Java for High Performance Computing
Multithreaded and Shared-Memory
Programming in Java
http://www.hpjava.org/courses/arl
Instructor: Bryan Carpenter
Pervasive Technology Labs
Indiana University
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1
Java as a Threaded Language

In C, C++, etc it is possible to do multithreaded programming,
given a suitable library.
– e.g. the pthreads library.

Thread libraries provide one approach to doing parallel
programming on computers with shared memory.
– Another approach is OpenMP, which uses compiler directives. This
will be discussed later.

Unlike these (traditional HPC) languages, Java integrates
threads into the basic language specification in a much tighter
way.
– Every Java Virtual Machine must support threads.

Although this close integration doesn’t exactly make
multithreaded programming in Java easy, it does help avoid
common programming errors, and keeps the semantics clean.
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2
Features of Java Threads

Java provides a set of synchronization primitives based on
monitor and condition variable paradigm of C.A.R. Hoare.
– Underlying functionality is similar to POSIX threads, for example.

Syntactic extension for threads is (deceptively?) small:
–
–
–
–

synchronized attribute on methods.
synchronized statement.
volatile keyword.
Other thread management and synchronization captured in the Thread
class and related classes.
But the presence of threads has a more wide-ranging effect on
the language specification and JVM implementation.
– e.g., the Java memory model.
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3
Contents of this Lecture Set

Introduction to Java Threads.
– Mutual Exclusion.
– Synchronization between Java Threads using wait() and notify().
– Other features of Java Threads.

Shared Memory Parallel Computing with Java Threads
– We review select parallel applications and benchmarks of Java on
SMPs from the recent literature.

Special Topic: JOMP
– JOMP is a prototype implementation of the OpenMP standard for
Java.

Suggested Exercises
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4
Java Thread Basics
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5
Creating New Threads in a Java Program

Any Java thread of execution is associated with an instance of
the Thread class. Before starting a new thread, you must
create a new instance of this class.

The Java Thread class implements the interface Runnable.
So every Thread instance has a method:
public void run() { . . . }

When the thread is started, the code executed in the new
thread is the body of the run() method.
– Generally speaking the new thread ends when this method returns.
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6
Making Thread Instances

There are two ways to create a thread instance (and define the thread
run() method). Choose at your convenience:
1. Extend the Thread class and override the run() method, e.g.:
class MyThread extends Thread {
public void run() {
System.out.println(“Hello from another thread”) ;
}
}
...
Thread thread = new MyThread() ;
2. Create a separate Runnable object and pass it to the Thread constructor,
e.g.:
class MyRunnable implements Runnable {
public void run() {
System.out.println(“Hello from another thread”) ;
}
}
...
Thread thread = new MyThread(new MyRunnable()) ;
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7
Starting a Thread


Creating the Thread instance does not in itself start the
thread running.
To do that you must call the start() method on the new
instance:
thread.start() ;


This operation causes the run() method to start executing
concurrently with the original thread.
In our example the new thread will print the message “Hello
from another thread” to standard output, then immediately
terminate.
You can only call the start() method once on any Thread
instance. Trying to “restart” a thread causes an exception to
be thrown.
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Example: Multiple Threads
class MyThread extends Thread {
MyThread(int id) {
this.id = id ;
}
public void run() {
System.out.println(“Hello from thread ” + id) ;
}
private int id ;
}
...
Thread [] threads = new Thread [p] ;
for(int i = 0 ; i < p ; i++)
threads [i] = new MyThread(i) ;
for(int i = 0 ; i < p ; i++)
threads [i].start() ;
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Remarks

This is one way of creating and starting p new threads to run
concurrently.

The output might be something like (for p = 4):
Hello from thread 3
Hello from thread 4
Hello from thread 2
Hello from thread 1
Of course there is no guarantee of order (or atomicity) of
outputs, because the threads are concurrent.

