Note that attachments are generally stripped from Apache mailing lists, it is
usually better to just cut and paste inline
Since you CC’d me directly I did get the attachments, the most interesting of
which is the stack trace including here for the benefit of the rest of the list
with some analysis interspersed
default task-38
at java.lang.OutOfMemoryError.<init>()V (OutOfMemoryError.java:48)
at
org.apache.jena.ext.com.google.common.cache.LocalCache$Strength$1.referenceValue(Lorg/apache/jena/ext/com/google/common/cache/LocalCache$Segment;Lorg/apache/jena/ext/com/google/common/cache/LocalCache$ReferenceEntry;Ljava/lang/Object;I)Lorg/apache/jena/ext/com/google/common/cache/LocalCache$ValueReference;
(LocalCache.java:382)
at
As I expected it does appear to be in the cache where the stack trace
originates, however since this is the standard Google Guava cache that is
happily used in many production installations across many different companies
across many different projects far beyond Jena I would suspect that is actually
something else that is the root cause.
org.apache.jena.ext.com.google.common.cache.LocalCache$Segment.setValue(Lorg/apache/jena/ext/com/google/common/cache/LocalCache$ReferenceEntry;Ljava/lang/Object;Ljava/lang/Object;J)V
(LocalCache.java:2165)
at
org.apache.jena.ext.com.google.common.cache.LocalCache$Segment.put(Ljava/lang/Object;ILjava/lang/Object;Z)Ljava/lang/Object;
(LocalCache.java:2883)
at
org.apache.jena.ext.com.google.common.cache.LocalCache.put(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;
(LocalCache.java:4149)
at
org.apache.jena.ext.com.google.common.cache.LocalCache$LocalManualCache.put(Ljava/lang/Object;Ljava/lang/Object;)V
(LocalCache.java:4754)
at
org.apache.jena.atlas.lib.cache.CacheGuava.put(Ljava/lang/Object;Ljava/lang/Object;)V
(CacheGuava.java:76)
at
org.apache.jena.tdb.store.nodetable.NodeTableCache.cacheUpdate(Lorg/apache/jena/graph/Node;Lorg/apache/jena/tdb/store/NodeId;)V
(NodeTableCache.java:207)
at
org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(Lorg/apache/jena/tdb/store/NodeId;)Lorg/apache/jena/graph/Node;
(NodeTableCache.java:129)
at
org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(Lorg/apache/jena/tdb/store/NodeId;)Lorg/apache/jena/graph/Node;
(NodeTableCache.java:82)
at
org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(Lorg/apache/jena/tdb/store/NodeId;)Lorg/apache/jena/graph/Node;
(NodeTableWrapper.java:50)
at
org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(Lorg/apache/jena/tdb/store/NodeId;)Lorg/apache/jena/graph/Node;
(NodeTableInline.java:67)
at
org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(Lorg/apache/jena/tdb/store/NodeId;)Lorg/apache/jena/graph/Node;
(NodeTableWrapper.java:50)
at
org.apache.jena.tdb.solver.BindingTDB.get1(Lorg/apache/jena/sparql/core/Var;)Lorg/apache/jena/graph/Node;
(BindingTDB.java:122)
at
org.apache.jena.sparql.engine.binding.BindingBase.get(Lorg/apache/jena/sparql/core/Var;)Lorg/apache/jena/graph/Node;
(BindingBase.java:121)
at
org.apache.jena.sparql.expr.ExprLib.evalOrElse(Lorg/apache/jena/sparql/expr/Expr;Lorg/apache/jena/sparql/engine/binding/Binding;Lorg/apache/jena/sparql/function/FunctionEnv;Lorg/apache/jena/sparql/expr/NodeValue;)Lorg/apache/jena/sparql/expr/NodeValue;
(ExprLib.java:70)
at
org.apache.jena.sparql.expr.ExprLib.evalOrNull(Lorg/apache/jena/sparql/expr/Expr;Lorg/apache/jena/sparql/engine/binding/Binding;Lorg/apache/jena/sparql/function/FunctionEnv;)Lorg/apache/jena/sparql/expr/NodeValue;
(ExprLib.java:38)
at
org.apache.jena.sparql.expr.aggregate.AccumulatorExpr.accumulate(Lorg/apache/jena/sparql/engine/binding/Binding;Lorg/apache/jena/sparql/function/FunctionEnv;)V
(AccumulatorExpr.java:50)
at
org.apache.jena.sparql.engine.iterator.QueryIterGroup$1.initializeIterator()Ljava/util/Iterator;
(QueryIterGroup.java:111)
This shows that you are using grouping, this wasn’t in the example query you
sent so this is not a stack trace associated with that specific query.
