ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 #308

fmannhardt · 2014-03-25T20:17:32Z

I updated to MapDB 0.9.11 and I'm now getting a ArrayIndexOutOfBoundsException on BTreeMap.put after adding several entries. Looking at the MapDB file while adding entries it never exceed the size of 16 MB, whereas it was growing bigger before (~800MB).

I'm running on Win7 64bit, Java JDK 1.7.0_25 using DBMaker.newFileDB to create the DB. The same error happens also if I disable the cache or the asyncWrite feature. I will try to create a test case, but maybe this helps already.

java.lang.ArrayIndexOutOfBoundsException: 147448
    at org.mapdb.Volume$ByteBufferVol.getLong(Volume.java:327)
    at org.mapdb.StoreDirect.get2(StoreDirect.java:440)
    at org.mapdb.StoreDirect.get(StoreDirect.java:428)
    at org.mapdb.EngineWrapper.get(EngineWrapper.java:60)
    at org.mapdb.AsyncWriteEngine.get(AsyncWriteEngine.java:399)
    at org.mapdb.Caches$HashTable.get(Caches.java:230)
    at org.mapdb.BTreeMap.put2(BTreeMap.java:664)
    at org.mapdb.BTreeMap.put(BTreeMap.java:644)

The ArrayIndexOutOfBoundsException is always at different sizes.

The text was updated successfully, but these errors were encountered:

fmannhardt · 2014-03-26T09:22:46Z

~~I found that the error is gone, if I don't select the option valuesOutsideNodesEnable().~~ (Sometimes the error is gone, but it does not depend on that option.)
Moreover, if I use the option checksumEnable(), then the following IOError is thrown:

java.io.IOError: java.io.IOException: Checksum does not match, data broken
    at org.mapdb.StoreDirect.get(StoreDirect.java:430)
    at org.mapdb.EngineWrapper.get(EngineWrapper.java:60)
    at org.mapdb.AsyncWriteEngine.get(AsyncWriteEngine.java:399)
    at org.mapdb.Caches$HashTable.get(Caches.java:230)
    at org.mapdb.BTreeMap.put2(BTreeMap.java:661)
    at org.mapdb.BTreeMap.put(BTreeMap.java:644)
    at org.test.SimpleMapDBTestCase.testCreateReadRandomLogDisk(SimpleMapDBTestCase.java:42)
Caused by: java.io.IOException: Checksum does not match, data broken
    at org.mapdb.Store.deserialize(Store.java:238)
    at org.mapdb.StoreDirect.get2(StoreDirect.java:475)
    at org.mapdb.StoreDirect.get(StoreDirect.java:428)
    ... 28 more

This is how I create the DBMaker:

File tempFile = File.createTempFile("test", ".db");
DBMaker dbMaker = DBMaker.newFileDB(tempFile)
                // .closeOnJvmShutdown(), we do not use this, as it causes memory leaks
                .deleteFilesAfterClose().transactionDisable()
                .mmapFileEnableIfSupported();
dbMaker = dbMaker.cacheSize(1024 * 16);
dbMaker = dbMaker.asyncWriteEnable().asyncWriteFlushDelay(100).asyncWriteQueueSize(1024 * 64);
dbMaker = dbMaker.checksumEnable();
DB db = dbMaker.make();

And this is how I create the Map:

KeyStringPool keyPool = new KeyStringPool();        
ConcurrentNavigableMap<Long, XAttributeExternalImpl> mapStorage = db.createTreeMap("attributeStore").keySerializer(BTreeKeySerializer.ZERO_OR_POSITIVE_LONG)
                .valueSerializer(new MapDBXAttributeSerializer(keyPool)).valuesOutsideNodesEnable().nodeSize(64)
                .make();

I prepared a small example project that I could send you by mail.

