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From Hasan Hasan <ha...@trialox.org>
Subject Re: leak but where after parsing rdf files?
Date Thu, 13 Jan 2011 20:02:18 GMT
The size is not precise, since I only print out every increase to
multiplication of 100

hasan

On Thu, Jan 13, 2011 at 8:58 PM, Hasan Hasan <hasan@trialox.org> wrote:

> Hi all,
>
> the problem seems to lie in the JenaGraphAdaptor class
> It has a member:
> final BidiMap<BNode, Node> tria2JenaBNodes = new BidiMapImpl<BNode,
> Node>();
>
> which grows each time a serialized graph get parsed.
>
> My experiments with my test data show
>
> At the end of the 1st parsing: Size of tria2JenaBNodes = 87200
> At the end of the 2nd parsing: Size of tria2JenaBNodes = 130800
> At the end of the 3rd parsing: Size of tria2JenaBNodes = 174400
>
> Hasan
>
> On Thu, Jan 13, 2011 at 11:54 AM, Hasan Hasan <hasan@trialox.org> wrote:
>
>> Hi Andy
>>
>> Except that there are quite some bnodes, there's nothing special about the
>> data.
>>
>> Hasan
>>
>>
>> On Thu, Jan 13, 2011 at 9:40 AM, Andy Seaborne <
>> andy.seaborne@epimorphics.com> wrote:
>>
>>> The RIOT parsers should have no state build-up except the necessary bNode
>>> label map - that gets dropped across files.
>>>
>>> Is there anything characteristic about the data?
>>>
>>>        Andy
>>>
>>>
>>> On 13/01/11 07:24, Reto Bachmann-Gmuer wrote:
>>>
>>>> Hi Hasan
>>>>
>>>> great thing to have an alternative parsing provider. I've been takling
>>>> to
>>>> Andy Seaborne about the leak. He's aware of an issue when using the a
>>>> jena-riot parser he thinks it might be caused by a dependency of it.
>>>> Investigating further and doing profiling is high on my TODO-List.
>>>>
>>>> Cheers,
>>>> reto
>>>>
>>>> On Thu, Jan 13, 2011 at 12:08 AM, Hasan Hasan<hasan@trialox.org>
>>>>  wrote:
>>>>
>>>>  Hi all,
>>>>>
>>>>> We experienced out of memory error after parsing rdf files. Assuming
>>>>> (or
>>>>> rather guessing?) leak in the jena parsing provider, I implemented a
>>>>> sesame-based parsing provider.
>>>>> However, using sesame-based parsing provider, I also get out of memory
>>>>> error. I carried out some experiments with jena-based as well as
>>>>> sesame-based parsing providers.
>>>>> The results are shown below. There is a memory leak but where? Maybe
>>>>> during
>>>>> storing the triples into the mgraph? I'll check this tomorrow... too
>>>>> tired
>>>>> now to continue...
>>>>>
>>>>> regards
>>>>> hasan
>>>>>
>>>>> Test setup:
>>>>> - The serialized graph contains 148163 triples
>>>>> - The serialized graph is an n-triples file (each line is a triple) but
>>>>> parsed with a turtle parser
>>>>> - The serialized graph is parsed several times and in each time the
>>>>> result
>>>>> is always stored to the same mgraph replacing old contents
>>>>>
>>>>> A. With Jena-based Parser
>>>>>
>>>>> A1. Options used: -Xmx256m -XX:MaxPermSize=128M
>>>>>
>>>>> Parsing the first time results in:
>>>>>
>>>>> INFO Thread-26 org.apache.clerezza.platform.BootMonitor - The Apache
>>>>> Clerezza Platform is now operational.
