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From "Clinton Begin" <clinton.be...@gmail.com>
Subject Re: select * causing " OutOfMemoryError: Java heap space"
Date Mon, 17 Mar 2008 22:18:59 GMT
Wow, I just read that other thread on the Compass site.... This is not
directly an iBATIS problem at all...

at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1268)
at com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:843)

This line tells me that the execution is never returning from the prepared
statement.  iBATIS never has a chance to even see the ResultSet, let alone
get to the RowHandler. So swapping out the GpsDevice here won't make any
difference at all. This is odd behavior for a JDBC driver and tells me that
something is very wrong with the configuration.

Which version of the JDBC driver are you using?  What are the rest of the
iBATIS convfiguration details?

Clinton


On Mon, Mar 17, 2008 at 4:12 PM, Clinton Begin <clinton.begin@gmail.com>
wrote:

> Thanks for the summary.  A few things:
>
> * PaginatedList was definitely the wrong solution for that, so I'm glad
> it's gone.
>
> * A RowHandler is possibly the right solution, but will only store as many
> records in memory as you tell it to.  iBATIS does not just arbitrarily keep
> records around.  Quite the opposite actually.  Unless you keep a reference
> or configure a cache, iBATIS will not keep the object around at all.
>
> Looking at your implementation, there are a couple of things going on...
>
> session.create(o);
> if(currentItem== pageSize){
>   if (log.isDebugEnabled()) {
>     log.debug("Indexing page number ["+ pageCount++ + "]");
>   }
> session.evictAll();
>
> Things to Try:
>
> 1)  These lines of code must be treated as guilty until proven innocent
> (especially the logging).  The easiest way to do that is to delete them.
> Create an empty handler/GpsDevice and run the test to see what happens.
>
> 2) Look at the iBATIS configuration files.  Is a cache configured for this
> query?  What kind of cache?
>
> 3) You could try multiple queries of fixed sizes with
> queryForList(String,Object,int offset,int limit) ... but I can't see how
> that would be better than a RowHandler.
>
> 4) Next, just in case the driver's default fetch size is ridiculously high
> (or unlimited), try setting <select ... fetchSize="100"/>.  You could also
> try a scrollable SesultSet with <statement ... resultSetType /> of
> SCROLL_INSENSITIVE or SCROLL_SENSITIVE.
>
> Finally, please know that I've used iBATIS to load tens of millions of
> rows for ETL and even analysis (NetFlix Prize) and was able to do so with a
> RowHandler or even simply multiple calls to queryForList(String,Object,int
> offset,int limit).  I don't recall having to even think about the
> configuration, although I did manage to optimize it to achieve a read/insert
> performance of 15,000 records per second between two databases (on a single
> machine too).
>
> I'm sure there's something about the configuration here that is causing
> the problem, and it can be solved.
>
> I hope one of these helps.
>
> Clinton
>
>
> On Mon, Mar 17, 2008 at 1:53 PM, nch <underscore_dot@yahoo.com> wrote:
>
> >
> > Hi, there. :-)
> >
> > The thing is, I'm testing a search engine called Compass. One of the
> > tests consists of indexing a Wikipedia dump. In this case only the text of
> > the articles, so I downloaded it and imported it into a MySQL database
> > (about 650000 records - 1.5GB).
> >
> > You can configure Compass to access a database and index it's contents
> > by configuring what they call a GPS Device. You can do that through an ORM
> > such as iBatis, Hibernate or JPA.
> >
> > Compass provides an implementation of such a GPS Device called
> > SqlMapClientGpsDevice which uses iBatis queryForPaginatedList to get the
> > results of a query and, so, index them. The query is just a "select * from
> > articles_table".
> >
> > So I wired everything up and ran several tests with different amounts of
> > data to be indexed and JVM stack space sizes. The result was an
> > "OutOfMemoryError: java heap space" error message whenever the size of the
> > selected rows was bigger than the amount of available heap space (I can not
> > index the 650000 records having 1GB of stack).
> >
> > After doing some profiling I concluded iBatis was loading the whole
> > amount of results into memory. So I decided to try Hibernate, which worked
> > just fine.
