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Subject: RE: Tomcat OutOfMemoryError with OGSA-DAI clients

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From: Arijit Mukherjee (Arijit.Mukherjee@newcastle.ac.uk)
Date: May 16, 2006 13:45

Hi

The evaluators and OGSA-DAI are both on the same tomcat instance - may
that's a reason for going out of memory - note that this is not the case
for an end-to-end DAI client.

And secondly, the SAX parser inside the TableScanOp fails if the XML
data contains characters like "&" - and throws a parsing error. We know
about this issue, but unfortunately I didn't have time to fix it. Also,
I'm not quite sure on how to deal with this - the only reference I could
find in the web talked about putting all the stuff inside a CDATA
element - which I guess is somewhat odd for DQP.

Regards
Arijit

>-----Original Message-----
>From: owner-users@ogsadai.org.uk
>[mailto:owner-users@ogsadai.org.uk] On Behalf Of Ally Hume
>Sent: 16 May 2006 12:51
>To: lucas@dcs.bbk.ac.uk
>Cc: users@ogsadai.org.uk
>Subject: RE: Tomcat OutOfMemoryError with OGSA-DAI clients
>
>Hi Lucas,
>
>So it looks like DQP is being given some characters it cannot
>understand. Two reasons spring to mind that may cause this:
>
>1) There really is a bad character in the output of the query
>that is not being escaped correctly so it can pass as XML.
>
>2) An error message is appearing the in data being sent to DQP
>instead of the real data. DQP then throws an error when
>paring this error message.
>
>I'm not too familiar with the internals of DQP but my guess
>would be that some bad XML is being passed between services.
>One path to solving this may be to using axis's TCP monitor to
>view the messages being sent between this DQP server and the
>OGSA-DAI server(s). When viewing these messages you may be
>able to diagnose what is going wrong.
>
>I'm sorry I cannot offer much more help. Is there any error
>messages in the logs of the OGSA-DAI services being accessed by DQP?
>
>Ally
>
>-------------------------------------------------------------
>Ally Hume
>Software Architect
>EPCC, University of Edinburgh
>James Clerk Maxwell Building
>Mayfield Road E-mail: a.hume@epcc.ed.ac.uk
>Edinburgh, EH9 3JZ Phone: + 44 (0) 131 651 3397
>United Kingdom Fax: + 44 (0) 131 650 6555
>-------------------------------------------------------------
>
>
>-----Original Message-----
>From: Lucas Zamboulis [mailto:lucas@dcs.bbk.ac.uk]
>Sent: 16 May 2006 12:27
>To: Ally Hume
>Cc: users@ogsadai.org.uk
>Subject: Re: Tomcat OutOfMemoryError with OGSA-DAI clients
>
>Hi Ally,
>
>I increased the memory for the end-to-end client through the
>ant file and it worked - so this is not a DAI problem.
>
>Back to my original problem: I am trying to use the DQP query client.
>It
>works fine with queries that return small results, but throws
>the following error when it's supposed to return large result
>sets (this is from the tomcat log - the error is output after
>the DQP has returned -
>
>in the log, not the command line - about 4000 tuples).
>
>I wrote the first e-mail because I thought maybe DAI stopped providing
>
>results to DQP, which crashed as a result, giving this error message.
>Now it seems it's a DQP issue?
>
>Regards,
>Lucas
>
>- Could not parse row: Illegal character or entity reference syntax.
>- Could not parse row: Illegal character or entity reference syntax.
>org.xml.sax.SAXParseException: Illegal character or entity
>reference syntax.
> at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3376)
> at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3364)
> at
>org.apache.crimson.parser.Parser2.maybeReferenceInContent(Parser2.java
>:2604)
> at
>org.apache.crimson.parser.Parser2.content(Parser2.java:2017)
> at
>org.apache.crimson.parser.Parser2.maybeElement(Parser2.java:1691)
> at
>org.apache.crimson.parser.Parser2.content(Parser2.java:1963)
> at
>org.apache.crimson.parser.Parser2.maybeElement(Parser2.java:1691)
> at
>org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:667)
