Develop Reference

Dataproc Hive Job - Tez Java heap OOM

I have a problem with my cluster.
the cluster have
2 worker primary
2 secondary worker
30 gb di ram
The cluster runs correctly and launches the job hives for at least about 10h.
After 10h I have an error of :Java heap space
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_292]
Caused by: java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3236) ~[?:1.8.0_292]
at java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191) ~[?:1.8.0_292]
at org.apache.hadoop.ipc.ResponseBuffer.toByteArray(ResponseBuffer.java:53) ~[hadoop-common-3.2.2.jar:?]
at org.apache.hadoop.ipc.Client$Connection$3.run(Client.java:1159) ~[hadoop-common-3.2.2.jar:?]
... 5 more
ERROR : FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.tez.TezTask
INFO : Completed executing command(queryId=hive_20210923102707_66b4cd11-7cfb-4910-87bc-7f062ce1b00e); Time taken: 75.101 seconds
INFO : Concurrency mode is disabled, not creating a lock manager
Error: Error while processing statement: FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.tez.TezTask (state=08S01,code=1)
i tried to set this cofiguration but it didn't help.
SET hive.execution.engine = tez;
SET hive.exec.dynamic.partition = true;
SET hive.exec.dynamic.partition.mode = nonstrict;
SET mapreduce.job.reduces=1;
SET hive.auto.convert.join=false;
set hive.stats.column.autogather=false;
set hive.optimize.sort.dynamic.partition=true;
is there any way to clean the java heap space or I have got some configuration wrong?
the problem is solved by restarting the cluster

It seems that the default Tez container and heap sizes set by Dataproc are too small for your job. You can update the following Hive properties to increase them:
hive.tez.container.size: The YARN container size in MB for Tez. If set to "-1" (default value), it picks the value of mapreduce.map.memory.mb. Consider increasing the value if the query / Tez app fails with something like "Container is running beyond physical memory limits. Current usage: 4.1 GB of 4 GB physical memory used; 6.0 GB of 20 GB virtual memory used. Killing container.". Example: SET hive.tez.container.size=8192 in Hive, or --properties hive:hive.tez.container.size=8192 when creating the cluster.
hive.tez.java.opts: The JVM options for the Tez YARN application. If not set, it picks the value of mapreduce.map.java.opts. This value should be less or equal to the container size. Consider increasing the JVM heap size if the query / Tez app fails with an OOM exception. Example: SET hive.tez.java.opts=-Xmx8g or --properties hive:hive.tez.java.opts=-Xmx8g when creating the cluster.
You can check /etc/hadoop/conf/mapred-site.xml to get the value of mapreduce.map.java.opts, and /etc/hive/conf/hive-site.xml for the 2 Hive properties mentioned above.