> >
> > Finally I found queryForPaginatedList was deprecated and that I should
> > use queryWithRowHandler instead, so I made my own implementation of the
> > SqlMapClientGpsDevice based on queryWithRowHandler and tested it, but I had
> > the same result (I profiled the application stack usage and I could see a
> > line growing steadily and finally crash against the stack ceiling while
> > performing the select statement).
> >
> > Shay Banon, Compass project leader, is planning to patch
> > SqlMapClientGpsDevice by replacing queryForPaginatedList with
> > queryWithRowHandler, but I'm doubtful it's gonna work.
> >
> > Finally you can, of course, devide the select stament into several
> > selects (and it works) but, in my opinion, that shouldn't be necessary.
> > You can read more on
> > http://forum.compass-project.org/thread.jspa?threadID=215278
> >
> > Thanks!
> >
> >
> > ----- Original Message ----
> > From: Clinton Begin <clinton.begin@gmail.com>
> > To: user-java@ibatis.apache.org
> > Sent: Monday, March 17, 2008 2:22:39 PM
> > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> >
> > Wow, this thread is interesting.   I suppose I could read the past
> > emails, but could someone summarize the problem and progress to date?  I may
> > be able to shed some light on what is happening.
> >
> > Clinton
> >
> > On Sun, Mar 16, 2008 at 11:49 PM, nch <underscore_dot@yahoo.com> wrote:
> >
> > >
> > > Another thing I forgot. This works perfectly well if we replace iBatis
> > > by Hibernate, so I don't think this is being caused by the MySQL driver.
> > >
> > > ----- Original Message ----
> > > From: nch <underscore_dot@yahoo.com>
> > > To: user-java@ibatis.apache.org
> > > Sent: Sunday, March 16, 2008 10:18:42 PM
> > > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> > >
> > >
> > > Well, I modified the mediumblob into a mediumtext and removed all
> > > other fields except the id one.
> > >
> > > ----- Original Message ----
> > > From: nch <underscore_dot@yahoo.com>
> > > To: user-java@ibatis.apache.org
> > > Sent: Sunday, March 16, 2008 10:06:34 PM
> > > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> > >
> > >
> > > You're probably right. I'm using the table called "text" which
> > > contains a field of type "mediumblob".
> > >
> > > CREATE TABLE /*$wgDBprefix*/text (
> > >   old_id int unsigned NOT NULL auto_increment,
> > >   old_text mediumblob NOT NULL,
> > >   old_flags tinyblob NOT NULL,
> > >   PRIMARY KEY old_id (old_id)
> > > ) /*$wgDBTableOptions*/ MAX_ROWS=10000000 AVG_ROW_LENGTH=10240;
> > >
> > > You can find it's definition here:
> > >
> > > http://svn.wikimedia.org/viewvc/mediawiki/trunk/phase3/maintenance/tables.sql?view=markup
> > >
> > > I'll try to modify that field, first, and see what happens.
> > > I've already tried "select * from your_wikipedia_dump limit $start$,
> > > $size$" and it seems to work fine, but I see a possible issue with this, you
> > > can not remove any of the records you've already read during the whole
> > > process. This might not be an option.
> > >
> > > Thank you.
> > >
> > > ----- Original Message ----
> > > From: Larry Meadors <larry.meadors@gmail.com>
> > > To: user-java@ibatis.apache.org
> > > Sent: Sunday, March 16, 2008 4:19:43 PM
> > > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> > >
> > > Yeah, I just noticed that - it looks like it's failing in the jdbc
> > > driver when it tries to read a blob, maybe?
> > >
> > > I know that some versions of the postgresql jdbc driver load the
> > > entire contents of a resultset into a massive byte[][] structure. I
> > > wonder if that is what is happening here? I think you can get the
> > > source for the MySQL driver and check that if you want to.
> > >
> > > If it is, you may need to structure your app to take smaller bites of
> > > this elephant.
> > >
> > > Try "select * from your_wikipedia_dump limit $start$, $size$" instead
> > > - that will limit the size of the results to $size$ rows, starting on
> > > row $start$ (the $start$ value is zero-based). If you experiment to
> > > see how big $size$ can get, you should be able to get pretty decent
> > > performance out of this.