One might worry about the efficiency of this approach for
large numbers of threads (massive parallelism).
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10
JVM Termination and Daemon Threads


When a Java application is started, the main() method of the application
is executed in a singled-out thread called the main thread.
In the simplest case—if the main method never creates any new
threads—the JVM keeps running until the main() method completes (and
the main thread terminates).
–



If the JVM was started with the java command, the command finishes.
If the main() method creates new threads, then by default the JVM
terminates when all user-created threads have terminated.
More generally there are system threads executing in the background,
concurrent with the user threads (e.g. threads might be associated with
garbage collection). These threads are marked as daemon threads—
meaning just that they don’t have the property of “keeping the JVM
alive”. So, more strictly, the JVM terminates when all non-daemon
threads terminate.
Ordinary user threads can create daemon threads by applying the
setDaemon() method to the thread instance before starting it.
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11
Mutual Exclusion
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12
Avoiding Interference

In any non-trivial multithreaded (or shared-memory-parallel) program,
interference between threads is an issue.

Generally interference (or a race condition) occurs if two threads are
trying to do operations on the same variables at the same time. This often
results in corrupt data.
–
But not always. It depends on the exact interleaving of instructions. This
non-determinism is the worst feature of race conditions.

A popular solution is to provide some kind of lock primitive. Only one
thread can acquire a particular lock at any particular time. The
concurrent program can then be written so that operations on a given
group of variables are only ever performed by threads that hold the lock
associated with that group.

In POSIX threads, for example, the lock objects are called mutexes.
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13
Example use of a Mutex (in C)
Thread A
Thread B
pthread_mutex_lock(&my_mutex) ;
/* critical region */
tmp1 = count ;
count = tmp1 + 1 ;
pthread_mutex_lock(&my_mutex) ;
Blocked
pthread_mutex_unlock(&my_mutex) ;
/* critical region */
tmp2 = count ;
count = tmp2 - 1 ;
pthread_mutex_unlock(&my_mutex) ;
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14
Pthreads-style mutexes




In POSIX threads, a mutex is allocated then initialized with
pthread_mutex_init().
Once a mutex is initialized, a thread can acquire a lock on it by calling
e.g. pthread_mutex_lock(). While it holds the lock it performs some
update on the variables guarded by the lock (critical region). Then the
thread calls pthread_mutex_unlock() to release the lock.
Other threads that try to call pthread_mutex_lock() while the critical
region is being executed are blocked until the first thread releases the
lock.
This is fine, but opportunities for error include:
–
–
There is no built-in association between the lock object (mutex) and the set of
variables it guards—it is up to the program to maintain a consistent
association.
If you forget to call pthread_mutex_unlock() after pthread_mutex_lock(),
deadlocks will occur.
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15
Monitors

Java addresses these problems by adopting a version of the monitors proposed
by C.A.R. Hoare.

Every Java object is created with its own lock (and every lock is associated
with an object—there is no way to create an isolated mutex). In Java this lock
is often called the monitor lock.

Methods of a class can be declared to be synchronized.

The object’s lock is acquired on entry to a synchronized method, and
released on exit from the method.
–
Synchronized static methods need slightly different treatment.

Assuming methods generally modify the fields (instance variables) of the
objects they are called on, this leads to a natural and systematic association
between locks and the variables they guard: viz. a lock guards the instance
variables of the object it is attached to.

