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Hibernate associations using too much memory

I have a table "class" which is linked to tables "student" and "teachers".
A "class" is linked to multiple students and teachers via foriegn key relationship.
When I use hibernate associations and fetch large number of entities(tried for 5000) i am seeing that it is taking 4 times more memory than if i just use foreign key place holders.
Is there something wrong in hibernate association?
Can i use any memory profiler to figure out what's using too much memory?
This is how the schema is:
class(id,className)
student(id,studentName,class_id)
teacher(id,teacherName,class_id)
class_id is foreign key..
Case #1 - Hibernate Associations
1)in Class Entity , mapped students and teachers as :
#Entity
#Table(name="class")
public class Class {
private Integer id;
private String className;
private Set<Student> students = new HashSet<Student>();
private Set<Teacher> teachers = new HashSet<Teacher>();
#OneToMany(fetch = FetchType.EAGER, mappedBy = "classRef")
#Cascade({ CascadeType.ALL })
#Fetch(FetchMode.SELECT)
#BatchSize(size=500)
public Set<Student> getStudents() {
return students;
}
2)in students and teachers , mapped class as:
#Entity
#Table(name="student")
public class Student {
private Integer id;
private String studentName;
private Class classRef;
#ManyToOne
#JoinColumn(name = "class_id")
public Class getClassRef() {
return classRef;
}
Query used :
sessionFactory.openSession().createQuery("from Class where id<5000");
This however was taking a Huge amount of memory.
Case #2- Remove associations and fetch seperately
1)No Mapping in class entity
#Entity
#Table(name="class")
public class Class {
private Integer id;
private String className;
2)Only a placeholder for Foreign key in student, teachers
#Entity
#Table(name="student")
public class Student {
private Integer id;
private String studentName;
private Integer class_id;
Queries used :
sessionFactory.openSession().createQuery("from Class where id<5000");
sessionFactory.openSession().createQuery("from Student where class_id = :classId");
sessionFactory.openSession().createQuery("from Teacher where class_id = :classId");
Note - Shown only imp. part of the code. I am measuring memory usage of the fetched entities via JAMM library.
I also tried marking the query as readOnly in case #1 as below, which does not improve memory usage very much ; just a very little. So that's not the solve.
Query query = sessionFactory.openSession().
createQuery("from Class where id<5000");
query.setReadOnly(true);
List<Class> classList = query.list();
sessionFactory.getCurrentSession().close();
Below are the heapdump snapshots sorted by sizes. Looks like the Entity maintained by hibernate is creating the problem..
Snapshot of Heapdump for hibernate associations program
Snapshot of heapdump for fetching using separate entities

You are doing a EAGER fetch with the below annotation. This will in turn fetch all the students without even you accessing the getStudents(). Make it lazy and it will fetch only when needed.
From
#OneToMany(fetch = FetchType.EAGER, mappedBy = "classRef")
To
#OneToMany(fetch = FetchType.LAZY, mappedBy = "classRef")

When Hibernate loads a Class entity containing OneToMany relationships, it replaces the collections with its own custom version of them. In the case of a Set, it uses a PersistentSet. As can be seen on grepcode, this PersistentSet object contains quite a bit of stuff, much of it inherited from AbstractPersistentCollection, to help Hibernate manage and track things, particularly dirty checking.
Among other things, the PersistentSet contains a reference to the session, a boolean to track whether it's initialized, a list of queued operations, a reference to the Class object that owns it, a string describing its role (not sure what exactly that's for, just going by the variable name here), the string uuid of the session factory, and more. The biggest memory hog among the lot is probably the snapshot of the unmodified state of the set, which I would expect to approximately double memory consumption by itself.
There's nothing wrong here, Hibernate is just doing more than you realized, and in more complex ways. It shouldn't be a problem unless you are severely short on memory.
Note, incidentally, that when you save a new Class object that Hibernate previously was unaware of, Hibernate will replace the simple HashSet objects you created with new PersistentSet objects, storing the original HashSet wrapped inside the PersistentSet in its set field. All Set operations will be forwarded to the wrapped HashSet, while also triggering PersistentSet dirty tracking and queuing logic, etc. With that in mind, you should not keep and use any external references to the Set from before saving, and should instead fetch a new reference to Hibernate's PersistentSet instance and use that if you need to make any changes (to the set, not to the students or teachers within it) after the initial save.