Apache Ignite IGFS Not using Non Heap Space

I am using Apache Ignite 2.6. I am using Ignite Filesystem, and when I write a specific file, which is about 25 MB, to IGFS, over and over, the data is not saved into the non-heap space. Instead, it goes into heap, which is subject to Garbage Collection, and it is relatively slow. How do I get IGFS to save a file into the large heap space I have allocated for it?
High level architecture--I have a client ignite node running inside of a tomcat for now, and a server ignite node, on which I intend this data to be stored. Scaling can occur once I get this working as expected--but it is very slow because of the aforementioned problem. It also OOMs when it runs out of heap space very quickly. Thing is, I want it to use the 30G of NON HEAP space I have allocated!
I intend this it to be an in memory cache. I am allocating 2 G of heap space and 30G of non heap space to the JVM. The non heap space never gets used and it runs out of memory as a result. I have confirmed that the non-heap space is not used using the JMX Console Memory tab--non heap space stays well below 100M, while heap space quickly balloons to 2G and then the JVM crashes.
The details: First, my ignite configuration (spring xml):
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd">
<bean id="propertyConfigurer" class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
<property name="systemPropertiesModeName" value="SYSTEM_PROPERTIES_MODE_FALLBACK"/>
<property name="searchSystemEnvironment" value="true"/>
</bean>
<bean id="ignite.cfg" class="org.apache.ignite.configuration.IgniteConfiguration">
<property name="marshaller">
<bean class="org.apache.ignite.internal.binary.BinaryMarshaller" />
</property>
<property name="fileSystemConfiguration">
<list>
<bean class="org.apache.ignite.configuration.FileSystemConfiguration">
<property name="name" value="igfs"/>
<property name="blockSize" value="#{128 * 1024}"/>
<property name="perNodeBatchSize" value="512"/>
<property name="perNodeParallelBatchCount" value="16"/>
<property name="prefetchBlocks" value="32"/>
</bean>
</list>
</property>
<property name="discoverySpi">
<bean class="org.apache.ignite.spi.discovery.tcp.TcpDiscoverySpi">
<property name="ipFinder">
<bean class="org.apache.ignite.spi.discovery.tcp.ipfinder.multicast.TcpDiscoveryMulticastIpFinder">
<property name="addresses">
<list>
<value>127.0.0.1:47500..47509</value>
</list>
</property>
</bean>
</property>
</bean>
</property>
<property name="dataStorageConfiguration">
<bean class="org.apache.ignite.configuration.DataStorageConfiguration" >
<!-- if I don't set this, the system region runs out of memory almost immediately -->
<property name="systemRegionMaxSize" value="#{6L * 1024 * 1024 * 1024"} />
<property name="systemRegionInitialSize" value="#{6L * 1024 * 1024 * 1024"} />
</bean>
</property>
</bean>
Here is the script I use to start up my ignite server process. It's a shell script running on a Linux machine with 64 G RAM and 40 G disk space.
IGNITE_HOME=/data/apache-ignite
export IGNITE_HOME
IGNITE_JMX_PORT=1234
export IGNITE_JMX_PORT
$IGNITE_HOME/bin/ignite.sh $IGNITE_HOME/ignite-media-server.xml -J-Xmx2G -J-Xms2G -J-XX::+HeapDumpOnOutOfMemoryError -J-XX:HeapDumpPath=$IGNITE_HOME -J-XX:+PrintGC -J-XX:+PrintGCTimeStamps -J-XX:+PrintGCDateStamps -J-Xloggc:$IGNITE_HOME/gc.log-$(date +%m%d-%H%M%S) -J-XX:+UseG1GC -J-XX:DisableExplicitGC -J-XX:MaxDirectMemorySize=30G
This is the code that creates my client igfs object, through which I save files to ignite. They tend to be on the large side.
public void init() throws Exception{
igniteInstanceName = "client-name=" + hostInfo.getLocalHost();
Ignition.setClientMode(true);
// reading in the same config file as the server uses to start up above. The big difference is the clientMode set to true here.
try(InputStream configFileInputStream = new FileInputStream(ResourceUtils.getFile("ignite-media-server.xml"));){
ignite = IgnitionEx.start(configFileInputStream, igniteInstanceName, null, null);
igfs = ignite.fileSystem("igfs");
}
catch(Throwable t){ /* do log */}
}
Here is a save method, that saves my files to ignite:
public saveStream(String cachePath, AudioInputStream toCache){
OutputStream os = null;
try{
IgfsPath cacheFile = new IgfsPath(cachePath);
os = igfs.create(cacheFile, true);
AudioSystem.write(toCache.getDataStream, AudioFileFormat.TYPE.WAVE, os);
}
finally{
// close streams
}
}
Why doesn't my data get saved to the speedy off-heap space? What am I missing? my server.config comes almost straight from the igfs provided example.
In other confusion, when I use ignitevisor.cmd to inspect memory usage on the server node before and after a shorter test (that doesn't make it crash) I see the following:
Look at memory allocation while ignite is empty in ignitevisor.cmd. See that my igfs region says:
Heap Memory Initialized: 2g
Heap Memory Used: 56mb
Non-heap memory initialized: 2mb
Non Heap memory used: 49 mb
Non heap memory maximum: 744mb
Create JUST SHY 2 G worth of files saved in IGFS--just short of an OOM since from bitter experience I know it will blow up shortly. Use ignitevisor.cmd to look at the memory allocation of the nodes. This is what ... – MeowCode 2 mins ago
Heap memory initialized: 2gb
Heap memory used: 1gb
Non Heap memory used 64 MB
Non heap memory maximum: 744mb
Why is there still almost nothing in non-heap? And why does ignitevisor think that the non-heap maximum is 744 MB when it should be 30 GB?
In other points of interest, if I increase my heap size to 6 GB, it runs longer, but still the server crashes with an "OutOfMemoryError:Java heap space". Interestingly, I can reproduce this even when I enable disk persistence. Inspecting the heap dump file reveals a lot of ConcurrentLinkedHashMap entries. The entries themselves are "org.apache.ignite.internal.GridTopic" objects. Each one has a uuid and most appear to be of type TOPIC_DATASTREAM.

