> > > > > >> > > > > >> > Hi, > > > >> > > > > >> > What log files of the Neo4J REST server can I use to check what's > > > going > > > >> on > > > >> > in the server? The log/console.log and neo4j.x.x.log do not show > > > >> > transactions in the run time. I also looked into > > graph.db/tm_tx_log.x > > > >> but I > > > >> > did not learn anything from there. Can somebody give me some > > pointers? > > > >> > > > > >> > Thanks, > > > >> > _______________________________________________ > > > >> > 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 > > > >> > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > -- > > David Montag <david.mon...@neotechnology.com> > > Neo Technology, www.neotechnology.com > > Cell: 650.556.4411 > > Skype: ddmontag > > _______________________________________________ > > 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 > > > > > > -- > David Montag <david.mon...@neotechnology.com> > Neo Technology, www.neotechnology.com > Cell: 650.556.4411 > Skype: ddmontag > _______________________________________________ > 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 > > -- David Montag <david.mon...@neotechnology.com> Neo Technology, www.neotechnology.com Cell: 650.556.4411 Skype: ddmontag _______________________________________________ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