Regarding the huge memory consumption you are noticing, one potential reason is Hibernate Session has to maintain the state of each entity it has loaded the form of EntityEntry object i.e., one extra object, EntityEntry, for each loaded entity. This is needed for hibernate automatic dirty checking mechanism during the flush stage to compare the current state of entity with its original state (one that is stored as EntityEntry).
Note that this EntityEntry is different from the object that we get to access in our application code when we call session.load/get/createQuery/createCriteria. This is internal to hibernate and stored in the first level cache.
Quoting form the javadocs for EntityEntry :
We need an entry to tell us all about the current state of an object
with respect to its persistent state Implementation Warning: Hibernate
needs to instantiate a high amount of instances of this class,
therefore we need to take care of its impact on memory consumption.
One option, assuming the intent is only to read and iterate through the data and not perform any changes to those entities, you can consider using StatelessSession instead of Session.
The advantage as quoted from Javadocs for Stateless Session:
A stateless session does not implement a first-level cache nor
interact with any second-level cache, nor does it implement
transactional write-behind or automatic dirty checking
With no automatic dirty checking there is no need for Hibernate to create EntityEntry for each entity of loaded entity as it did in the earlier case with Session. This should reduce pressure on memory utilization.
Said that, it does have its own set of limitations as mentioned in the StatelessSession javadoc documentation.
One limitation that is worth highlighting is, it doesn't lazy loading the collections. If we are using StatelessSession and want to load the associated collections we should either join fetch them using HQL or EAGER fetch using Criteria.
Another one is related to second level cache where it doesn't interact with any second-level cache, if any.
So given that it doesn't have any overhead of first-level cache, you may want to try with Stateless Session and see if that fits your requirement and helps in reducing the memory consumption as well.

Yes, you can use a memory profiler, like visualvm or yourkit, to see what takes so much memory. One way is to get a heap dump and then load it in one of these tools.
However, you also need to make sure that you compare apples to apples. Your queries in case#2 sessionFactory.openSession().createQuery("from Student where class_id = :classId");
sessionFactory.openSession().createQuery("from Teacher where class_id = :classId");
select students and teachers only for one class, while in case #1 you select way more. You need to use <= :classId instead.
In addition, it is a little strange that you need one student and one teacher record per one class. A teacher can teach more than one class and a student can be in more than one class. I do not know what exact problem you're solving but if indeed a student can participate in many classes and a teacher can teach more than one class, you will probably need to design your tables differently.

Try #Fetch(FetchMode.JOIN), This generates only one query instead of multiple select queries. Also review the generated queries. I prefer using Criteria over HQL(just a thought).
For profiling, use freewares like visualvm or jconsole. yourkit is good for advanced profiling, but it is not for free. I guess there is a trail version of it.
You can take the heapdump of your application and analyze it with any memory analyzer tools to check for any memory leaks.
BTW, I am not exactly sure about the memory usage for current scenario.

Its likely the reason is the bi-directional link from Student to Class and Class to Students. When you fetch Class A (id 4500), The Class object must be hydrated, in turn this must go and pull all the Student objects (and teachers presumably) associated with this class. When this happens each Student Object must be hydrated. Which causes the fetch of every class the Student is a part of. So although you only wanted class A, you end up with:
Fetch Class A (id 4900)
Returns Class A with reference to 3 students, Student A, B, C.
Student A has ref to Class A, B (id 5500)
Class B needs hydrating
Class B has reference to Students C,D
Student C needs hydrating
Student C only has reference to Class A and B
Student C hydration complete.
Student D needs hydrating
Student D only has reference to Class B
Student B hydration complete
Class B hydration complete
Student B needs hydrating (from original class load class A)
etc... With eager fetching, this continues until all links are hydrated. The point being that its possible you end up with Classes in memory that you didn't actually want. Or whose id is not less than 5000.
This could get worse fast.
Also, you should make sure you are overriding the hashcode and equals methods. Otherwise you may be getting redundant objects, both in memory and in your set.
One way to improve is either change to LAZY loading as other have mentioned or break the bidirectional links. If you know you will only ever access students per class, then don't have the link from student back to class. For student/class example it makes sense to have the bidirectional link, but maybe it can be avoided.

as you say you "I want "all" the collections". so lazy-loading won't help.
Do you need every field of every entity? In which case use a projection to get just the bits you want. See when to use Hibernate Projections.
Alternatively consider having minimalist Teacher-Lite and Student-Lite entity that the full-fat versions extend.

Json and Java - Circular Reference

I'm having and issue with the Circular reference.
I have Rest Webservices which returns objects to the front end, the issue is when I try to return objects that have several references so as the result I get an infinite response, which generate
java.lang.IllegalStateException:
Cannot call sendError() after the response has been committed
The objects are generated automatically by Hibernate Code Generation and I need to have the circular reference in the backend, I've just need to remove it before send the information to the frontend using Jackson.
The controller method header is:
#RequestMapping(value="/list", method=RequestMethod.POST)
public #ResponseBody eventResponse list(#RequestBody String sessionID) {
I'm not doing anything explicite to convert to Json, I'm a newby with this and I think that jackson resolved this automatically.