Data is saved to Off-Heap all right, but you should be aware that a lot of transient objects involved in IGFS operation will still be briefly held on heap (and GCed after that).
"JMX Console Memory tab--non heap space" is the wrong metric. I don't think that there are any JVM metrics for Off-Heap. However, Ignite will print Off-Heap statistics at regular intervals.
Why you would run out of memory is not obvious. Have you tried collecting heap dump and analyzing it?

Oracle Coherence eviction not working

I am working on implementing Oracle Coherence replicated cache. The implementation is as follows:
<?xml version="1.0"?>
<!DOCTYPE cache-config SYSTEM "cache-config.dtd">
<cache-config>
<caching-scheme-mapping>
<cache-mapping>
<cache-name>EntryList</cache-name>
<scheme-name>ENTRY_ITEMS</scheme-name>
</cache-mapping>
</caching-scheme-mapping>
<caching-schemes>
<replicated-scheme>
<scheme-name>ENTRY_ITEMS</scheme-name>
<backing-map-scheme>
<local-scheme>
<scheme-name>ENTRY_ITEMS</scheme-name>
<unit-calculator>FIXED</unit-calculator>
<expiry-delay>60m</expiry-delay> <!-- expire after 60 minutes -->
<high-units>2000</high-units>
<eviction-policy>LFU</eviction-policy>
</local-scheme>
</backing-map-scheme>
<autostart>true</autostart>
</replicated-scheme>
</caching-schemes>
</cache-config>
tangasol-coherence-override.xml
<coherence xmlns:xsi="http://www.w4.org/2001/XMLSchema-instance"
xmlns="http://xmlns.oracle.com/coherence/coherence-operational-config"
xsi:schemaLocation="http://xmlns.oracle.com/coherence/coherence-operational-config
coherence-operational-config.xsd">
<cluster-config>
<member-identity>
<cluster-name>clusterName</cluster-name>
<!-- Name of the first member of the cluster -->
<role-name>RoleName</role-name>
</member-identity>
<unicast-listener xml-override=coherence-environment.xml/>
</cluster-config>
</coherence>
coherence-environment.xml
<unicast-listener xmlns:xsi="http://www.w4.org/2001/XMLSchema-instance"
xmlns="http://xmlns.oracle.com/coherence/coherence-operational-config"
xsi:schemaLocation="http://xmlns.oracle.com/coherence/coherence-operational-config
coherence-operational-config.xsd">
<well-known-addresses>
<socket-address id="1">
<address>member1</address>
<port>7777</port>
</socket-address>
</well-known-addresses>
<well-known-addresses>
<socket-address id="2">
<address>member2</address>
<port>7777</port>
</socket-address>
</well-known-addresses>
</unicast-listener>
This is implemented and tested to be working perfectly.
We were testing the eviction policy of the cache. To ease out testing I did the following:
I keep the size of cache as 4 by setting high-units as 4. Now add 4 entries in the cache. This should fill the cache completely.
Now if I make one more entry number 5 in the cache, I was expecting the lease frequently used entry to be kicked out of the cache to make room for the entry number 5.
The next time I access the cache for the new entry number 5, I should get a cache HIT.
But that's not happening, I always get a Cache MISS.
I ran my java code in debug mode and I see that the code PUT's entry number 5 in the cache but this PUT operation does not reflect on the cache.
Now I am definitely not the first person testing the coherence cache eviction policies. Am I missing anything in the configuration? Am I testing the eviction in a wrong way. Any inputs are welcome.
Thanks.