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - REQUEST
>>>>> /graph
>>>>> on
>>>>> org.eclipse.jetty.server.nio.SelectChannelConnector$2@3de8fe
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log -
>>>>>
>>>>> sessionManager=org.eclipse.jetty.server.session.HashSessionManager@891d76
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - session=null
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log -
>>>>> servlet=org.eclipse.equinox.http.servlet.HttpServiceServlet-33258683
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - servlet
>>>>> holder=
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - chain=
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.auth.AuthenticationCheckerImpl
-
>>>>> user
>>>>> admin successfully authenticated
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Get permissions
>>>>> for
>>>>> user admin
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.security.AllPermission "" "")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.util.PropertyPermission "*" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "resource")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "metadata")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/content.graph" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/documentation.graph" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/config.graph" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.a.graph" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.b.graph" "read")
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl -
>>>>> Accept-Header: [text/html, application/xhtml+xml,
>>>>> application/xml;q=0.9,
>>>>> */*;q=0.8]
>>>>> DEBUG qtp11927727-23 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter org.apache.clerezza.jaxrs.utils.form.MultiPartBody has
>>>>> annotations: 0
>>>>> WARN qtp11927727-23 - /graph org.eclipse.jetty.util.log - Error for
>>>>> /graph
>>>>> java.lang.OutOfMemoryError: Java heap space
>>>>> at java.util.Arrays.copyOf(Arrays.java:2786)
>>>>> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:71)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.DelimiterInputStream.readTill(DelimiterInputStream.java:68)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.readFields(MultiPartBodyImpl.java:358)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:222)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:239)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:60)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:43)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl.getBodyObject(WebRequestImpl.java:194)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities.createParametersForRequest(InjectionUtilities.java:201)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.handleWithMethod(RootResourceExecutorImpl.java:461)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.execute(RootResourceExecutorImpl.java:119)
>>>>> at
>>>>> org.apache.clerezza.triaxrs.JaxRsHandler.handle(JaxRsHandler.java:503)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler$RegisteredHandler.handle(PathMappingHandler.java:127)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler.handle(PathMappingHandler.java:102)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:94)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter.handle(AuthenticatingFilter.java:90)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.xhtml2html.Xhtml2HtmlFilter.handle(Xhtml2HtmlFilter.java:73)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.osgi.OsgiWebServerFactory$1.service(OsgiWebServerFactory.java:78)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ServletRegistration.handleRequest(ServletRegistration.java:90)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.processAlias(ProxyServlet.java:109)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.service(ProxyServlet.java:75)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:532)
>>>>> at
>>>>>
>>>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:227)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:965)
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - [POST
>>>>> /graph]@5006061 org.eclipse.jetty.server.Request@4c62ed
>>>>> DEBUG qtp11927727-23 - /graph org.eclipse.jetty.util.log - RESPONSE
>>>>> /graph
>>>>>  500
>>>>> DEBUG qtp11927727-17 - Acceptor0
>>>>> SelectChannelConnector@0.0.0.0:8080org.eclipse.jetty.util.log -
>>>>> org.eclipse.jetty.io.nio.SelectorManager$SelectSet@2f63c JVM BUG(s) -
>>>>> cancelled keys 1 times
>>>>> DEBUG qtp11927727-18 org.eclipse.jetty.util.log - EOF
>>>>>
>>>>>
>>>>> A2. Options used: -Xmx320m -XX:MaxPermSize=128M
>>>>>
>>>>> Parsing the second time results in:
>>>>>
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - REQUEST
>>>>> /graph
>>>>> on
>>>>> org.eclipse.jetty.server.nio.SelectChannelConnector$2@e64ba2
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log -
>>>>>
>>>>> sessionManager=org.eclipse.jetty.server.session.HashSessionManager@1abdb8a
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - session=null
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log -
>>>>> servlet=org.eclipse.equinox.http.servlet.HttpServiceServlet-24612108
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - servlet
>>>>> holder=
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - chain=
>>>>> DEBUG qtp29719186-20 - /graph
>>>>> org.apache.clerezza.platform.security.auth.AuthenticationCheckerImpl
-
>>>>> user
>>>>> admin successfully authenticated
>>>>> DEBUG qtp29719186-20 - /graph
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl -
>>>>> Accept-Header: [text/html, application/xhtml+xml,
>>>>> application/xml;q=0.9,
>>>>> */*;q=0.8]
>>>>> DEBUG qtp29719186-20 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter org.apache.clerezza.jaxrs.utils.form.MultiPartBody has
>>>>> annotations: 0
>>>>> WARN qtp29719186-20 - /graph org.eclipse.jetty.util.log - Error for
>>>>> /graph
>>>>> java.lang.OutOfMemoryError: Java heap space
>>>>> at java.util.Arrays.copyOf(Arrays.java:2786)
>>>>> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:71)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.DelimiterInputStream.readTill(DelimiterInputStream.java:68)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.readFields(MultiPartBodyImpl.java:358)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:222)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:239)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:60)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:43)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl.getBodyObject(WebRequestImpl.java:194)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities.createParametersForRequest(InjectionUtilities.java:201)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.handleWithMethod(RootResourceExecutorImpl.java:461)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.execute(RootResourceExecutorImpl.java:119)