jankotek · 2014-03-27T14:46:24Z

Hi,

there was a race condition in BTreeMap.put fixed recently in #304. So perhaps try with newest 1.0.0 snapshot. If that does not help, please send me example project, my email is in github profile.

reuschling · 2014-03-28T16:06:57Z

I have a similar error with 9.11, also tried with 1.0.0 snapshot

java.lang.RuntimeException: Writer thread failed
    at org.mapdb.AsyncWriteEngine.checkState(AsyncWriteEngine.java:328)
    at org.mapdb.AsyncWriteEngine.close(AsyncWriteEngine.java:491)
    at org.mapdb.EngineWrapper.close(EngineWrapper.java:82)
    at org.mapdb.Caches$HashTable.close(Caches.java:312)
    at org.mapdb.EngineWrapper.close(EngineWrapper.java:82)
    at org.mapdb.EngineWrapper$CloseOnJVMShutdown.close(EngineWrapper.java:659)
    at org.mapdb.EngineWrapper$CloseOnJVMShutdown$1.run(EngineWrapper.java:644)
    at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 3108142
    at org.mapdb.Volume$ByteBufferVol.getByte(Volume.java:336)
    at org.mapdb.Volume.getUnsignedShort(Volume.java:96)
    at org.mapdb.StoreDirect.longStackTake(StoreDirect.java:932)
    at org.mapdb.StoreDirect.freePhysTake(StoreDirect.java:1065)
    at org.mapdb.StoreDirect.physAllocate(StoreDirect.java:655)
    at org.mapdb.StoreDirect.update2(StoreDirect.java:535)
    at org.mapdb.StoreDirect.update(StoreDirect.java:491)
    at org.mapdb.EngineWrapper.update(EngineWrapper.java:65)
    at org.mapdb.AsyncWriteEngine.access$101(AsyncWriteEngine.java:74)
    at org.mapdb.AsyncWriteEngine.runWriter(AsyncWriteEngine.java:220)
    at org.mapdb.AsyncWriteEngine$WriterRunnable.run(AsyncWriteEngine.java:170)
    ... 1 more

I create my db as follows:

DB db = DBMaker.newFileDB(new File("dbPath")).closeOnJvmShutdown().asyncWriteEnable().deleteFilesAfterClose()
                        .transactionDisable().mmapFileEnableIfSupported().make();

Map<String, NerEntity> hsId2Entity = db.getTreeMap("id2entity");

public class NerEntity extends Entity implements Serializable, Comparable<NerEntity>
{
    private static final long serialVersionUID = 1334795226689152608L;
    public float score = 0f;
    public String textTrigger;
    public String textTriggerTermPOS;
...}

JensBee · 2014-03-31T07:29:30Z

Looks like the error gets triggered when using AsyncWriteEngine. Disabling all .async* options does not trigger the error and may be used as workaround.

ghost · 2014-03-31T22:04:57Z

Hi, I have the problem when I Pump data to a BTree and I have too much data. I tried to disable async stuff but it doesn't seem to help in that case

ghost · 2014-03-31T22:27:28Z

I did a very simple test and I could reproduce the issue.

It seems this option causes the problem
.mmapFileEnableIfSupported()

Here is my test code

@Test
    public void test(){
        DB db = DBMaker.newTempFileDB()
                .mmapFileEnableIfSupported()
                .compressionEnable()
                .transactionDisable()
                .checksumEnable()
                .syncOnCommitDisable()
                .make();
        Iterator<Fun.Tuple2<Long,String>> newIterator = new Iterator<Fun.Tuple2<Long, String>>() {
            private AtomicLong value = new AtomicLong(10000000);
            @Override
            public boolean hasNext() {
                return value.get() > 0 ;
            }

            @Override
            public Fun.Tuple2<Long, String> next() {
                Long v = value.decrementAndGet();
                return new Fun.Tuple2<Long,String>(v,v.toString());
            }
        };
        BTreeMap<Long,String> cubeData = db.createTreeMap("data").pumpSource(newIterator).make();

