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Posted to xindice-users@xml.apache.org by ch...@ebi.ac.uk on 2006/12/14 16:49:02 UTC
OutOfMemory
Hello,
I am stuck with an OutOfMemoryError. We have around 100 xml documents
stored in two collections which located in one xindice. Biggest document
is around 800k(not that monster big, right?). I would say it worked well.
But if I query them with some general key-words. Xindice will throw out
the following outOfMemoryErrors, and really exhausted the server. So I had
restart tomcat in that case.
Any idea or hints to resolve it or handle the error. I appreciate the
experience you share.
Regards,
----------------------------------------
Caused by: org.xmldb.api.base.XMLDBException: Failed to execute command
'Query' on server: http://localhost:9971/xindice/, message:
java.lang.Exception: java.lang.OutOfMemoryError
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
at
org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
at
org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
... 5 more
Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
java.lang.OutOfMemoryError
at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
... 8 more
Re: OutOfMemory
Posted by Vadim Gritsenko <va...@reverycodes.com>.
chenli@ebi.ac.uk wrote:
> Hi, Todd,
>
> We are using Xindice 1.13. And each file usually is 100kb except some huge
> file is 1MB each.
>
> The erro message is pasted below. It is exactly as same as posted before.
Chen,
According to the stacktrace you sent, it happened in the xml-rpc library and
unfortunately it has no line numbers for xml-rpc classes. Also, there is a
nested Exception with no trace printed at all.
However, the trace you sent is not from the Xindice server. It is actually a
trace from the Xindice XML-RPC client. So actual OutOfMemory exception might be
happening either on server or client.
I would suggest you to check memory settings on both client and server JVM, and
if this does not help, check logs on Xindice server.
> Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
> java.lang.OutOfMemoryError
> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
> at
>
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
Vadim
Re: OutOfMemory
Posted by ch...@ebi.ac.uk.
Hi, Todd,
We are using Xindice 1.13. And each file usually is 100kb except some huge
file is 1MB each.
The erro message is pasted below. It is exactly as same as posted before.
Thank you,
Chen
Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
java.lang.OutOfMemoryError
at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
... 8 more
[B@1876e5dorg.apache.xmlrpc.XmlRpcException: java.lang.Exception:
java.lang.OutOfMemoryError
at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
at
org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
at
org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
at uk.ac.ebi.compneur.xml.XindiceDB.doSearch(Unknown Source)
at uk.ac.ebi.compneur.xml.XindiceDB.search(Unknown Source)
at
uk.ac.ebi.biomodels.PublModelsDatabase.listModelsBySBMLElements(PublModelsDatabase.java:182)
at
uk.ac.ebi.biomodels.SearchModelsBean$SBMLElementsSearcher.doRun(SearchModelsBean.java:922)
at
uk.ac.ebi.biomodels.SearchModelsBean$Searcher.run(SearchModelsBean.java:845)
Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
java.lang.OutOfMemoryError
at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
at
org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
at
org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
at
org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
at uk.ac.ebi.compneur.xml.XindiceDB.doSearch(Unknown Source)
at uk.ac.ebi.compneur.xml.XindiceDB.search(Unknown Source)
at
uk.ac.ebi.biomodels.PublModelsDatabase.listModelsBySBMLElements(PublModelsDatabase.java:182)
at
uk.ac.ebi.biomodels.SearchModelsBean$SBMLElementsSearcher.doRun(SearchModelsBean.java:922)
at
uk.ac.ebi.biomodels.SearchModelsBean$Searcher.run(SearchModelsBean.java:845)
Re: OutOfMemory
Posted by by...@cns.montana.edu.
Hi Brendan,
What version of Xindice are you using? The lastest out of SVN has several
bug fixes.
Second what size are the files that your adding?
Mind re-running the query and posting the server log with the
execption trace?
Todd Byrne
On Thu, 14 Dec 2006 chenli@ebi.ac.uk wrote:
> Thank you, Brendan.
>
> But I suspect that it was not caused by that, since the memory had been
> set to 1024MB already by that "JAVA_OPTS=-Xmx1024m" way.
>
> > Is it java that's out of memory? I had a problem like this and need to
> > set the memory using mx256 command... see similar post:
> > http://www-128.ibm.com/developerworks/forums/dw_thread.jsp?forum=176&thread=48015&cat=10
> >
> > Brendan
> >
> > On 14/12/06, chenli@ebi.ac.uk <ch...@ebi.ac.uk> wrote:
> >> Hello,
> >>
> >> I am stuck with an OutOfMemoryError. We have around 100 xml documents
> >> stored in two collections which located in one xindice. Biggest document
> >> is around 800k(not that monster big, right?). I would say it worked
> >> well.