> > >
> > > Psuedo-code would be like this...
> > >
> > > int start = 0;
> > > int size = 1000; // see how big you can make this to improve
> > > performance
> > > while(still_more_data){
> > >   still_more_data = index(start, size);
> > >   start += size;
> > > }
> > >
> > > Your index method will return true if the query returned any data. If
> > > the query returns no data, it'll return false.
> > >
> > > I can't imagine what Hibernate is doing differently here to make this
> > > work if the JDBC driver is failing when executing the query.
> > >
> > > Larry
> > >
> > >
> > > On Sun, Mar 16, 2008 at 4:12 AM, nch <underscore_dot@yahoo.com> wrote:
> > > >
> > > >
> > > > Sure. Please, see attached.
> > > > I don't think the problem is in the RowHandler, though, because the
> > > > OutOfMemoryError occurs before invoking RowHandle#handleRow.
> > > >
> > > > Cheers
> > > >
> > > >
> > > > ----- Original Message ----
> > > > From: Larry Meadors <larry.meadors@gmail.com>
> > > > To: user-java@ibatis.apache.org
> > > >
> > > > Sent: Sunday, March 16, 2008 3:13:27 AM
> > > > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> > > >
> > > >  Can you post the row handler you are using.
> > > >
> > > > Larry
> > > >
> > > >
> > > > On Sat, Mar 15, 2008 at 1:14 PM, nch <underscore_dot@yahoo.com>
> > > wrote:
> > > > >
> > > > >
> > > > > Hi, Nathan.
> > > > > I did so, but I'm still having the same issue. Perhaps I'm not
> > > using it
> > > > > correctly?
> > > > > See my last post to this forum entry:
> > > > >
> > > > > http://forum.compass-project.org/thread.jspa?threadID=215278
> > > > >
> > > > > See the stack trace:
> > > > >
> > > > > MemoryError: Java heap space:
> > > > > java.lang.OutOfMemoryError: Java heap space
> > > > >        at com.mysql.jdbc.Buffer.getBytes(Buffer.java:198)
> > > > >        at com.mysql.jdbc.Buffer.readLenByteArray(Buffer.java:318)
> > > > >        at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1366)
> > > > >        at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java
> > > :2333)
> > > > >        at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:435)
> > > > >        at
> > > > > com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java
> > > :2040)
> > > > >        at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1443)
> > > > >        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1777)
> > > > >        at com.mysql.jdbc.Connection.execSQL(Connection.java:3249)
> > > > >        at
> > > > >
> > > > com.mysql.jdbc.PreparedStatement.executeInternal(
> > > PreparedStatement.java:1268)
> > > > >        at
> > > > > com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java
> > > :843)
> > > > >        at
> > > > >
> > > > org.apache.commons.dbcp.DelegatingPreparedStatement.execute(
> > > DelegatingPreparedStatement.java:169)
> > > > >        at
> > > > >
> > > > org.apache.commons.dbcp.DelegatingPreparedStatement.execute(
> > > DelegatingPreparedStatement.java:169)
> > > > >        at
> > > > >
> > > > com.ibatis.sqlmap.engine.execution.SqlExecutor.executeQuery(
> > > SqlExecutor.java:186)
> > > > >        at
> > > > >
> > > >
> > > com.ibatis.sqlmap.engine.mapping.statement.GeneralStatement.sqlExecuteQuery
> > > (GeneralStatement.java:205)
> > > > >        at
> > > > >
> > > >
> > > com.ibatis.sqlmap.engine.mapping.statement.GeneralStatement.executeQueryWithCallback
> > > (GeneralStatement.java:173)
> > > > >        at
> > > > >
> > > >
> > > com.ibatis.sqlmap.engine.mapping.statement.GeneralStatement.executeQueryWithRowHandler
> > > (GeneralStatement.java:133)
> > > > >        at
> > > > >
> > > >
> > > com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate.queryWithRowHandler
> > > (SqlMapExecutorDelegate.java:649)