>>>>> at
>>>>> org.apache.clerezza.triaxrs.JaxRsHandler.handle(JaxRsHandler.java:503)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler$RegisteredHandler.handle(PathMappingHandler.java:127)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler.handle(PathMappingHandler.java:102)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:94)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter.handle(AuthenticatingFilter.java:90)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.xhtml2html.Xhtml2HtmlFilter.handle(Xhtml2HtmlFilter.java:73)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.osgi.OsgiWebServerFactory$1.service(OsgiWebServerFactory.java:78)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ServletRegistration.handleRequest(ServletRegistration.java:90)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.processAlias(ProxyServlet.java:109)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.service(ProxyServlet.java:75)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:532)
>>>>> at
>>>>>
>>>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:227)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:965)
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - [POST
>>>>> /graph]@31032394 org.eclipse.jetty.server.Request@1d9844a
>>>>> DEBUG qtp29719186-20 - /graph org.eclipse.jetty.util.log - RESPONSE
>>>>> /graph
>>>>>  500
>>>>>
>>>>>
>>>>> A3. Options used: -Xmx380m -XX:MaxPermSize=128M
>>>>> Still no problem after parsing 5 times
>>>>>
>>>>>
>>>>> B. With Sesame-based Parser
>>>>>
>>>>> B1. Options used: -Xmx256m -XX:MaxPermSize=128M
>>>>>
>>>>> Parsing the first time results in:
>>>>>
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - REQUEST
>>>>> /graph
>>>>> on
>>>>> org.eclipse.jetty.server.nio.SelectChannelConnector$2@119e3ab
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log -
>>>>>
>>>>> sessionManager=org.eclipse.jetty.server.session.HashSessionManager@116c054
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - session=null
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log -
>>>>> servlet=org.eclipse.equinox.http.servlet.HttpServiceServlet-30926038
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - servlet
>>>>> holder=
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - chain=
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.auth.AuthenticationCheckerImpl
-
>>>>> user
>>>>> admin successfully authenticated
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Get permissions
>>>>> for
>>>>> user admin
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.security.AllPermission "" "")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.util.PropertyPermission "*" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "resource")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "metadata")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/content.graph" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/documentation.graph" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/config.graph" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.a.graph" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.b.graph" "read")
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl -
>>>>> Accept-Header: [text/html, application/xhtml+xml,
>>>>> application/xml;q=0.9,
>>>>> */*;q=0.8]
>>>>> DEBUG qtp18102317-19 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter org.apache.clerezza.jaxrs.utils.form.MultiPartBody has
>>>>> annotations: 0
>>>>> WARN qtp18102317-19 - /graph org.eclipse.jetty.util.log - Error for
>>>>> /graph
>>>>> java.lang.OutOfMemoryError: Java heap space
>>>>> at java.util.Arrays.copyOf(Arrays.java:2786)
>>>>> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:71)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.DelimiterInputStream.readTill(DelimiterInputStream.java:68)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.readFields(MultiPartBodyImpl.java:358)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:222)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:239)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:60)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:43)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl.getBodyObject(WebRequestImpl.java:194)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities.createParametersForRequest(InjectionUtilities.java:201)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.handleWithMethod(RootResourceExecutorImpl.java:461)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.execute(RootResourceExecutorImpl.java:119)
>>>>> at
>>>>> org.apache.clerezza.triaxrs.JaxRsHandler.handle(JaxRsHandler.java:503)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler$RegisteredHandler.handle(PathMappingHandler.java:127)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler.handle(PathMappingHandler.java:102)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:94)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter.handle(AuthenticatingFilter.java:90)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.xhtml2html.Xhtml2HtmlFilter.handle(Xhtml2HtmlFilter.java:73)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.osgi.OsgiWebServerFactory$1.service(OsgiWebServerFactory.java:78)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ServletRegistration.handleRequest(ServletRegistration.java:90)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.processAlias(ProxyServlet.java:109)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.service(ProxyServlet.java:75)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:532)
>>>>> at
>>>>>
>>>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:227)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:965)
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - [POST
>>>>> /graph]@33413638 org.eclipse.jetty.server.Request@1fdda06
>>>>> DEBUG qtp18102317-19 - /graph org.eclipse.jetty.util.log - RESPONSE
>>>>> /graph
>>>>>  500
>>>>>
>>>>>
>>>>>
>>>>> B2. Options used: -Xmx320m -XX:MaxPermSize=128M
>>>>>
>>>>> Parsing the first time results in:
>>>>>
>>>>> INFO Thread-26 org.apache.clerezza.platform.BootMonitor - The Apache
>>>>> Clerezza Platform is now operational.