> >> But if I query them with some general key-words. Xindice will throw out
> >> the following outOfMemoryErrors, and really exhausted the server. So I
> >> had
> >> restart tomcat in that case.
> >>
> >> Any idea or hints to resolve it or handle the error. I appreciate the
> >> experience you share.
> >>
> >> Regards,
> >>
> >>
> >> ----------------------------------------
> >> Caused by: org.xmldb.api.base.XMLDBException: Failed to execute command
> >> 'Query' on server: http://localhost:9971/xindice/, message:
> >> java.lang.Exception: java.lang.OutOfMemoryError
> >> at
> >> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124)
> >> at
> >> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
> >> at
> >> org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
> >> at
> >> org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
> >> ... 5 more
> >> Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
> >> java.lang.OutOfMemoryError
> >> at
> >> org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
> >> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
> >> at
> >> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
> >> ... 8 more
> >>
> >>
> >
>
>
Re: OutOfMemory
Posted by ch...@ebi.ac.uk.
Thank you, Brendan.
But I suspect that it was not caused by that, since the memory had been
set to 1024MB already by that "JAVA_OPTS=-Xmx1024m" way.
> Is it java that's out of memory? I had a problem like this and need to
> set the memory using mx256 command... see similar post:
> http://www-128.ibm.com/developerworks/forums/dw_thread.jsp?forum=176&thread=48015&cat=10
>
> Brendan
>
> On 14/12/06, chenli@ebi.ac.uk <ch...@ebi.ac.uk> wrote:
>> Hello,
>>
>> I am stuck with an OutOfMemoryError. We have around 100 xml documents
>> stored in two collections which located in one xindice. Biggest document
>> is around 800k(not that monster big, right?). I would say it worked
>> well.
>> But if I query them with some general key-words. Xindice will throw out
>> the following outOfMemoryErrors, and really exhausted the server. So I
>> had
>> restart tomcat in that case.
>>
>> Any idea or hints to resolve it or handle the error. I appreciate the
>> experience you share.
>>
>> Regards,
>>
>>
>> ----------------------------------------
>> Caused by: org.xmldb.api.base.XMLDBException: Failed to execute command
>> 'Query' on server: http://localhost:9971/xindice/, message:
>> java.lang.Exception: java.lang.OutOfMemoryError
>> at
>> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124)
>> at
>> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
>> at
>> org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
>> at
>> org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
>> ... 5 more
>> Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
>> java.lang.OutOfMemoryError
>> at
>> org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
>> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
>> at
>> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
>> ... 8 more
>>
>>
>
Re: OutOfMemory
Posted by Brendan Laing <br...@googlemail.com>.
Is it java that's out of memory? I had a problem like this and need to
set the memory using mx256 command... see similar post:
http://www-128.ibm.com/developerworks/forums/dw_thread.jsp?forum=176&thread=48015&cat=10
Brendan
On 14/12/06, chenli@ebi.ac.uk <ch...@ebi.ac.uk> wrote:
> Hello,
>
> I am stuck with an OutOfMemoryError. We have around 100 xml documents
> stored in two collections which located in one xindice. Biggest document
> is around 800k(not that monster big, right?). I would say it worked well.
> But if I query them with some general key-words. Xindice will throw out
> the following outOfMemoryErrors, and really exhausted the server. So I had
> restart tomcat in that case.
>
> Any idea or hints to resolve it or handle the error. I appreciate the
> experience you share.
>
> Regards,
>
>
> ----------------------------------------
> Caused by: org.xmldb.api.base.XMLDBException: Failed to execute command
> 'Query' on server: http://localhost:9971/xindice/, message:
> java.lang.Exception: java.lang.OutOfMemoryError
> at
> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124)
> at
> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.query(CollectionImpl.java:515)
> at
> org.apache.xindice.client.xmldb.XindiceCollection.query(XindiceCollection.java:259)
> at
> org.apache.xindice.client.xmldb.services.QueryService.query(QueryService.java:90)
> ... 5 more
> Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception:
> java.lang.OutOfMemoryError
> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java)
> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java)
> at
> org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112)
> ... 8 more
>
>