DDevelopment & Design

mount.ntfs high cpu ubuntu

My computer suffers from sudden and continous hard drive load strokes. Sometimes it lasts for a few minutes and hence work is impossible because everything goes very slow.I’m trying to locate the cause because it makes me nervous :)Today I found one of…

My computer suffers from sudden and continous hard drive load strokes. Sometimes it lasts for a few minutes and hence work is impossible because everything goes very slow.
I’m trying to locate the cause because it makes me nervous :)

Today I found one of the causes. It’s updatedb.mlocate script which is responsible for scanning hard drives and build locate (a location of files) database. But due to some NTFS driver limitations that poor thing thinks that NTFS share is always new and needs to be rescan at every scheduled scan.

How to make sure that you have the same problem? When hard drive starts to choke check all IO processes with

sudo iotop

and look for updatedb.mlocate or mount.ntfs processes with high IO load. If this is the case try to fix it.
The solution is to point NTFS shares as non-scannable. To do this edit

/etc/updatedb.conf

and add your NTFS mount paths to PRUNEPATHS list. Although NTFS is listed in PRUNEFS entry that dummy mlocate script still would scan NTFS shares.

All that I found on Ubuntu forum.

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DDevelopment & Design

JBoss Envers and Spring transaction managers

I've stumbled upon a bug with my configuration for JBoss Envers today, despite having integration tests all over the application. I have to admit, it casted a dark shadow of doubt about the value of all the tests for a moment. I've been practicing TDD since 2005, and frankly speaking, I should have been smarter than that.

My fault was simple. I've started using Envers the right way, with exploratory tests and a prototype. Then I've deleted the prototype and created some integration tests using in-memory H2 that looked more or less like this example:

@Test
public void savingAndUpdatingPersonShouldCreateTwoHistoricalVersions() {
    //given
    Person person = createAndSavePerson();
    String oldFirstName = person.getFirstName();
    String newFirstName = oldFirstName + "NEW";

    //when
    updatePersonWithNewName(person, newFirstName);

    //then
    verifyTwoHistoricalVersionsWereSaved(oldFirstName, newFirstName);
}

private Person createAndSavePerson() {
    Transaction transaction = session.beginTransaction();
    Person person = PersonFactory.createPerson();
    session.save(person);
    transaction.commit();
    return person;
}    

private void updatePersonWithNewName(Person person, String newName) {
    Transaction transaction = session.beginTransaction();
    person.setFirstName(newName);
    session.update(person);
    transaction.commit();
}

private void verifyTwoHistoricalVersionsWereSaved(String oldFirstName, String newFirstName) {
    List<Object[]> personRevisions = getPersonRevisions();
    assertEquals(2, personRevisions.size());
    assertEquals(oldFirstName, ((Person)personRevisions.get(0)[0]).getFirstName());
    assertEquals(newFirstName, ((Person)personRevisions.get(1)[0]).getFirstName());
}

private List<Object[]> getPersonRevisions() {
    Transaction transaction = session.beginTransaction();
    AuditReader auditReader = AuditReaderFactory.get(session);
    List<Object[]> personRevisions = auditReader.createQuery()
            .forRevisionsOfEntity(Person.class, false, true)
            .getResultList();
    transaction.commit();
    return personRevisions;
}

Because Envers inserts audit data when the transaction is commited (in a new temporary session), I thought I have to create and commit the transaction manually. And that is true to some point.

My fault was that I didn't have an end-to-end integration/acceptance test, that would call to entry point of the application (in this case a service which is called by GWT via RPC), because then I'd notice, that the Spring @Transactional annotation, and calling transaction.commit() are two, very different things.

Spring @Transactional annotation will use a transaction manager configured for the application. Envers on the other hand is used by subscribing a listener to hibernate's SessionFactory like this:

<bean id="sessionFactory" class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean" >        
...
 <property name="eventListeners">
     <map key-type="java.lang.String" value-type="org.hibernate.event.EventListeners">
         <entry key="post-insert" value-ref="auditEventListener"/>
         <entry key="post-update" value-ref="auditEventListener"/>
         <entry key="post-delete" value-ref="auditEventListener"/>
         <entry key="pre-collection-update" value-ref="auditEventListener"/>
         <entry key="pre-collection-remove" value-ref="auditEventListener"/>
         <entry key="post-collection-recreate" value-ref="auditEventListener"/>
     </map>
 </property>
</bean>

<bean id="auditEventListener" class="org.hibernate.envers.event.AuditEventListener" />

Envers creates and collects something called AuditWorkUnits whenever you update/delete/insert audited entities, but audit tables are not populated until something calls AuditProcess.beforeCompletion, which makes sense. If you are using org.hibernate.transaction.JDBCTransaction manually, this is called on commit() when notifying all subscribed javax.transaction.Synchronization objects (and enver's AuditProcess is one of them).