This throws an ArrayOutOfBoundsException IIF mmap is enabled

I use Java 8 btw if it has any importance

jankotek · 2014-04-01T09:32:07Z

Thanks, last test case is very helpful. I will fix it very soon.

ghost · 2014-04-01T14:03:44Z

great! keep in touch and keep up the good work

jankotek · 2014-04-05T19:03:31Z

This is now fixed.

jankotek · 2014-04-16T07:56:51Z

0.9.13 released with fix

abarnashankar · 2015-08-27T18:36:16Z

I am using MapDB version (1.0.1) and in PRODUCTION I am getting the following error.
I need help from some one as this is in PRODUCTION and i have a strict SLA. Any help is appreciated.

I am getting error java.lang.ArrayIndexOutOfBoundsException: 238011748
at org.mapdb.Volume$ByteBufferVol.getByte(Volume.java:385) and also Exception in thread "main" java.lang.AssertionError: data were not fully read, check your serializer when i use MapDB

abarnashankar · 2015-08-27T18:38:22Z

I am using MapDB version 1.0.1 and my code is pasted below. Please let me know whether i need to modify any thing in the below code. It would be great if some one helps me on this one.

db = DBMaker
.newFileDB(new File("file"))
.mmapFileEnable()
.closeOnJvmShutdown()
.transactionDisable()
.cacheSize(1000)
.make();

jankotek · 2015-08-27T19:46:42Z

@abarnashankar 1.0.1 is way too old, there were number of issues fixed since than. I would recommend to backup your data for start.

abarnashankar · 2015-08-27T22:50:53Z

Hi,
Thanks for your response.. I am happy to see your response… some one there to help me :)

It would be great if you could advice me of the steps I need to do. I even tried to use MapDB version 1.0.8 in my pom.xml and then when I tested, the error is the same.
Please let me know what may be the reason for this error. I even tried to take the same file from PRODUCTION which is used by MapDB and test in my QA region, I am getting the same error.
You suggested me to take a backup of the file… I have a copy of this file… But please tell me whether I need to restart my QA or PRODUCTION server ? it is difficult for me to ask for restarting production server.

NOTE : It was working fine till few weeks back but then all of a sudden, it stopped working

Code :
db = DBMaker

            .newFileDB(new File(“file"))

            .mmapFileEnable()

            .closeOnJvmShutdown()

            .transactionDisable()

            .cacheSize(1000)

            .make();


 Map<Long, String> treeMap = db.getTreeMap(“<string>"); //this line is throwing error at some point of time.


Exception Stack Trace:

java.lang.ArrayIndexOutOfBoundsException: 238011748
at org.mapdb.Volume$ByteBufferVol.getByte(Volume.java:385)
at org.mapdb.Volume.getUnsignedShort(Volume.java:97)
at org.mapdb.StoreDirect.longStackTake(StoreDirect.java:1027)
at org.mapdb.StoreDirect.freePhysTake(StoreDirect.java:1160)
at org.mapdb.StoreDirect.physAllocate(StoreDirect.java:741)
15/08/27 19:18:48 INFO compress.CodecPool: Got brand-new compressor [.deflate]
Exception in thread "main" java.lang.AssertionError: data were not fully read, check your serializer
at org.mapdb.Store.deserialize(Store.java:332)
at org.mapdb.StoreDirect.get2(StoreDirect.java:532)

Thanks and Regards
Shankar V
612-226-1845 (Cell)
SCJP, PMP, Cloudera Certified Hadoop Developer, Datastax Certified Cassandra Developer
From: Jan Kotek <notifications@github.com mailto:notifications@github.com>
Reply-To: jankotek/mapdb <reply@reply.github.com mailto:reply@reply.github.com>
Date: Thursday, August 27, 2015 at 12:46 PM
To: jankotek/mapdb <mapdb@noreply.github.com mailto:mapdb@noreply.github.com>
Cc: Shankar Viswanathan <shviswanathan@stubhub.com mailto:shviswanathan@stubhub.com>
Subject: Re: [mapdb] ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 (#308)