The critical region becomes the body of the synchronized method.
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16
Example use of Synchronized Methods
Thread A
Thread B
… call to counter.increment() …
// body of synchronized method
tmp1 = count ;
count = tmp1 + 1 ;
… call to counter.decrement() …
Blocked
… counter.increment() returns …
// body of synchronized method
tmp2 = count ;
count = tmp2 - 1 ;
… counter.decrement() returns …
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17
Caveats


This approach helps to encourage good practices, and make multithreaded
Java programs less error-prone than, say, multithreaded C programs.
But it isn’t magic:
–
–
–
–

It still depends on correct identification of the critical regions, to avoid race
conditions.
The natural association between the lock of the object and its fields relies on the
programmer following conventional patterns of object oriented programming
(which the language encourages but doesn’t enforce).
By using the synchronized construct (see later), programs can break this
association altogether.
There are plenty more insidious ways to introduce deadlocks, besides accidentally
forgetting to release a lock!
Concurrent programming is hard, and if you start with the assumption Java
somehow makes concurrent programming “easy”, you are probably going to
write some broken programs!
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18
Example: A Simple Queue
public class SimpleQueue {
private Node front, back ;
public synchronized void add(Object data) {
if (front != null) {
back.next = new Node(data) ;
back = back.next ;
}
else {
front = new Node(data) ;
back = front ;
}
}
public synchronized Object rem() {
Object result = null ;
if (front != null) {
result = front.data ;
front = front.next ;
}
return result ;
}
}
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19
Remarks





This queue is implemented as a linked list with a front pointer
and a back pointer.
The method add() adds a node to the back of the list; the
method rem() removes a node from the front of the list.
The Node class just has a data field (type Object) and a next
field (type Node).
The rem() method immediately returns null when the queue
is empty.
The following slide gives an example of what could go wrong
without mutual exclusion. It assumes two threads
concurrently add nodes to the queue.
– In the initial state, Z is the last item in the queue. In the final state, the
X node is orphaned, and the back pointer is null.
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The Need for Synchronized Methods
Thread A: add(X)
null
Z
back
back.next = new Node(X) ;
X
Thread B: add(Y)
null
back.next = new Node(Y) ;
Z
X
back
null
Z
Y
null
back
back = back.next ;
null
X
Z
Y
back = back.next ;
null
back
X
null
Z
Y
back
null
Corrupt data structure!
null
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21
The synchronized construct

The keyword synchronized also appears in the synchronized
statement, which has syntax like:
synchronized (object) {
… critical region …
}



Here object is a reference to any object. The synchronized
statement first acquires the lock on this object, then executes
the critical region, then releases the lock.
Typically you might use this for the lock object, somewhere
inside a none-synchronized method, when the critical region
is smaller than the whole method body.
In general, though, the synchronized statement allows you to
use the lock in any object to guard any code.
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22
Performance Overheads of synchronized

Acquiring locks obviously introduces an overhead in
execution of synchronized methods. See, for example:
“Performance Limitations of the Java Core Libraries”,
Allan Heydon and Marc Najork (Compaq),
Proceedings of ACM 1999 Java Grande Conference.


Many of the utility classes in the Java platform (e.g. Vector,
etc) were originally specified to have synchronized methods,
to make them safe for the multithreaded environment.
This is now generally thought to have been a mistake: newer
replacement classes (e.g. ArrayList) usually don’t have
synchronized methods—it is left to the user to provide the
synchronization, as needed, e.g. through wrapper classes.
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23
General Synchronization
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Beyond Mutual Exclusion




The mutual exclusion provided by synchronized methods and
statements is an important special sort of synchronization.
But there are other interesting forms of synchronization
between threads. Mutual exclusion by itself is not enough to
implement these more general sorts of thread interaction (not
efficiently, at least).
POSIX threads, for example, provides a second kind of
synchronization object called a condition variable to
implement more general inter-thread synchronization.
In Java, condition variables (like locks) are implicit in the
definition of objects: every object effectively has a single
condition variable associated with it.
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25
A Motivating Example




Consider the simple queue from the previous example.
If we try to remove an item from the front of the queue when
the queue is empty, SimpleQueue was specified to just return
null.
This is reasonable if our queue is just meant as a data structure
buried somewhere in an algorithm. But what if the queue is a
message buffer in a communication system?
In that case, if the queue is empty, it may be more natural for
the “remove” operation to block until some other thread added
a message to the queue.
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26
Busy Waiting

One approach would be to add a method that polls the queue until data is
ready:
public synchronized Object get() {
while(true) {
Object result = rem() ;
if (result != null)
return result ;
}
}

This works, but it may be inefficient to keep doing the basic rem()
operation in a tight loop, if these machine cycles could be used by other
threads.
– This isn’t clear cut: sometimes busy waiting is the most efficient approach.