The problem was, that I used a wrong transaction manager.

<bean id="transactionManager" class="org.springframework.jdbc.datasource.DataSourceTransactionManager" >
    <property name="dataSource" ref="dataSource"/>
</bean>

This transaction manager doesn't know anything about hibernate and doesn't use org.hibernate.transaction.JDBCTransaction. While Synchronization is an interface from javax.transaction package, DataSourceTransactionManager doesn't use it (maybe because of simplicity, I didn't dig deep enough in org.springframework.jdbc.datasource), and thus Envers works fine except not pushing the data to the database.

Which is the whole point of using Envers.

Use right tools for the task, they say. The whole problem is solved by using a transaction manager that is well aware of hibernate underneath.

<bean id="transactionManager" class="org.springframework.orm.hibernate3.HibernateTransactionManager" >
    <property name="sessionFactory" ref="sessionFactory"/>
</bean>

Lesson learned: always make sure your acceptance tests are testing the right thing. If there is a doubt about the value of your tests, you just don't have enough of them,
DDevelopment & Design

Zookeeper + Curator = Distributed sync

An application developed for one of my recent projects at TouK involved multiple servers. There was a requirement to ensure failover for the system’s components. Since I had already a few separate components I didn’t want to add more of that, and since there already was a Zookeeper ensemble running - required by one of the services, I’ve decided to go that way with my solution.

What is Zookeeper?

Just a crude distributed synchronization framework. However, it implements Paxos-style algorithms (http://en.wikipedia.org/wiki/Paxos_(computer_science)) to ensure no split-brain scenarios would occur. This is quite an important feature, since I don’t have to care about that kind of problems while using this app. You just need to create an ensemble of a couple of its instances - to ensure high availability. It is basically a virtual filesystem, with files, directories and stuff. One could ask why another filesystem? Well this one is a rather special one, especially for distributed systems. The reason why creating all the locking algorithms on top of Zookeeper is easy is its Ephemeral Nodes - which are just files that exist as long as connection for them exists. After it disconnects - such file disappears.

With such paradigms in place it’s fairly easy to create some high level algorithms for synchronization.

Having that in place, it can safely integrate multiple services ensuring loose coupling in a distributed way.

Zookeeper from developer’s POV

With all the base services for Zookeeper started, it seems there is nothing else, than just connect to it and start implementing necessary algorithms. Unfortunately, the API is quite basic and offers files and directories abstractions with the addition of different node type (file types) - ephemeral and sequence. It is also possible to watch a node for changes.

Using bare Zookeeper is hard!

Creating connections is tedious - and there is lots of things to take care of. Handling an established connection is hard - when establishing connection to ensemble, it’s necessary to negotiate a session also. During the whole process a number of exceptions can occur - these are “recoverable” exceptions, that can be gracefully handled and not break the connection.

    class="c8"><span>So, Zookeeper API is hard.</span></p><p class="c1"><span></span></p><p class="c8"><span>Even if one is proficient with that API, then there come recipes. The reason for using Zookeeper is to be able to implement some more sophisticated algorithms on top of it. Unfortunately those aren&rsquo;t trivial and it is again quite hard to implement them without bugs.</span>

And since distributed systems are hard, why would anyone want another difficult to handle tool?

Enter Curator

<p 
    class="c8"><span>Happily, guys from Netflix implemented a nice abstraction for dealing with Zookeeper internals. They called it Curator and use it extensively in the company&rsquo;s environment. Curator offers consistent API for Zookeeper&rsquo;s functionality. It even implements a couple of recipes for distributed systems.</span>

File read/write

<p 
    class="c8"><span>The basic use of Zookeeper is as a distributed configuration repository. For this scenario I only need read/write capabilities, to be able to write and read files from the Zookeeper filesystem. This code snippet writes a sample json to a file on ZK filesystem.</span>

<a href="#" 
                                                                                                  name="0"></a>


EnsurePath ensurePath = new EnsurePath(markerPath);
ensurePath.ensure(client.getZookeeperClient());
String json = “...”;
if (client.checkExists().forPath(statusFile(core)) != null)
     client.setData().forPath(statusFile(core), json.getBytes());
else
     client.create().forPath(statusFile(core), json.getBytes());