> > > > >        at
> > > > >
> > > > com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl.queryWithRowHandler(
> > > SqlMapSessionImpl.java:156)
> > > > >        at
> > > > >
> > > > org.myorg.compass.SqlMapClientGpsDeviceWithRowHandler.doIndex(
> > > SqlMapClientGpsDeviceWithRowHandler.java:33)
> > > > >        at
> > > > >
> > > > org.compass.gps.device.AbstractGpsDevice$1.doInCompassWithoutResult(
> > > AbstractGpsDevice.java:93)
> > > > >        at
> > > > >
> > > > org.compass.core.CompassCallbackWithoutResult.doInCompass(
> > > CompassCallbackWithoutResult.java:29)
> > > > >        at
> > > > > org.compass.core.CompassTemplate.execute(CompassTemplate.java:132)
> > > > >        at
> > > > >
> > > > org.compass.gps.impl.SingleCompassGps.executeForIndex(
> > > SingleCompassGps.java:161)
> > > > >        at
> > > > > org.compass.gps.device.AbstractGpsDevice.index(
> > > AbstractGpsDevice.java:91)
> > > > >        at
> > > > >
> > > >
> > > org.compass.spring.device.SpringSyncTransactionGpsDeviceWrapper$1.doInTransactionWithoutResult
> > > (SpringSyncTransactionGpsDeviceWrapper.java:98)
> > > > >        at
> > > > >
> > > >
> > > org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction
> > > (TransactionCallbackWithoutResult.java:33)
> > > > >        at
> > > > >
> > > > org.springframework.transaction.support.TransactionTemplate.execute(
> > > TransactionTemplate.java:128)
> > > > >        at
> > > > >
> > > >
> > > org.compass.spring.device.SpringSyncTransactionGpsDeviceWrapper.index(
> > > SpringSyncTransactionGpsDeviceWrapper.java:96)
> > > > >        at
> > > > >
> > > > org.compass.gps.impl.SingleCompassGps$1.buildIndexIfNeeded(
> > > SingleCompassGps.java:133)
> > > > >        at
> > > > >
> > > >
> > > org.compass.core.lucene.engine.manager.DefaultLuceneSearchEngineIndexManager$8.firstStep
> > > (DefaultLuceneSearchEngineIndexManager.java:233)
> > > > >        at
> > > > >
> > > >
> > > org.compass.core.lucene.engine.manager.DefaultLuceneSearchEngineIndexManager.doOperate
> > > (DefaultLuceneSearchEngineIndexManager.java:182)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ----- Original Message ----
> > > > > From: Nathan Maves <nathan.maves@gmail.com>
> > > > > To: user-java@ibatis.apache.org
> > > > >
> > > > > Sent: Saturday, March 15, 2008 5:43:04 PM
> > > > > Subject: Re: select * causing " OutOfMemoryError: Java heap space"
> > > > >
> > > > >  this is only my 2 cents but I would throw that class out.  Write
> > > your own
> > > > > implementation which uses a row handler.  This is the type of
> > > situation in
> > > > > which a row handler could really help.  almost no memory would be
> > > used.
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Mar 13, 2008 at 4:57 PM, nch <underscore_dot@yahoo.com>
> > > wrote:
> > > > > >
> > > > > > Yes, I agree that dividing the query into several queries should
> > > do as
> > > > > long as none of them uses more memory than available. Gracias,
> > > Carlos.
> > > > > >
> > > > > > Nevertheless, I looked into
> > > > > org.compass.gps.device.ibatis.SqlMapClientGpsDevice#doIndex and,
> > > > > fundamentally, what it does is a queryForPaginatedList and
> > > iterates
> > > > through
> > > > > the resulting PaginatedList with nextPage()
> > > > > >
> > > > > > I guess that the reason why pages are kept in memory after
> > > performing
> > > > > paginatedList.nextPage() is because a paginatedList.previousPage()
> > > can be
> > > > > issued but, should't it free pages if heap space is running out?
> > > > > >
> > > > > >
> > > > > > Carlos de Luna Saenz <cdelunasaenz@yahoo.com.mx> wrote:
> > > > > >
> > > > > > Since we have a similar trouble around here i must say that
you
> > > have lot
> > > > > of options when going to compass..