Try to isolate the problem:
change<expiry-delay>1</expiry-delay> (1ms)
add <low-units>0</low-units> (default value is 75% which is 3 entries).
try another policy <eviction-policy>LRU</eviction-policy>
If those won't help, try to add custom eviction policy class to see wheter eviction triggered. see here:

I have tried your example with 3 as High Units. My observation:
Eviction works as soon as I put 4th entry item. So, it works!!
You can start Coherence Server (coherence.sh) for command-line monitoring with same override & cache config file. See details, which gets printed when I put following command to see cache:
Map (?): cache EntryList
Cache Configuration: EntryList
SchemeName: ENTRY_ITEMS
AutoStart: true
ServiceName: ReplicatedCache
ServiceDependencies
EventDispatcherThreadPriority: 10
ThreadPriority: 10
WorkerThreadsMax: 2147483647
WorkerPriority: 5
EnsureCacheTimeout: 30000
BackingMapScheme
InnerScheme (LocalScheme)
SchemeName: ENTRY_ITEMS
UnitCalculatorBuilder
Calculator: FIXED
EvictionPolicyBuilder
Policy: LFU
ExpiryDelay: 1h
HighUnits
Units: 3
UnitFactor: 1

How to trace and prevent the deadlock appeared in c3po which is running in seperate processes?

I have a very simple computation which produces letter matrices finds probably all the words in the matrix. The letters in the word are adjacent cells.
for (int i = 0; i < 500; i++) {
System.out.println(i);
Matrix matrix = new Matrix(4);
matrix.scanWordsRandomly(9);
matrix.printMatrix();
System.out.println(matrix.getSollSize());
matrix.write_to_db();
}
Here is the persisting code.
public void write_to_db() {
Session session = null;
try {
session = HibernateUtil.getSessionFactory().openSession();
session.beginTransaction();
Matrixtr onematrixtr = new Matrixtr();
onematrixtr.setDimension(dimension);
onematrixtr.setMatrixstr(this.toString());
onematrixtr.setSolsize(getSollSize());
session.save(onematrixtr);
for (Map.Entry<Kelimetr, List<Cell>> sollution : sollutions.entrySet()) {
Kelimetr kelimetr = sollution.getKey();
List<Cell> solpath = sollution.getValue();
Solstr onesol = new Solstr();
onesol.setKelimetr(kelimetr);
onesol.setMatrixtr(onematrixtr);
onesol.setSoltext(solpath.toString().replace("[", "").replace("]", "").replace("true", "").replace("false", ""));
session.save(onesol);
}
session.getTransaction().commit();
session.close();
}
catch (HibernateException he) {
System.out.println("DB Error : " + he.getMessage());
session.close();
}
catch (Exception ex) {
System.out.println("General Error : " + ex.getMessage());
}
}
Here is the hibernate configuration file.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-configuration PUBLIC "-//Hibernate/Hibernate Configuration DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/kelimegame_db_dev?autoReconnect=true&useUnicode=true&characterEncoding=UTF-8</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password">!.Wlu9RrCA</property>
<property name="hibernate.show_sql">false</property>
<property name="hibernate.query.factory_class">org.hibernate.hql.classic.ClassicQueryTranslatorFactory</property>
<property name="hibernate.format_sql">false</property>
<!-- Use the C3P0 connection pool provider -->
<property name="hibernate.c3p0.acquire_increment">50</property>
<property name="hibernate.c3p0.min_size">10</property>
<property name="hibernate.c3p0.max_size">100</property>
<property name="hibernate.c3p0.timeout">300</property>
<property name="hibernate.c3p0.max_statements">5</property>
<property name="hibernate.c3p0.idle_test_period">3000</property>
<mapping resource="kelimegame/entity/Progress.hbm.xml"/>
<mapping resource="kelimegame/entity/Solstr.hbm.xml"/>
<mapping resource="kelimegame/entity/Kelimetr.hbm.xml"/>
<mapping resource="kelimegame/entity/User.hbm.xml"/>
<mapping resource="kelimegame/entity/Achievement.hbm.xml"/>
<mapping resource="kelimegame/entity/Matrixtr.hbm.xml"/>
</session-factory>
</hibernate-configuration>
After finding all possible solutions I persist the matrix and the solutions using hibernate. I am also using c3pO library. I am not spawning any thread. All the work is being done in a very simple iterative way. But I am running the jar in separate processes.
From different terminals I am executing this :
java -jar NewDB.jar
I got a deadlock as follows :
Apr 25, 2013 8:38:05 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
Apr 25, 2013 9:08:23 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2933f261
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#116dd369
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#41529b6f
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#165ab5ea
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#1d5d211d
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#4d2905fa
Pool thread stack traces:
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Apr 25, 2013 9:41:29 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
Apr 25, 2013 9:55:18 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#5a337b7d
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#69f079ce
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#2accf9b8
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#771eb4fb
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#fc07d6
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2266731b
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#740f0341
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#59edbee
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#78e924
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2123aba
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#7acd8a65
Pool thread stack traces:
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0,5,main]
java.text.NumberFormat.getInstance(NumberFormat.java:769)
java.text.NumberFormat.getInstance(NumberFormat.java:393)
java.text.MessageFormat.subformat(MessageFormat.java:1262)
java.text.MessageFormat.format(MessageFormat.java:860)
java.text.Format.format(Format.java:157)
java.text.MessageFormat.format(MessageFormat.java:836)
com.mysql.jdbc.Messages.getString(Messages.java:106)
com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2552)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3002)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2991)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3532)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:943)
com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4113)
com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1308)
com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2336)
com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2176)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2158)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:792)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
sun.reflect.GeneratedConstructorAccessor7.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:525)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:381)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:134)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:183)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:172)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:188)Killed
caglar#ubuntu:~/NetBeansProjects/NewDB/dist$
My question is as follows :
Can this deadlock in c3po happen since I am running the program in
separate processes?
Should I use one process and multiple threads inside of this
process?
How can I trace this deadlock understand the cause of it? Is there a way to trace multiple JVMs causing deadlocks?