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log - REQUEST
>>>>> /graph
>>>>> on
>>>>> org.eclipse.jetty.server.nio.SelectChannelConnector$2@1214c4e
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log -
>>>>>
>>>>> sessionManager=org.eclipse.jetty.server.session.HashSessionManager@dc135d
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log - session=null
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log -
>>>>> servlet=org.eclipse.equinox.http.servlet.HttpServiceServlet-1848812
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log - servlet
>>>>> holder=
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log - chain=
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.auth.AuthenticationCheckerImpl
-
>>>>> user
>>>>> admin successfully authenticated
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Get permissions
>>>>> for
>>>>> user admin
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.security.AllPermission "" "")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (java.util.PropertyPermission "*" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "resource")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.osgi.framework.AdminPermission "*" "metadata")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/content.graph" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/documentation.graph" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/config.graph" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.a.graph" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.platform.security.UserAwarePolicy - Add permission
>>>>> (org.apache.clerezza.rdf.core.access.security.TcPermission "
>>>>> http://tpf.localhost/live.b.graph" "read")
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl -
>>>>> Accept-Header: [text/html, application/xhtml+xml,
>>>>> application/xml;q=0.9,
>>>>> */*;q=0.8]
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter org.apache.clerezza.jaxrs.utils.form.MultiPartBody has
>>>>> annotations: 0
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter javax.ws.rs.core.UriInfo has annotations: 1
>>>>> DEBUG qtp18195096-19 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Inject parameter 1 to
>>>>> org.apache.clerezza.triaxrs.util.UriInfoImpl@12bdf9
>>>>> WARN qtp18195096-19 - /graph org.apache.clerezza.triaxrs.JaxRsHandler
-
>>>>> Exception (with no exception mapper)
>>>>> java.lang.OutOfMemoryError: GC overhead limit exceeded
>>>>> at java.util.LinkedHashMap.createEntry(LinkedHashMap.java:424)
>>>>> at java.util.LinkedHashMap.addEntry(LinkedHashMap.java:406)
>>>>> at java.util.HashMap.put(HashMap.java:385)
>>>>> at org.openjena.atlas.lib.cache.CacheLRU.put(CacheLRU.java:47)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheUpdate(NodeTableCache.java:156)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:87)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:57)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:43)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:55)
>>>>> at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:108)
>>>>> at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:103)
>>>>> at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:32)
>>>>> at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:64)
>>>>> at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:60)
>>>>> at org.openjena.atlas.iterator.Iter$4.next(Iter.java:265)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.store.GraphTDBBase$MapperIteratorTriples.next(GraphTDBBase.java:227)
>>>>> at
>>>>>
>>>>>
>>>>> com.hp.hpl.jena.tdb.store.GraphTDBBase$MapperIteratorTriples.next(GraphTDBBase.java:186)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:108)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.remove(JenaGraphAdaptor.java:120)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.remove(AbstractTripleCollection.java:88)
>>>>> at java.util.AbstractCollection.clear(AbstractCollection.java:396)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.core.impl.util.PrivilegedTripleCollectionWrapper$14.run(PrivilegedTripleCollectionWrapper.java:198)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.core.impl.util.PrivilegedTripleCollectionWrapper.clear(PrivilegedTripleCollectionWrapper.java:194)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.rdf.core.access.LockableMGraphWrapper.clear(LockableMGraphWrapper.java:218)
>>>>> at
>>>>>
>>>>> org.apache.clerezza.rdf.web.core.WebAccess.postTriples(WebAccess.java:183)
>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>> at
>>>>>
>>>>>
>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>>> at
>>>>>
>>>>>
>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.handleWithMethod(RootResourceExecutorImpl.java:469)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.execute(RootResourceExecutorImpl.java:119)
>>>>> WARN qtp18195096-19 - /graph
>>>>> org.wymiwyg.wrhapi.osgi.OsgiWebServerFactory -
>>>>> Exception handling requestorg.wymiwyg.wrhapi.HandlerException:
>>>>> java.lang.OutOfMemoryError: GC overhead limit exceeded
>>>>> DEBUG qtp18195096-19 - /graph org.eclipse.jetty.util.log - RESPONSE
>>>>> /graph
>>>>>  500
>>>>> DEBUG qtp18195096-23 org.eclipse.jetty.util.log - EOF
>>>>>
>>>>>
>>>>> B3. Options used: -Xmx380m -XX:MaxPermSize=128M
>>>>>
>>>>> Parsing the 3rd time results in
>>>>>
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - REQUEST
>>>>> /graph on
>>>>> org.eclipse.jetty.server.nio.SelectChannelConnector$2@1ff9440
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log -
>>>>>
>>>>> sessionManager=org.eclipse.jetty.server.session.HashSessionManager@35b5e8
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - session=null
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log -
>>>>> servlet=org.eclipse.equinox.http.servlet.HttpServiceServlet-14065888
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - servlet
>>>>> holder=
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - chain=
>>>>> DEBUG qtp7908994-20 - /graph
>>>>> org.apache.clerezza.platform.security.auth.AuthenticationCheckerImpl
-
>>>>> user
>>>>> admin successfully authenticated
>>>>> DEBUG qtp7908994-20 - /graph org.apache.clerezza.triaxrs.WebRequestImpl
>>>>> -
>>>>> Accept-Header: [text/html, application/xhtml+xml,
>>>>> application/xml;q=0.9,
>>>>> */*;q=0.8]
>>>>> DEBUG qtp7908994-20 - /graph
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities
>>>>> - Parameter org.apache.clerezza.jaxrs.utils.form.MultiPartBody has
>>>>> annotations: 0
>>>>> WARN qtp7908994-20 - /graph org.eclipse.jetty.util.log - Error for
>>>>> /graph
>>>>> java.lang.OutOfMemoryError: Java heap space
>>>>> at java.util.Arrays.copyOf(Arrays.java:2786)
>>>>> at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:71)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.DelimiterInputStream.readTill(DelimiterInputStream.java:68)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.readFields(MultiPartBodyImpl.java:358)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:222)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartBodyImpl.<init>(MultiPartBodyImpl.java:239)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:60)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.jaxrs.utils.form.MultiPartFormMessageBodyReader.readFrom(MultiPartFormMessageBodyReader.java:43)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.WebRequestImpl.getBodyObject(WebRequestImpl.java:194)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.InjectionUtilities.createParametersForRequest(InjectionUtilities.java:201)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.handleWithMethod(RootResourceExecutorImpl.java:461)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.triaxrs.RootResourceExecutorImpl.execute(RootResourceExecutorImpl.java:119)
>>>>> at
>>>>> org.apache.clerezza.triaxrs.JaxRsHandler.handle(JaxRsHandler.java:503)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler$RegisteredHandler.handle(PathMappingHandler.java:127)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.util.pathmappings.PathMappingHandler.handle(PathMappingHandler.java:102)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:94)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.security.auth.AuthenticatingFilter.handle(AuthenticatingFilter.java:90)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.apache.clerezza.platform.xhtml2html.Xhtml2HtmlFilter.handle(Xhtml2HtmlFilter.java:73)
>>>>> at
>>>>> org.wymiwyg.wrhapi.filter.impl.FilterRunner.handle(FilterRunner.java:56)
>>>>> at
>>>>>
>>>>>
>>>>> org.wymiwyg.wrhapi.osgi.OsgiWebServerFactory$1.service(OsgiWebServerFactory.java:78)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ServletRegistration.handleRequest(ServletRegistration.java:90)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.processAlias(ProxyServlet.java:109)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.equinox.http.servlet.internal.ProxyServlet.service(ProxyServlet.java:75)
>>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>>>>> at
>>>>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:532)
>>>>> at
>>>>>
>>>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:453)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:227)
>>>>> at
>>>>>
>>>>>
>>>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:965)
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - [POST
>>>>> /graph]@14584367 org.eclipse.jetty.server.Request@de8a2f
>>>>> DEBUG qtp7908994-20 - /graph org.eclipse.jetty.util.log - RESPONSE
>>>>> /graph
>>>>>  500
>>>>> DEBUG qtp7908994-17 - Acceptor0
>>>>> SelectChannelConnector@0.0.0.0:8080org.eclipse.jetty.util.log -
>>>>> org.eclipse.jetty.io.nio.SelectorManager$SelectSet@1d0a5f9 JVM BUG(s)
>>>>> -
>>>>> cancelled keys 1 times
>>>>> DEBUG qtp7908994-23 org.eclipse.jetty.util.log - EOF
>>>>>
>>>>>
>>>>> B4. Options used: -Xmx512m -XX:MaxPermSize=128M
>>>>> Still no problem after parsing 5 times
>>>>>
>>>>>
>>>>
>>
>

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