Distributed locking

Having multiple systems there may be a need of using an exclusive lock for some resource, or perhaps some big system requires it’s components to synchronize based on locks. This “recipe” is an ideal match for those situations.

ref="#"
                                                                                    name="b0329bbbf14b79ffaba1139881914aea887ef6a3"></a>




lock = new InterProcessSemaphoreMutex(client, lockPath);
lock.acquire(5, TimeUnit.MINUTES);
… do sth …
lock.release();

 (from https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/LockingRemotely.java)

Sevice Advertisement

<p

    class="c8"><span>This is quite an interesting use case. With many small services on different servers it is not wise to exchange ip addresses and ports between them. When some of those services may go down, while other will try to replace them - the task gets even harder. </span>

That’s why, with Zookeeper in place, it can be utilised as a registry of existing services.

If a service starts, it registers into the ServiceRegistry, offering basic information, like it’s purpose, role, address, and port.

Services that want to use a specific kind of service request an access to some instance. This way of configuring easily decouples services from their configuration.

Basically this scenario needs ? steps:

<span>1. Service starts and registers its presence (</span><span class="c5"><a class="c0"
                                                                               href="https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerAdvertiser.java#L44">https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerAdvertiser.java#L44</a></span><span>)</span><span>:</span>




ServiceDiscovery discovery = getDiscovery();
            discovery.start();
            ServiceInstance si = getInstance();
            log.info(si);
            discovery.registerService(si);

2. Another service - on another host or in another JVM on the same machine tries to discover who is implementing the service (https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerFinder.java#L50):

<a href="#"

                                                                                                  name="3"></a>


instances = discovery.queryForInstances(serviceName);

The whole concept here is ridiculously simple - the service advertising its presence just stores a file with its whereabouts. The service that is looking for service providers just look into specific directory and read stored definitions.

In my example, the structure advertised by services looks like this (+ some getters and constructor - the rest is here: https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/model/WorkerMetadata.java): 



public final class WorkerMetadata {
    private final UUID workerId;
    private final String listenAddress;
    private final int listenPort;
}

Source code

<p

    class="c8"><span>The above recipes are available in Curator library (</span><span class="c5"><a class="c0"
                                                                                                    href="http://curator.incubator.apache.org/">http://curator.incubator.apache.org/</a></span><span>). Recipes&rsquo;
usage examples are in my github repo at </span><span class="c5"><a class="c0"
                                                                   href="https://github.com/zygm0nt/curator-playground">https://github.com/zygm0nt/curator-playground</a></span>

Conclusion

<p 
    class="c8"><span>If you&rsquo;re in need of a reliable platform for exchanging data and managing synchronization, and you need to do it in a distributed fashion - just choose Zookeeper. Then add Curator for the ease of using it. Enjoy!</span>

  1. image comes from: http://www.flickr.com/photos/jfgallery/2993361148
  2. all source code fragments taken from this repo: https://github.com/zygm0nt/curator-playground

An application developed for one of my recent projects at TouK involved multiple servers. There was a requirement to ensure failover for the system’s components. Since I had already a few separate components I didn’t want to add more of that, and since there already was a Zookeeper ensemble running - required by one of the services, I’ve decided to go that way with my solution.

What is Zookeeper?

Just a crude distributed synchronization framework. However, it implements Paxos-style algorithms (http://en.wikipedia.org/wiki/Paxos_(computer_science)) to ensure no split-brain scenarios would occur. This is quite an important feature, since I don’t have to care about that kind of problems while using this app. You just need to create an ensemble of a couple of its instances - to ensure high availability. It is basically a virtual filesystem, with files, directories and stuff. One could ask why another filesystem? Well this one is a rather special one, especially for distributed systems. The reason why creating all the locking algorithms on top of Zookeeper is easy is its Ephemeral Nodes - which are just files that exist as long as connection for them exists. After it disconnects - such file disappears.

With such paradigms in place it’s fairly easy to create some high level algorithms for synchronization.

Having that in place, it can safely integrate multiple services ensuring loose coupling in a distributed way.

Zookeeper from developer’s POV

With all the base services for Zookeeper started, it seems there is nothing else, than just connect to it and start implementing necessary algorithms. Unfortunately, the API is quite basic and offers files and directories abstractions with the addition of different node type (file types) - ephemeral and sequence. It is also possible to watch a node for changes.

Using bare Zookeeper is hard!