this is an interesting one.
you've published two distinct APPARENT DEADLOCKS. the first one is being caused by c3p0 attempting to close() Connections, and those close() operations are neither succeeding nor failing with an Exception in a timely manner. the second APPARENT DEADLOCK shows problems with Connection acquisition: c3p0 is attempting to acquire new Connections, and those attempts are neither succeeding nor failing with an Exception in a timely manner. the fact that very different operations are freezing suggests that it might be a more general problem with your dbms locking up under the stress of what you are doing or somesuch. it should be no problem to run multiple processes against your database, but you need to stay cognizant of limits.
there are a few interesting things about your configuration:
1) hibernate.c3p0.max_statements=5 is a very bad idea, on almost any pool and particularly on pools this large. you've got up to 100 Connections, and you're only allowing a total of 5 Statements to be cached between all of them. this might stress both the pool and the DBMS, as you will constantly be churning through PreparedStatements and the statement cache does a lot of bookkeeping about that. you may have meant that to be 5 cached statements per connection, but that's not what you have configured. you have set a global maximum for your pool. maybe try hibernate.c3p0.maxStatementsPerConnection=5 instead? or set max_statements to zero to turn statement caching off, at least until you resolve your deadlock. see http://www.mchange.com/projects/c3p0/#configuring_statement_pooling
2) if you are running your computation in multiple processes rather than multiple Threads, do you really need each process to hold 50 - 100 Connections? things may well be freezing up simply because you are stressing the dbms with too many Connections outstanding as each of your multiple processes acquire lots of resource-heavy Connections. you don't need more Connections in any process than you might have client Threads running concurrently within that process. i'd set hibernate.c3p0.acquire_increment and probably hibernate.c3p0.max_size to much smaller values.
3) if you really do need all those Connections running simultaneously, you can reduce the vulnerability of your pools to deadlock by increasing the config parameter numHelperThreads to some value greater than its default of 3. you probably want numHelperThreads to be something like twice the number of cores available on your machine. given that you are running multiple processes though, you might find that you are saturating your CPU, and that is freezing things up. so watch for that.
basically, try updating your configuration so that you are using resources -- file handles, network connections, CPU -- as efficiently as possible and so that you are not unnecessarily stressing the pool / statement cache / dbms more than you need to be.
if these suggestions don't resolve the problem, please post the fill config of your pools. c3p0 dumps its config at INFO level on pool initialization.
good luck!