There are two ways you can go about this. If you must expose your entity to the outside world, I recommend adding #JsonIgnore on the property that is causing the circular reference. This will tell Jackson not to serialize that property.
Another way is to use the bidirectional features provided by Jackson. You can either use #JsonManagedReference or #JsonBackReference. #JsonManagedReference is the "forward" part of the property and it will get serialized normally. #JsonBackReference is the "back" part of the reference; it will not be serialized, but will be reconstructed when the "forward" type is deserialized.
You can check out the examples here.
This addresses your comment: I think what you might want to do in this case is use a DTO that is visible to the outside world. I like this approach because I don't want to expose my entities to the outside. This means that the Jackson annotations would be on the DTO and not on the enity. You would need some sort of mapper or converter that converts the entity to the DTO. Now when you make changes to your entity, they won't get propagated to the DTO unless you modify your mapper/converter. I think this is ok, because when you make a change to your entity you can decide if you want that change to be exposed or not.
UPDATE
There is a good blog post here that goes into detail about the various ways you can handle bidirectional relationships in Jackson. It describes solutions that use #JsonIgnore, #JsonManagedReference and #JsonBackReference, #JsonIdentityInfo, #JsonView and a custom serializer as well. It's a pretty comprehensive writeup of the various techniques that you can use.

A single annotation #JsonIdentityInfo solves the problem. It handles circular references also.Reference

A #JsonbTransient solved my problem to handel circular references:
#JsonbTransient // javax.json.bind.annotation.JsonbTransient
#ManyToOne
#JoinColumn(name = "userId", referencedColumnName = "id", nullable = false)
public AContainedEntity getAContainedEntity() {
return aContainedEntity;
}

Grails. Hibernate lazy loading multiple objects

I'm having difficulties with proxied objects in Grails.
Assuming I've got the following
class Order {
#ManyToMany(fetch = FetchType.EAGER)
#JoinTable(name="xxx", joinColumns = {#JoinColumn(name = "xxx")}, inverseJoinColumns = {#JoinColumn(name = "yyy")})
#OrderBy("id")
#Fetch(FetchMode.SUBSELECT)
private List<OrderItem> items;
}
class Customer {
#ManyToOne(cascade = CascadeType.ALL, fetch = FetchType.LAZY, optional = true)
#JoinColumn(name = "xxx",insertable = false, nullable = false)
private OrderItem lastItem;
private Long lastOrderId;
}
And inside some controller class
//this all happens during one hibernate session.
def currentCustomer = Customer.findById(id)
//at this point currentCustomer.lastItem is a javassist proxy
def lastOrder = Order.findById(current.lastOrderId)
//lastOrder.items is a proxy
//Some sample actions to initialise collections
lastOrder.items.each { println "${it.id}"}
After the iteration lastOrder.items still contains a proxy of currentCustomer.lastItem. For example if there are 4 items in the lastOrder.items collection, it looks like this:
object
object
javassist proxy (all fields are null including id field). This is the same object as in currentCustomer.lastItem.
object
Furthermore, this proxy object has all properties set to null and it's not initialized when getters are invoked. I have to manually call GrailsHibernateUtils.unwrapIdProxy() on every single element inside lastOrder.items to ensure that there are no proxies inside (which basically leads to EAGER fetching).
This one proxy object leads to some really weird Exceptions, which are difficult to track on testing phase.
Interesting fact: if I change the ordering of the operations (load the order first and the customer second) every element inside lastOrder.items is initialized.
The question is: Is there a way to tell Hibernate that it should initialize the collections when they are touched, no matter if any elements from the collection is already proxied in the session?