Creating connections is tedious - and there is lots of things to take care of. Handling an established connection is hard - when establishing connection to ensemble, it’s necessary to negotiate a session also. During the whole process a number of exceptions can occur - these are “recoverable” exceptions, that can be gracefully handled and not break the connection.

    class="c8"><span>So, Zookeeper API is hard.</span></p><p class="c1"><span></span></p><p class="c8"><span>Even if one is proficient with that API, then there come recipes. The reason for using Zookeeper is to be able to implement some more sophisticated algorithms on top of it. Unfortunately those aren&rsquo;t trivial and it is again quite hard to implement them without bugs.</span>

And since distributed systems are hard, why would anyone want another difficult to handle tool?

Enter Curator

<p 
    class="c8"><span>Happily, guys from Netflix implemented a nice abstraction for dealing with Zookeeper internals. They called it Curator and use it extensively in the company&rsquo;s environment. Curator offers consistent API for Zookeeper&rsquo;s functionality. It even implements a couple of recipes for distributed systems.</span>

File read/write

<p 
    class="c8"><span>The basic use of Zookeeper is as a distributed configuration repository. For this scenario I only need read/write capabilities, to be able to write and read files from the Zookeeper filesystem. This code snippet writes a sample json to a file on ZK filesystem.</span>

<a href="#" 
                                                                                                  name="0"></a>


EnsurePath ensurePath = new EnsurePath(markerPath);
ensurePath.ensure(client.getZookeeperClient());
String json = “...”;
if (client.checkExists().forPath(statusFile(core)) != null)
     client.setData().forPath(statusFile(core), json.getBytes());
else
     client.create().forPath(statusFile(core), json.getBytes());

Distributed locking

Having multiple systems there may be a need of using an exclusive lock for some resource, or perhaps some big system requires it’s components to synchronize based on locks. This “recipe” is an ideal match for those situations.

ref="#"
                                                                                    name="b0329bbbf14b79ffaba1139881914aea887ef6a3"></a>




lock = new InterProcessSemaphoreMutex(client, lockPath);
lock.acquire(5, TimeUnit.MINUTES);
… do sth …
lock.release();

 (from https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/LockingRemotely.java)

Sevice Advertisement

<p

    class="c8"><span>This is quite an interesting use case. With many small services on different servers it is not wise to exchange ip addresses and ports between them. When some of those services may go down, while other will try to replace them - the task gets even harder. </span>

That’s why, with Zookeeper in place, it can be utilised as a registry of existing services.

If a service starts, it registers into the ServiceRegistry, offering basic information, like it’s purpose, role, address, and port.

Services that want to use a specific kind of service request an access to some instance. This way of configuring easily decouples services from their configuration.

Basically this scenario needs ? steps:

<span>1. Service starts and registers its presence (</span><span class="c5"><a class="c0"
                                                                               href="https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerAdvertiser.java#L44">https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerAdvertiser.java#L44</a></span><span>)</span><span>:</span>




ServiceDiscovery discovery = getDiscovery();
            discovery.start();
            ServiceInstance si = getInstance();
            log.info(si);
            discovery.registerService(si);

2. Another service - on another host or in another JVM on the same machine tries to discover who is implementing the service (https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/curator/WorkerFinder.java#L50):

<a href="#"

                                                                                                  name="3"></a>


instances = discovery.queryForInstances(serviceName);

The whole concept here is ridiculously simple - the service advertising its presence just stores a file with its whereabouts. The service that is looking for service providers just look into specific directory and read stored definitions.

In my example, the structure advertised by services looks like this (+ some getters and constructor - the rest is here: https://github.com/zygm0nt/curator-playground/blob/master/src/main/java/pl/touk/model/WorkerMetadata.java): 



public final class WorkerMetadata {
    private final UUID workerId;
    private final String listenAddress;
    private final int listenPort;
}

Source code

<p

    class="c8"><span>The above recipes are available in Curator library (</span><span class="c5"><a class="c0"
                                                                                                    href="http://curator.incubator.apache.org/">http://curator.incubator.apache.org/</a></span><span>). Recipes&rsquo;
usage examples are in my github repo at </span><span class="c5"><a class="c0"
                                                                   href="https://github.com/zygm0nt/curator-playground">https://github.com/zygm0nt/curator-playground</a></span>

Conclusion

<p 
    class="c8"><span>If you&rsquo;re in need of a reliable platform for exchanging data and managing synchronization, and you need to do it in a distributed fashion - just choose Zookeeper. Then add Curator for the ease of using it. Enjoy!</span>

  1. image comes from: http://www.flickr.com/photos/jfgallery/2993361148
  2. all source code fragments taken from this repo: https://github.com/zygm0nt/curator-playground