Many threads created using C3P0 with Hibernate/Spring

I do a project merging Hibernate and Spring in a Java web application, using Tomcat under Linux environment. Due to the Mysql 8 hours timeout problem, we want to use C3P0 to manage a connection pool with our Mysql database.
But when we use it, we have numerous threads that are created. I figured it out beacause I did on each request a print of all of them with a memory status that show me the increasing memory and that kind of threads:
name: C3P0PooledConnectionPoolManager[identityToken->1hged7o8r13kpj7n1h3ycia|39c446]-HelperThread-#0 daemon: true group! main groupParent: system alive: true interrupted: false
name: C3P0PooledConnectionPoolManager[identityToken->1hged7o8r13kpj7n1h3ycia|17ec0e8]-AdminTaskTimer daemon: true group! main groupParent: system alive: true interrupted: false
It can produce more than 500 threads like these ones, after enough time.
Here is my Hibernate.cfg.xml:
<property name="connection.provider_class">
org.hibernate.connection.C3P0ConnectionProvider</property>
<property name="hibernate.c3p0.acquire_increment">1</property>
<property name="hibernate.c3p0.idle_test_period">5</property>
<property name="hibernate.c3p0.max_size">100</property>
<property name="hibernate.c3p0.max_statements">100</property>
<property name="hibernate.c3p0.min_size">10</property>
<property name="hibernate.c3p0.timeout">5</property>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/myBase</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password"></property>
<property name="hibernate.hbm2ddl.auto">update</property>
<property name="hibernate.default_schema">myProject</property>
<property name="hibernate.query.factory_class">org.hibernate.hql.classic.ClassicQueryTranslatorFactory</property>
<property name="show_sql">false</property>
<property name="cache.provider_class">
org.hibernate.cache.NoCacheProvider
</property>
I also tried to add a C3P0 propeties file, but except reducing the helper thread number, it don't delete the unsused thread:
c3p0.maxStatements=5
c3p0.maxIdleTime=10
c3p0.numHelperThreads=1
c3p0.testConnectionOnCheckout=true
c3p0.preferredTestQuery=SELECT 1
c3p0.initialPoolSize=1
c3p0.minPoolSize=1
c3p0.maxPoolSize=10
c3p0.acquireIncrement=1
c3p0.idleConnectionTestPeriod=1
Does anyone have an idea of why this happen and how to solve this problem?
Thanks a lot.

if you are seeing a multiplication of c3p0 helper and timer threads, you are somehow creating a multitude of c3p0 DataSources when you want there to be just one. sometimes this happens if you are hot-reloading your app but forgetting to close() your old c3p0 DataSource when you recycle.
effectively it looks like you are "leaking" DataSources. you need to figure out why/where this is happening. for some clues, check out your logs for c3p0 DataSource initialization messages at INFO level. Search for the string "Initializing c3p0 pool", for example.
good luck!

Ok I found a combination of properties to solve my problem, keeping in mind that I don't need a lot of connection at a time:
c3p0.maxStatements=5
c3p0.maxIdleTime=10
c3p0.numHelperThreads=3
c3p0.testConnectionOnCheckout=true
c3p0.preferredTestQuery=SELECT 1
c3p0.initialPoolSize=1
c3p0.minPoolSize=1
c3p0.maxPoolSize=1
c3p0.acquireIncrement=1
c3p0.idleConnectionTestPeriod=1
c3p0.maxAdministrativeTaskTime=1
Thanks to everyone

I would expect it to create a number of threads proportional to c3p0.minPoolSize
and c3p0.maxPoolSize and your maximum is 10.
http://www.mchange.com/projects/c3p0/#other_ds_configuration
"numHelperThreads and maxAdministrativeTaskTime help to configure the behavior of DataSource thread pools. By default, each DataSource has only three associated helper threads. If performance seems to drag under heavy load, or if you observe via JMX or direct inspection of a PooledDataSource, that the number of "pending tasks" is usually greater than zero, try increasing numHelperThreads. maxAdministrativeTaskTime may be useful for users experiencing tasks that hang indefinitely and "APPARENT DEADLOCK" messages. (See Appendix A for more.) "
numHelperThreads defines how many threads per DataSource are used, therefore indeed you will have 10 threads with numHelperThreads=1.
The only way to make sure C3P0 consumes only one Thread is to set c3p0.minPoolSize
and c3p0.maxPoolSize to 1 but this defeats the purpose of connection pooling.