I think what's happening here is an interesting interaction between the first level cache (stored in Hibernate's Session instance) and having different FetchType on related objects.
When you load Customer, it gets put in to the Session cache, along with any objects that are loaded with it. This includes a proxy object for the OrderItem object, because you've got FetchType.LAZY. Hibernate only allows one instance to be associated with any particular ID, so any further operations that would be acting on the OrderItem with that ID would always be using that proxy. If you asked the same Session to get that particular OrderItem in another way, as you are by loading an Order containing it, that Order would have the proxy, because of Session-level identity rules.
That's why it 'works' when you reverse the order. Load the Order first, it's collection is FetchType.EAGER, and so it (and the first level cache) have fully realized instances of OrderItem. Now load a Customer which has it's lastItem set to one of the already-loaded OrderItem instances and presto, you have a real OrderItem, not a proxy.
You can see the identity rules documented in the Hibernate manual:
For objects attached to a particular Session... JVM identity for database identity is guaranteed by Hibernate.
All that said, even if you get an OrderItem proxy, it should work fine as long as the associated Session is still active. I wouldn't necessarily expect the proxy ID field to show up as populated in the debugger or similar, simply because the proxy handles things in a 'special' way (ie, it's not a POJO). But it should respond to method calls the same way it's base class would. So if you have an OrderItem.getId() method, it should certainly return the ID when called, and similarly on any other method. Because it's lazily initialized though, some of those calls may require a database query.
It's possible that the only real problem here is simply that it's confusing to have it so that any particular OrderItem could be a proxy or not. Maybe you want to simply change the relationships so that they're either both lazy, or both eager?
For what it's worth, it's a bit odd that you've got the ManyToMany relationship as EAGER and the ManyToOne as LAZY. That's exactly the reverse of the usual settings, so I would at least think about changing it (although I obviously don't know your entire use case). One way to think about it: If an OrderItem is so expensive to fetch completely that it's a problem when querying for Customer, surely it's also too expensive to load all of them at once? Or conversely, if it's cheap enough to load all of them, surely it's cheap enough to just grab it when you get a Customer?

I think you can force eager loading this way or using
def lastOrder = Order.withCriteria(uniqueResult: true) {
eq('id', current.lastOrderId)
items{}
}
or using HQL query with 'fetch all'

Changing from Collection to SortedSet

I'm changing a Collection to a SortedSet because I need it to always be in the same consistent order that they were created in. I've changed my model property from
#OneToMany(cascade = CascadeType.ALL, mappedBy = "contentId")
private Collection<Footnote> footnoteCollection;
to
#OneToMany(cascade = CascadeType.ALL, mappedBy = "contentId")
private SortedSet<Footnote> footnoteSortedSet;
and all relevant functions so Netbeans no longer shows any errors. When I run the app I get the error: Exception Description: Could not load the field named [footnoteSortedSet] on the class [class com.mysite.cmt.model.Content_]. Ensure there is a corresponding field with that name defined on the class.
Since I've just changed this properly and relaunched my app I'm struggling to figure out why it's saying it's not set...

The error you are getting seems to be coming from the JPA metamodel. I assume you are generating this in some way, if you don't use the metamodel in Criteria, then you don't need this and the error will go away.
The issue is that JPA only allows the collection interfaces, Map, List, Set, Collection. So, while you could use a SortedSet in your new instances, object read from the database will use a special lazy List implementation.
In EclipseLink, you can use a SortedSet if you mark the mapping as EAGER.
I think the metamodel error was fixed, try the latest release.

SortedSet javadoc to the rescue:
All elements inserted into a sorted set must implement the Comparable interface (or be accepted by the specified comparator).
Almost certainly, Footnote does not implement Comparable

JPA 2/Hibernate - Best way to update complex entities?

I'm new to JPA/Hibernate and I'm wondering, what is usually the best way of updating a complex entity?
For example, consider the entity below:
#Entity
public class Employee {
#Id
private long id;
#Column
private String name;
#ManyToMany
private List<Positions> positions;
// Getters and setters...
}
What is the best way to update the references to positions? Currently a service is passing me a list of positions that the employee should have. Creating them is easy:
for (long positionId : positionIdList) {
Position position = entityManager.find(positionId);
employee.getPositions.add(position);
}
entityManager.persist(employee);
However, when it comes to updating the employee, I'm not sure what the best way of updating the employees positions would be. I figure there is two options:
I parse through the list of position id's and determine if the position needs to be added/deleted (this doesn't seem like a fun process, and may end up with many delete queries)
I delete all positions and then re-add the specified positions. Is there a way in JPA/Hibernate to delete all children (in this case positions) with one sql command?
Am I thinking about this the wrong way? What do you guys recommend?

How about
employee.getPositions.clear(); // delete all existing one
// add all of them again
for (long positionId : positionIdList) {
Position position = entityManager.find(positionId);
employee.getPositions.add(position);
}
although it may not be the most efficient approach. For a detail discussion see here.
Cascading won't help here much because in ManyToMany relation the positions may not get orphaned as they may be attached to other employee (s), or even they shouldn't be deleted at all, because they can exists on their own.

JPA/Hibernate has support for this. It's called cascading. By using #ManyToMany(cascade=CascadeType.ALL) (or limit the cascade type to PERSIST and MERGE), you specify that the collection should be persisted (merged/deleted/etc) when the owning object is.
When deletion is concerned, there is a special case, when objects become "orphans" in the database. This is handled by setting orphanRemoval=true