> at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
> at
>org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
> at
>uk.org.ogsadai.dqp.gqes.utils.RowHandler.produceVectorFromRow(RowHandl
>er.java:137)
> at
>uk.org.ogsadai.dqp.gqes.utils.RowListHandler.endElement(RowListHandler
>.java:170)
> at
>org.apache.crimson.parser.Parser2.maybeElement(Parser2.java:1712)
> at
>org.apache.crimson.parser.Parser2.content(Parser2.java:1963)
> at
>org.apache.crimson.parser.Parser2.maybeElement(Parser2.java:1691)
> at
>org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:667)
> at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
> at
>org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
> at
>uk.org.ogsadai.dqp.gqes.utils.RowListHandler.produceVectorListFromRowL
>ist(RowListHandler.java:116)
> at
>uk.org.ogsadai.dqp.gqes.operators.AsynchGDSAccessor.run(TableScanOp.ja
>va:483)
>- 0: Exception in executeAsynchGDSRequest(): Illegal character
>or entity reference syntax.
>
>
>
>Ally Hume wrote:
>> Hi Lucas,
>>
>> It does sound like the client is a fault here.
>>
>> Let's start with the simple stuff first! Have you increased the
>> memory heap size for the client? Your notes seem to imply you have
>> done this only for the server.
>>
>> It sounds like you get the error when just using the data browser or
>> end to end client to talk to OGSA-DAI. In this case increasing the
>> memory of the server and/or the client should remove the out of
>memory
>> error.
>>
>> What exactly is the error you are seeing on the client? Do you have
>a
>> full stack trace?
>>
>> Regards,
>>
>> Ally
>>
>> -------------------------------------------------------------
>> Ally Hume
>> Software Architect
>> EPCC, University of Edinburgh
>> James Clerk Maxwell Building
>> Mayfield Road E-mail: a.hume@epcc.ed.ac.uk
>> Edinburgh, EH9 3JZ Phone: + 44 (0) 131 651 3397
>> United Kingdom Fax: + 44 (0) 131 650 6555
>> -------------------------------------------------------------
>>
>>
>> -----Original Message-----
>> From: owner-users@ogsadai.org.uk [mailto:owner-users@ogsadai.org.uk]
>> On Behalf Of Lucas Zamboulis
>> Sent: 12 May 2006 21:31
>> To: users@ogsadai.org.uk
>> Subject: Tomcat OutOfMemoryError with OGSA-DAI clients
>>
>> Hi,
>>
>> I'm having trouble retrieving a 200,000 integer result set from a
>> MySQL database. I'm using OGSA-DAI WSI 2.1 on a Linux FC4 with 2GB
>> RAM. I successfully retrieve data from other tables in the same DB
>> (and
>from
>> the same table when e.g. adding an Id<1000 constraint on the query).
>
>> This is therefore a problem having to do with the size of the result
>
>> set: both databrowser and end-to-end client exit with an
>> OutOfMemoryError, although the Tomcat log (see end of mail) .
>>
>> I then read the related issue in the DAI FAQ, which suggests:
>>
>> - increase the memory heap size for the virtual machine using the
>> Xms<size> flag.
>> --- Done that, raised both Xms and Xmx flags in the catalina.sh
>file,
>> using both CATALINA_OPTS and JAVA_OPTS, problem persists
>>
>> - may be a JDBC driver issue for specific db (loading whole results
>> set in memory prior to giving a handle to DAI), try using
>another DBMS
>> --- Using the latest driver, DBMS: MySQL version 4.1.
>>
>> - Try using asynchronous data transport functionalty to stream the
>> data to and from the service in chunks
>> --- I'm actually trying to use DQP over DAI, so it's out of my
>> control, but as I understand it, DQP 3 does use asynchronous data
>> transport functionalty and I still get an error when issuing
>the same
>> query on DQP (that's how I first noticed the problem - although the
>> problem
>appears
>>
>> in a different manner when using DQP).
>>
>> Do you think the error I'm getting is because neither the
>databrowser,
>>
>> nor the end-to-end client use asynchronous data transport? I'm
>asking
>> because the start of the log file (showing all three DAI process to
>> have
>> completed successfully) implies that DAI successfully processed the
