Can you describe how you see that it "stops"? Because the thread dump isn't showing anything of significance running.
David On Thu, Nov 10, 2011 at 3:28 PM, andrew ton <[email protected]> wrote: > > > Hi David, > > The total size of files stored into the db when the problem happened was > only 800KB. My RAM is 4G. > I ran the kill command when the problem happened because it just stopped > and I did not notice slowness. > > I will increase the heap to 512MB and test again. > > Thanks, > Andrew > > > ________________________________ > From: David Montag <[email protected]> > To: Neo4j user discussions <[email protected]> > Sent: Thursday, November 10, 2011 3:00 PM > Subject: Re: [Neo4j] Neo4j REST server's log files > > 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 <[email protected]> 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 <[email protected]> > > To: Neo4j user discussions <[email protected]> > > 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 <[email protected]> > 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 <[email protected]> > > > To: Peter Neubauer <[email protected]> > > > Cc: Neo4j user discussions <[email protected]> > > > 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 < > > > [email protected]> 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 <[email protected]> > > > 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 <[email protected]> > > > > > To: Neo4j user discussions <[email protected]> > > > > > 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" <[email protected]> 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 <[email protected]> > > > > >> To: Neo4j user discussions <[email protected]> > > > > >> 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" <[email protected]> > 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 > > > > >> > [email protected] > > > > >> > https://lists.neo4j.org/mailman/listinfo/user > > > > >> > > > > > >> _______________________________________________ > > > > >> Neo4j mailing list > > > > >> [email protected] > > > > >> https://lists.neo4j.org/mailman/listinfo/user > > > > >> _______________________________________________ > > > > >> Neo4j mailing list > > > > >> [email protected] > > > > >> https://lists.neo4j.org/mailman/listinfo/user > > > > >> > > > > > _______________________________________________ > > > > > Neo4j mailing list > > > > > [email protected] > > > > > https://lists.neo4j.org/mailman/listinfo/user > > > > > _______________________________________________ > > > > > Neo4j mailing list > > > > > [email protected] > > > > > https://lists.neo4j.org/mailman/listinfo/user > > > > > > > > > > > > > > > > > > > > > -- > > > David Montag <[email protected]> > > > Neo Technology, www.neotechnology.com > > > Cell: 650.556.4411 > > > Skype: ddmontag > > > _______________________________________________ > > > Neo4j mailing list > > > [email protected] > > > https://lists.neo4j.org/mailman/listinfo/user > > > _______________________________________________ > > > Neo4j mailing list > > > [email protected] > > > https://lists.neo4j.org/mailman/listinfo/user > > > > > > > > > > > -- > > David Montag <[email protected]> > > Neo Technology, www.neotechnology.com > > Cell: 650.556.4411 > > Skype: ddmontag > > _______________________________________________ > > Neo4j mailing list > > [email protected] > > https://lists.neo4j.org/mailman/listinfo/user > > > > _______________________________________________ > > Neo4j mailing list > > [email protected] > > https://lists.neo4j.org/mailman/listinfo/user > > > > > > > -- > David Montag <[email protected]> > Neo Technology, www.neotechnology.com > Cell: 650.556.4411 > Skype: ddmontag > _______________________________________________ > Neo4j mailing list > [email protected] > https://lists.neo4j.org/mailman/listinfo/user > _______________________________________________ > Neo4j mailing list > [email protected] > https://lists.neo4j.org/mailman/listinfo/user > -- David Montag <[email protected]> Neo Technology, www.neotechnology.com Cell: 650.556.4411 Skype: ddmontag _______________________________________________ Neo4j mailing list [email protected] https://lists.neo4j.org/mailman/listinfo/user