at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init()V
(IteratorDelayedInitialization.java:40)
at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext()Z
(IteratorDelayedInitialization.java:50)
at
org.apache.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding()Z
(QueryIterPlainWrapper.java:53)
at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext()Z
(QueryIteratorBase.java:114)
at
org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding()Z
(QueryIterProcessBinding.java:66)
at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext()Z
(QueryIteratorBase.java:114)
at org.apache.jena.sparql.engine.iterator.QueryIterConvert.hasNextBinding()Z
(QueryIterConvert.java:58)
at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext()Z
(QueryIteratorBase.java:114)
at
org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding()Z
(QueryIteratorWrapper.java:39)
at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext()Z
(QueryIteratorBase.java:114)
at
org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding()Z
(QueryIteratorWrapper.java:39)
at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext()Z
(QueryIteratorBase.java:114)
at org.apache.jena.sparql.engine.ResultSetStream.hasNext()Z
(ResultSetStream.java:74)
at org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext()Z
(ResultSetCheckCondition.java:55)
at
es.semantic.project.serialize.ResultSetSerializer.asJSON()Ljava/lang/String;
(ResultSetSerializer.java:161)
This looks suspect to me, this is a method from your own code that produces a
JSON string that encodes a result set. Depending on the results set the string
could be very large and occupy a large portion of memory. Or equally if you are
handling many requests in parallel storing many otherwise reasonably sized
strings could exhaust memory.
The general practice is to stream results directly back to the client, the
details of how you do that will be specific to the framework you are using.
This avoids buffering the entire results in memory which will also explain some
of your perceived performance issues because your users are always forced to
wait for the complete results set to be calculated before getting any response
at
es.semantic.project.serialize.Serializer.writeAs(Ljava/lang/String;)Ljava/lang/String;
(Serializer.java:98)
at
es.semantic.project.serialize.Serializer.writeAs(Ljavax/ws/rs/core/MediaType;)Ljava/lang/String;
(Serializer.java:69)
at
es.semantic.project.rest.QueryRestService.executeQuery(Les/semantic/project/storage/sql/SparqlQuery$Scope;Ljava/lang/String;Ljavax/ws/rs/core/Request;)Ljavax/ws/rs/core/Response;
(QueryRestService.java:340)
at
es.semantic.project.rest.QueryRestService$Proxy$_$$_WeldClientProxy.executeQuery(Les/semantic/project/storage/sql/SparqlQuery$Scope;Ljava/lang/String;Ljavax/ws/rs/core/Request;)Ljavax/ws/rs/core/Response;
(Unknown Source)
at
sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
(DelegatingMethodAccessorImpl.java:43)
at
java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
(Method.java:498)
at
org.jboss.resteasy.core.MethodInjectorImpl.invoke(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;Ljava/lang/Object;)Ljava/lang/Object;
(MethodInjectorImpl.java:139)
at
org.jboss.resteasy.core.ResourceMethodInvoker.invokeOnTarget(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;Ljava/lang/Object;)Lorg/jboss/resteasy/specimpl/BuiltResponse;
(ResourceMethodInvoker.java:295)
at
org.jboss.resteasy.core.ResourceMethodInvoker.invoke(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;Ljava/lang/Object;)Lorg/jboss/resteasy/specimpl/BuiltResponse;
(ResourceMethodInvoker.java:249)
at
org.jboss.resteasy.core.ResourceMethodInvoker.invoke(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;)Lorg/jboss/resteasy/specimpl/BuiltResponse;
(ResourceMethodInvoker.java:236)
at
org.jboss.resteasy.core.SynchronousDispatcher.invoke(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;Lorg/jboss/resteasy/core/ResourceInvoker;)V
(SynchronousDispatcher.java:395)
at
org.jboss.resteasy.core.SynchronousDispatcher.invoke(Lorg/jboss/resteasy/spi/HttpRequest;Lorg/jboss/resteasy/spi/HttpResponse;)V
(SynchronousDispatcher.java:202)
at
org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(Ljava/lang/String;Ljavax/servlet/http/HttpServletRequest;Ljavax/servlet/http/HttpServletResponse;Z)V
(ServletContainerDispatcher.java:221)
at
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(Ljava/lang/String;Ljavax/servlet/http/HttpServletRequest;Ljavax/servlet/http/HttpServletResponse;)V
(HttpServletDispatcher.java:56)
at
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(Ljavax/servlet/http/HttpServletRequest;Ljavax/servlet/http/HttpServletResponse;)V
(HttpServletDispatcher.java:51)
at
javax.servlet.http.HttpServlet.service(Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;)V
(HttpServlet.java:790)
at
io.undertow.servlet.handlers.ServletHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletHandler.java:85)
at
io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;)V