>> query and the result set, and therefore the error may be in the
>> application using DAI.
>>
>> If not, any ideas?
>>
>> Regards,
>> Lucas
>>
>>
>----------------------------------------------------------------------
>> -
>> Lucas Zamboulis
>> R.A./Ph.D. candidate
>> School of Computer Science and Information Systems
>> Birkbeck College, University of London
>> London Knowledge Lab Tel.: +44 20 7763 2102
>> 23-29 Emerald Street Fax: +44 20 7242 2756
>> London, WC1N 3QS http://www.dcs.bbk.ac.uk/~lucas
>>
>>
>> May 12, 2006 9:17:33 PM org.apache.catalina.startup.Catalina start
>> INFO: Server startup in 4814 ms
>> - statementOutputStatus : PROCESSING
>> - statementRSToXMLStatus : PROCESSING
>> - statementStatus : PROCESSING
>> - statementStatus : COMPLETED
>> - statementRSToXMLStatus : COMPLETED
>> - statementOutputStatus : COMPLETED
>> - java.io.IOException:
>> ClientAbortException: java.net.SocketException: Connection reset
>> at
>>
>org.apache.coyote.tomcat5.OutputBuffer.realWriteBytes(OutputBuffer.jav
>> a:373)
>> at
>> org.apache.tomcat.util.buf.ByteChunk.append(ByteChunk.java:294)
>> at
>>
>org.apache.coyote.tomcat5.OutputBuffer.writeBytes(OutputBuffer.java:40
>> 1)
>> at
>> org.apache.coyote.tomcat5.OutputBuffer.write(OutputBuffer.java:388)
>> at
>>
>org.apache.coyote.tomcat5.CoyoteOutputStream.write(CoyoteOutputStream.
>> java:76)
>> at org.apache.axis.utils.ByteArray.writeTo(ByteArray.java:375)
>> at org.apache.axis.SOAPPart.writeTo(SOAPPart.java:265)
>> at org.apache.axis.Message.writeTo(Message.java:528)
>> at
>>
>org.apache.axis.transport.http.AxisServlet.sendResponse(AxisServlet.ja
>> va:902)
>> at
>>
>org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:777
>> )
>> at
>> javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
>> at
>>
>org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase
>> .java:327)
>> at
>> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>> at
>>
>org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appli
>> cationFilterChain.java:237)
>> at
>>
>org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFi
>> lterChain.java:157)
>> at
>>
>org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVa
>> lve.java:214)
>> at
>>
>org.apache.catalina.core.StandardValveContext.invokeNext(StandardValve
>> Context.java:104)
>> at
>>
>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :520)
>> at
>>
>org.apache.catalina.core.StandardContextValve.invokeInternal(StandardC
>> ontextValve.java:198)
>> at
>>
>org.apache.catalina.core.StandardContextValve.invoke(StandardContextVa
>> lve.java:152)
>> at
>>
>org.apache.catalina.core.StandardValveContext.invokeNext(StandardValve
>> Context.java:104)
>> at
>>
>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :520)
>> at
>>
>org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.ja
>> va:137)
>> at
>>
>org.apache.catalina.core.StandardValveContext.invokeNext(StandardValve
>> Context.java:104)
>> at
>>
>org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.ja
>> va:118)
>> at
>>
>org.apache.catalina.core.StandardValveContext.invokeNext(StandardValve
>> Context.java:102)
>> at
>>
>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :520)
>> at
>>
>org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValv
>> e.java:109)
>> at
>>
>org.apache.catalina.core.StandardValveContext.invokeNext(StandardValve
>> Context.java:104)
>> at
>>
>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :520)
>> at
>>
>org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:929)
>> at
>>
>org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:160
>> )
>> at
>>
>org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
>> 799)
>> at
>>
>org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proces
>> sConnection(Http11Protocol.java:705)
>> at
>>
>org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:
>> 577)
>> at
>>
>org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPo
>> ol.java:683)
>> at java.lang.Thread.run(Thread.java:534)
>>
>>
>
>

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