@abarnashankarhttps://github.com/abarnashankar 1.0.1 is way too old, there were number of issues fixed since than. I would recommend to backup your data for start.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/308#issuecomment-135533621.

abarnashankar · 2015-08-27T22:52:38Z

Thanks for your response.. I am happy to see your response… some one there to help me :)

It would be great if you could advice me of the steps I need to do. I even tried to use MapDB version 1.0.8 in my pom.xml and then when I tested, the error is the same.
Please let me know what may be the reason for this error. I even tried to take the same file from PRODUCTION which is used by MapDB and test in my QA region, I am getting the same error.
You suggested me to take a backup of the file… I have a copy of this file… But please tell me whether I need to restart my QA or PRODUCTION server ? it is difficult for me to ask for restarting production server.

NOTE : It was working fine till few weeks back but then all of a sudden, it stopped working

Code :
db = DBMaker
.newFileDB(new File(“file"))
.mmapFileEnable()
.closeOnJvmShutdown()
.transactionDisable()
.cacheSize(1000)
.make();

 Map<Long, String> treeMap = db.getTreeMap(“<string>"); //this line is throwing error at some point of time.

Exception Stack Trace:

java.lang.ArrayIndexOutOfBoundsException: 238011748
at org.mapdb.Volume$ByteBufferVol.getByte(Volume.java:385)
at org.mapdb.Volume.getUnsignedShort(Volume.java:97)
at org.mapdb.StoreDirect.longStackTake(StoreDirect.java:1027)
at org.mapdb.StoreDirect.freePhysTake(StoreDirect.java:1160)
at org.mapdb.StoreDirect.physAllocate(StoreDirect.java:741)
15/08/27 19:18:48 INFO compress.CodecPool: Got brand-new compressor [.deflate]
Exception in thread "main" java.lang.AssertionError: data were not fully read, check your serializer
at org.mapdb.Store.deserialize(Store.java:332)
at org.mapdb.StoreDirect.get2(StoreDirect.java:532)

jankotek · 2015-08-28T06:15:42Z

That exception says that size of data is
different from number of bytes read
by serializer. So perhaps compression
or serializer has changed?

jankotek added the bug label Mar 27, 2014

jankotek added the fixed in trunk label Apr 5, 2014

jankotek added a commit that referenced this issue Apr 5, 2014

Volume: fix random errors at mmap files. See #308

97d7bb0

jankotek closed this as completed Apr 16, 2014

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ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 #308

ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 #308

fmannhardt commented Mar 25, 2014

fmannhardt commented Mar 26, 2014

jankotek commented Mar 27, 2014

reuschling commented Mar 28, 2014

JensBee commented Mar 31, 2014

ghost commented Mar 31, 2014

ghost commented Mar 31, 2014

jankotek commented Apr 1, 2014

ghost commented Apr 1, 2014

jankotek commented Apr 5, 2014

jankotek commented Apr 16, 2014

abarnashankar commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

jankotek commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

jankotek commented Aug 28, 2015

ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 #308

ArrayIndexOutOfBoundsException with BTreeMap.put using v0.9.11 #308

Comments

fmannhardt commented Mar 25, 2014

fmannhardt commented Mar 26, 2014

jankotek commented Mar 27, 2014

reuschling commented Mar 28, 2014

JensBee commented Mar 31, 2014

ghost commented Mar 31, 2014

ghost commented Mar 31, 2014

jankotek commented Apr 1, 2014

ghost commented Apr 1, 2014

jankotek commented Apr 5, 2014

jankotek commented Apr 16, 2014

abarnashankar commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

jankotek commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

abarnashankar commented Aug 27, 2015

jankotek commented Aug 28, 2015