(FilterHandler.java:129)
at
org.apache.logging.log4j.web.Log4jServletFilter.doFilter(Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;Ljavax/servlet/FilterChain;)V
(Log4jServletFilter.java:71)
at
io.undertow.servlet.core.ManagedFilter.doFilter(Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;Ljavax/servlet/FilterChain;)V
(ManagedFilter.java:60)
at
io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;)V
(FilterHandler.java:131)
at
io.undertow.servlet.handlers.FilterHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(FilterHandler.java:84)
at
io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletSecurityRoleHandler.java:62)
at
io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletDispatchingHandler.java:36)
at
org.wildfly.extension.undertow.security.SecurityContextAssociationHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(SecurityContextAssociationHandler.java:78)
at
io.undertow.server.handlers.PredicateHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(PredicateHandler.java:43)
at
io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(SSLInformationAssociationHandler.java:131)
at
io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletAuthenticationCallHandler.java:57)
at
io.undertow.server.handlers.PredicateHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(PredicateHandler.java:43)
at
io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(AbstractConfidentialityHandler.java:46)
at
io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletConfidentialityConstraintHandler.java:64)
at
io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(AuthenticationMechanismsHandler.java:60)
at
io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(CachedAuthenticatedSessionHandler.java:77)
at
io.undertow.security.handlers.NotificationReceiverHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(NotificationReceiverHandler.java:50)
at
io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(AbstractSecurityContextAssociationHandler.java:43)
at
io.undertow.server.handlers.PredicateHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(PredicateHandler.java:43)
at
org.wildfly.extension.undertow.security.jacc.JACCContextIdHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(JACCContextIdHandler.java:61)
at
io.undertow.server.handlers.PredicateHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(PredicateHandler.java:43)
at
io.undertow.server.handlers.PredicateHandler.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(PredicateHandler.java:43)
at
io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(Lio/undertow/server/HttpServerExchange;Lio/undertow/servlet/handlers/ServletChain;Lio/undertow/servlet/handlers/ServletRequestContext;Ljavax/servlet/ServletRequest;Ljavax/servlet/ServletResponse;)V
(ServletInitialHandler.java:284)
at
io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(Lio/undertow/server/HttpServerExchange;Lio/undertow/servlet/handlers/ServletRequestContext;Lio/undertow/servlet/handlers/ServletChain;Ljavax/servlet/DispatcherType;)V
(ServletInitialHandler.java:263)
at
io.undertow.servlet.handlers.ServletInitialHandler.access$000(Lio/undertow/servlet/handlers/ServletInitialHandler;Lio/undertow/server/HttpServerExchange;Lio/undertow/servlet/handlers/ServletRequestContext;Lio/undertow/servlet/handlers/ServletChain;Ljavax/servlet/DispatcherType;)V
(ServletInitialHandler.java:81)
at
io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(Lio/undertow/server/HttpServerExchange;)V
(ServletInitialHandler.java:174)
at
io.undertow.server.Connectors.executeRootHandler(Lio/undertow/server/HttpHandler;Lio/undertow/server/HttpServerExchange;)V
(Connectors.java:202)
at io.undertow.server.HttpServerExchange$1.run()V
(HttpServerExchange.java:793)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V
(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run()V
(ThreadPoolExecutor.java:617)
at java.lang.Thread.run()V (Thread.java:745)
Nothing looks obviously wrong with either your query or your sample data though
as I noted you didn’t provide the exact query that triggered this particular
stack trace
Rob
On 23/10/2017 15:59, "George News" <george.n...@gmx.net> wrote:
On 2017-10-11 15:47, Rob Vesse wrote:
> Comments inline:
>
> On 11/10/2017 11:57, "George News" <george.n...@gmx.net> wrote:
>
> Hi all,
>
> The project I'm working in currently has a TDB with approximately 100M
> triplets and the size is increasing quite quickly. When I make a
typical
> SPARQL query for getting data from the system, it takes ages,
sometimes
> more than 10-20 minutes. I think performance wise this is not really
> user friendly. Therefore I need to know how I can increase the speed,
etc.
We have made a tdbdump of the current TDB and the size for the figures
we pointed out are about 70GB in RDF/xml format.
> I'm running the whole system on a machine with Intel Xeon E312xx with
> 32Gb RAM and many times I'm getting OutofMemory Exceptions and the
> google.cache that Jena handles is the one that seems to be causing the
> problem.
