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From luc...@digiatlas.org
Subject Re: problems with large Lucene index (reason found)
Date Fri, 13 Mar 2009 14:26:33 GMT

Yes, I overrode the read() method in  
FSDirectory.FSIndexInput.Descriptor and forced it to read in 50Mb  
chunks and do an arraycopy() into the array created by Lucene. It now  
works with any heap size and doesn't get OOM.

There may be other areas this could happen in the Lucene code  
(although at present it seems to be working fine for me on our  
largest, 17Gb, index but I haven't tried accessing data yet - only  
getting the result size - so perhaps there are other calls to read()  
with large buffer sizes).

As this bug does not look like it will be fixed in the near future, it  
might be an idea to put in place a fix in the Lucene code. I think it  
would be safe to read in chunks of up to 100Mb without a problem and I  
don't think it will affect performance to any great degree.

It's pleasing to see that Lucene can easily handle such huge indexes,  
although this bug is obviously quite an impediment to doing so.

regards,
Cameron Newham

Quoting Michael McCandless <lucene@mikemccandless.com>:

>
> Gak, what a horrible bug!
>
> It seems widespread (JRE 1.5, 1.6, on Linux & Windows OSs).  And it's
> been open for almost 2.5 years.  I just added a comment & voted for the
> bug.
>
> Does it also occur on a 64 bit JRE?
>
> If you still allocate the full array, but read several smaller chunks
> into it, do you still hit the bug?
>
> Mike
>
> lucene@digiatlas.org wrote:
>
>>
>> I now know the cause of the problem. Increasing heap space actually  
>>  breaks Lucene when reading large indexes.
>>
>> Details on why can be found here:
>>
>> http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6478546
>>
>>
>> Lucene is trying to read a huge block (about 2580Mb) at the point   
>> of failure. While it allocates the required bytes in method   
>> MultiSegmentReader.norms(), line 334, just fine, it is only when it  
>>  attempts to use this array in a call to   
>> RandomAccessFile.readBytes() that it gets OOM. This is caused by a   
>> bug in the native code for the Java IO.
>>
>> As observed in the bug report, large heap space actually causes the  
>>  bug to appear. When I reduced my heap from 1200M to 1000M the   
>> exception was never generated and the code completed correctly and   
>> it reported the correct number of search hits in the Hibernate   
>> Search version of my program.
>>
>> This isn't good - I need as much memory as possible because I   
>> intend to run my search as a web service.
>>
>> The work-around would be to read the file in small chunks, but I am  
>>  not familiar with the Lucene code so I am unsure how that would be  
>>  done in a global sense (i.e.: does it really need to allocate a   
>> buffer of that size in MultiSegmentReader?)
>>
>> The obvious solution (which I haven't tried yet) would be to patch   
>> the point in FSDirectory where the java IO read occurs - looping   
>> with a small buffer for the read and then concatenating the result   
>> back into Lucene's byte array.
>>
>> Thanks for the comments on this problem from people on this list.
>>
>>
>>
>> Quoting Ted Dunning <ted.dunning@gmail.com>:
>>
>>> try running with verbose gc.  That will give you more details about what is
>>> happening.
>>>
>>> Even better, run with jconsole on the side so that you get really detailed
>>> information on memory pools.
>>>
>>> On Thu, Mar 12, 2009 at 7:30 AM, <lucene@digiatlas.org> wrote:
>>>
>>>> Thanks Mike and Jokin for your comments on the memory problem. I have
>>>> submitted the query to the Hibernate Search list although I haven't seen
a
>>>> response yet.
>>>>
>>>> In the meantime I did my own investigating in the code (I'd rather have
>>>> avoided this!). I'm seeing results that don't make any sense and maybe
>>>> someone here with more experience of Lucene and the way memory is  
>>>>  allocated