> > > > > > The first one is to index "object by object" by hand, the second
> > > one is
> > > > to
> > > > > use the Gps wich will use the complete bunch of data and make
> > > subindexes
> > > > > (making parts of your "main index" with diferent "maps" for each
> > > subindex
> > > > in
> > > > > your gpsDriver.
> > > > > > if your indexing is as strong as ours i should look forward
for
> > > numer 1
> > > > or
> > > > > number 3 depending of your needs. (More a Compass than iBatis
> > > issue)
> > > > > > Greetings
> > > > > > Carlos de Luna
> > > > > >
> > > > > > ----- Mensaje original ----
> > > > > > De: nch
> > > > > >
> > > > > > Para: user-java@ibatis.apache.org; larry.meadors@gmail.com
> > > > > > Enviado: jueves, 13 de marzo, 2008 9:37:04
> > > > > > Asunto: Re: select * causing " OutOfMemoryError: Java heap
> > > space"
> > > > > >
> > > > > >
> > > > > > Sorry. Yes, I need all the data at one time, because the Compass
> > > API
> > > > seems
> > > > > to be meant in that way.
> > > > > >
> > > > > > Larry Meadors wrote: OK, so the answer to the question is...[
> > > yes, i
> > > > need
> > > > > all the data at
> > > > > >
> > > > > >
> > > > > >
> > > > > > one time | no, i do not need all of the data at one time ].
> > > > > >
> > > > > > Larry
> > > > > >
> > > > > >
> > > > > > On Thu, Mar 13, 2008 at 9:04 AM, nch wrote:
> > > > > > >
> > > > > > > Hi!
> > > > > > >
> > > > > > > I'm doing tests both under tomcat and jetty. I set 1024MB
of
> > > heap
> > > > space
> > > > > in
> > > > > > > both cases. I am using a profiler to look into what's
> > > happening during
> > > > > > > execution of the indexing process and I can tell that's
the
> > > exact
> > > > amount
> > > > > it
> > > > > > > displays for the VM.
> > > > > > >
> > > > > > > As I describe in the Compass user forum (see link bellow),
I'm
> > > > indexing
> > > > > a
> > > > > > > Wikipedia dump of about 650000-675000 records. That's sort
of
> > > 1-1.5GB
> > > > of
> > > > > > > data.
> > > > > > >
> > > > > > > Hibernate can handle all that data, I guess it's using
some
> > > sort of
> > > > > > > pagination. iBatis seems to divide the select statement
into
> > > several
> > > > > select
> > > > > > > statements, but it also seems each of such statements
> > > surpasses the
> > > > > limit of
> > > > > > > 1024MB when trying to index only 300000 of the database
> > > records.
> > > > > > >
> > > > > > > Thank you
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Chris Lamey wrote:
> > > > > > > What is you JVM heap size set to and how much data is returned
> > > by
> > > > select
> > > > > *
> > > > > > > from table?
> > > > > > >
> > > > > > > If you're trying to pull back 1G worth of data into a JVM
with
> > > a heap
> > > > > size
> > > > > > > set to 64M, you will hit the heap limit pretty quick.
> > > > > > >
> > > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: nch [mailto:underscore_dot@yahoo..com]
> > > > > > > Sent: Thu 3/13/2008 8:03 AM
> > > > > > > To: user-java@ibatis.apache.org
> > > > > > > Subject: select * causing " OutOfMemoryError: Java heap
space"
> > > > > > >
> > > > > > >
> > > > > > > Hi, everybody.
> > > > > > > I'm testing the Compass search engine and, in particular,
how
> > > to index
> > > > a
> > > > > big
> > > > > > > set of documents from a table in a MySQL database. In order
to
> > > do this
> > > > I
> > > > > > > issue a "select * from table_name" using iBatis, but this
> > > seems to be
> > > > > > > causing the application to use all heap space available.
> > > > > > > I added a new entry into Compass user forum with details:
> > > > > > > http://forum.compass-project.org/thread.jspa?threadID=215278
> > > > > > >
> > > > > > > Can you figure out why is this happening?
> > > > > > >
> > > > > > > Many thanks
> > > > > > >
> > > > > > >
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> > Never miss a thing. Make Yahoo your homepage.<http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs>
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