>
> Specifics stack traces would be useful to understand where the cache is
being exploded. Certain kinds of query may use the cache more heavily than
others so some elaboration on the general construction of queries would be
interesting.
Find ExceptionStackTrace.txt file as an example. Most of the times the
error is quite similar.
>
> Are the figures I'm pointing normal (machine specs, response time,
> etc.)? Is it too big/too small?
>
> The size of the data seems small relative to the size of the machine.
You don’t specify whether you change the JVM heap size, most memory usage in
TDB is off-heap via memory mapped files so setting too large a heap can
negatively impact performance.
>
> The response times seems very poor but that may be the nature of your
queries and data structure, however since you are unable to show those we can
only provide generalisations
>
> For the moment, we have decided to split the graph in pieces, that is,
> generating a new named graph every now and then so the amount of
> information stored in a "current" graph is smaller. Then restricting
the
> query to a set of graphs things work better.
>
> Although this solution works, when we merge the graphs for historical
> queries, we are facing the same problem as before. Then, how can we
> increased the speed?
>
> I cannot disclosed the dataset or part of it, but I will try to
somehow
> explain it.
>
> - Ids for entities are approximately 255 random ASCII characters. Does
> the size of the ids affect the speed of the SPARQL queries? If yes,
can
> I apply a Lucene index to the IDs in order to reduce the query time?
>
> It depends on the nature of the query. All terms are mapped into 64-bit
internal identifiers, these are only mapped back to the original terms as and
when that query engine and/or results serialisation requires it. A cache is
used to speed up the mapping in both directions so depending on the nature of
the queries and your system loads you may be thrashing this cache.
>
> - The depth level of the graph or the information relationship is
around
> 7-8 level at most, but most of the times it is required to link 3-4
levels.
>
> Difficult to say how this impacts performance because it really depends
on how you are querying that structure
>
> - Most of the queries include several:
> ?x myont:hasattribute ?b.
> ?a rdf:type ?b.
>
> Therefore checking the class and subclasses of entities. Is there
anyway
> to speed up the inference as if I'm asking for the parent class I will
> get also the children ones defined in my ontology.
>
> So are you actively using inference? If you are then that will
significantly degrade performance because the inference closure is done
entirely in memory i.e. not in TDB if inference is turned on and you will get
minimal performance benefit from using TDB.
>
> If you only need simple inference like class and property hierarchy you
may be better served by asserting those statically using SPARQL updates and not
using dynamic inference
sorry for the delay on providing examples of data and SPARQL queries we
usually make.
The data we are using is following the ontology that is publicly
available at [1].
Using this ontology, a sample of a semantic document in JSON-LD format
can be found in the files attached (Observation.jsonld and
Resource.jsonld). These individuals are stored in a TDB using JENA, and
are stored in different graphs that can be merged within the code using
MultiUnion in order to make queries. Then we are requesting for data by
using SPARQL Select queries with quite a lot of inference required
(SPARQL.txt).
As you suggested, we have made some tries including more properties
(mainly rdf:type) for the individual descriptions in order to disable
inference from the requests. For instance, whenever I register a
m3-lite#AirThermometer I'm always including it is also a
ssn#SensingDevice. This way this device can be easily discovered by its
more descriptive name and/or by its generic one.
However, the results are not the expected using the same SPARQL
sentences and I have to create specific SPARQL queries to properly
discover the data. Is this the way you suggested to work? Should then I
inform the users of our system about the way we are registering data?
[1]: http://ontology.fiesta-iot.eu/ontologyDocs/fiesta-iot/doc
> - I know the "." in a query acts as more or less like an AND logical
> operation. Does the order of sentences have implications in the
> performance? Should I start with the most restrictive ones? Should I
> start with the simplest ones, i.e. checking number values, etc.?
>
> yes and no. TDB Will attempt to do the necessary scans in an optimal
order based on its knowledge of the statistics of the data. However this only
applies within a single query pattern i.e. { } so depending on the structure of
your query you may need to do some manual reordering. Also if inference is
involved then that may interact.
>
> - Some of the queries uses spatial and time filtering? Is is worth
> implementing the support for spatial searches with SPARQL? Is there
any
> kind of index for time searches?
>
> There is a geospatial indexing extension but there is no temporal
indexing provided by Jena.
As you can see from the Resource.jsonld, we are using location. Do you
think indexing will help on locating the individuals?
>
> Any help is more than welcome.
>
> Without more detail it is difficult to provide more detailed help.
>
> Rob
>
> Regards,
> Jorge
>
>
>
>
>
>