>>>> by the JVM may shed light on, what to me, are quite illogical   
>>>> observations.
>>>>
>>>> As you may recall I had a stand-alone Lucene search and a Hibernate Search
>>>> version.  Looking in the HS code did not shed any light on the   
>>>> issue. I took
>>>> my stand-alone Lucene code and put it in a method and replaced   
>>>> the search in
>>>> the HS class (the constructor of QueryHits.java) with the call to  
>>>>  my method.
>>>> Bear in mind this method is the same code as posted in my earlier  
>>>>  message -
>>>> it sets up the Lucene search from scratch (i.e.: no data   
>>>> structures created
>>>> by HS were used). So, effectively I was calling my stand-alone code after
>>>> any setup done by Hibernate and any memory it may have allocated (which
>>>> turned out to be a few Mb).
>>>>
>>>> I get OOM!  Printing the free memory at this point shows bags of memory
>>>> left. Indeed, the same free memory (+/- a few Mb) as the   
>>>> stand-alone Lucene
>>>> version!
>>>>
>>>> I then instrumented the Lucene method where the OOM is occuring
>>>> (FSDirectory.readInternal()).  I cannot understand the results I   
>>>> am seeing.
>>>> Below is a snippet of the output of each with the code around FSDirectory
>>>> line 598 as follows:
>>>>
>>>> ...
>>>>      do {
>>>>              long tot = Runtime.getRuntime().totalMemory();
>>>>              long free =Runtime.getRuntime().freeMemory();
>>>> System.out.println("LUCENE: offset="+offset+"  total="+total+"
>>>> len-total="+(len-total)+"   free mem="+free+"  used ="+(tot-free));
>>>>        int i = file.read(b, offset+total, len-total);
>>>> ...
>>>>
>>>>
>>>>
>>>> The stand-alone version:
>>>>
>>>> ...
>>>> LUCENE: offset=0  total=0  len-total=401   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=883   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=918576864  used
>>>> =330080544
>>>> LUCENE: offset=0  total=0  len-total=209000000   free mem=631122912  used
>>>> =617534496
>>>> LUCENE: offset=209000000  total=0  len-total=20900000   free mem=631122912
>>>> used =617534496
>>>> LUCENE: offset=229900000  total=0  len-total=20900000   free mem=631122912
>>>> used =617534496
>>>> LUCENE: offset=250800000  total=0  len-total=20900000   free mem=631122912
>>>> used =617534496
>>>> ...
>>>> completes successfully!
>>>>
>>>>
>>>> The method called via Hibernate Search:
>>>>
>>>> ...
>>>> LUCENE: offset=0  total=0  len-total=401   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=883   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=1024   free mem=924185480  used
>>>> =334892152
>>>> LUCENE: offset=0  total=0  len-total=209000000   free mem=636731528  used
>>>> =622346104
>>>> Exception in thread "main" java.lang.OutOfMemoryError
>>>>      at java.io.RandomAccessFile.readBytes(Native Method)
>>>>      at java.io.RandomAccessFile.read(Unknown Source)
>>>>      at
>>>> org.apache.lucene.store.FSDirectory$FSIndexInput.readInternal(FSDirectory.java:599)
>>>> ... fails with exception!
>>>>
>>>>
>>>> Note that the HS version has slightly more free memory because I ran it
>>>> with -Xms1210M as opposed to -Xms1200M for the stand-alone to offset any
>>>> memory used by HS when it starts up.
>>>>
>>>> As you can see, these are identical for all practical purposes.  So what
>>>> gives?
>>>>
>>>> I'm stumped, so any suggestions appreciated.
>>>>
>>>> Thanks.
>>>>
>>>>
>>>> Quoting Michael McCandless <lucene@mikemccandless.com>:
>>>>
>>>>
>>>>> Unfortunately, I'm not familiar with exactly what Hibernate search does
>>>>> with the Lucene APIs.
>>>>>
>>>>> It must be doing something beyond what your standalone Lucene test case
>>>>> does.
>>>>>
>>>>> Maybe ask this question on the Hibernate list?
>>>>>
>>>>> Mike
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Ted Dunning, CTO
>>> DeepDyve
>>>
>>> 111 West Evelyn Ave. Ste. 202
>>> Sunnyvale, CA 94086
>>> www.deepdyve.com
>>> 408-773-0110 ext. 738
>>> 858-414-0013 (m)
>>> 408-773-0220 (fax)
>>>
>>
>>
>>




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