Another possibility is to put a sleep() operation in the loop, to deschedule
the thread for some fixed interval between polling operations. But then we
lose responsiveness.
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27
wait() and notify()



In general a more elegant approach is to use the wait() and
notify() family of methods. These are defined in the Java
Object class.
Typically a call to a wait() method puts the calling thread to
sleep until another thread wakes it up again by calling a
notify() method.
In our example, if the queue is currently empty, the get()
method would invoke wait(). This causes the get() operation
to block. Later when another thread calls add(), putting data
on the queue, the add() method invokes notify() to wake up
the “sleeping” thread. The get() method can then return.
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28
A Simplified Example
public class Semaphore {
int s ;
public Semaphore(int s) { this.s = s ; }
public synchronized void add() {
s++ ;
notify() ;
}
public synchronized void get() throws InterruptedException {
while(s == 0)
wait() ;
s-- ;
}
}
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Remarks I

Rather than a linked list we have a simple counter, which is
required always to be non-negative.
– add() increments the counter.
– get() decrements the counter, but if the counter was zero it blocks until
another thread increments the counter.


The data structures are simplified, but the synchronization
features used here are essentially identical to what would be
needed in a blocking queue (left as an exercise).
You may recognize this as an implementation of a classical
semaphore—an important synchronization primitive in its
own right.
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Remarks II






wait() and notify() must be used inside synchronized methods of the
object they are applied to.
The wait() operation “pauses” the thread that calls it. It also releases the
lock which the thread holds on the object (for the duration of the wait()
call: the lock will be claimed again before continuing, after the pause).
Several threads can wait() simultaneously on the same object.
If any threads are waiting on an object, the notify() method “wakes up”
exactly one of those threads. If no threads are waiting on the object,
notify() does nothing.
A wait() method may throw an InterruptedException (rethrown by by
get() in the example). This will be discussed later.
Although the logic in the example doesn’t strictly require it, universal lore
has it that one should always put a wait() call in a loop, in case the
condition that caused the thread to sleep has not been resolved when the
wait() returns (a programmer flaunting this rule might use if in place of
while).
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31
Another Example
public class Barrier {
private int n, generation = 0, count = 0 ;
public Barrier(int n) { this.n = n ; }
public synchronized void synch() throws InterruptedException {
int genNum = generation ;
count++ ;
if(count == n) {
count = 0 ;
generation++ ;
notifyAll() ;
}
else
while(generation == genNum)
wait() ;
}
}
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Remarks



This class implements barrier synchronization—an important operation in
shared memory parallel programming.
It synchronizes n processes: when n threads make calls to synch() the first
n-1 block until the last one has entered the barrier.
The method notifyAll() generalizes notify(). It wakes up all threads
currently waiting on this object.
– Many authorities consider use of notifyAll() to be “safer” than notify(), and
recommend always to use notifyAll().

In the example, the generation number labels the current, collective barrier
operation: it is only really needed to control the while loop round wait().
– And this loop is only really needed to conform to the standard pattern of
wait()-usage, mentioned earlier.
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33
Concluding Remarks on Synchronization


We illustrated with a couple of simple examples that wait()
and notify() allow various interesting patterns of thread
synchronization (or thread communication) to be
implemented.
In some sense these primitives are sufficient to implement
“general” concurrent programming—any pattern of thread
synchronization can be implemented in terms of these
primitives.
– For example you can easily implement message passing between
threads (left as an exercise…)

This doesn’t mean these are necessarily the last word in
synchronization: e.g. for scalable parallel processing one
would like a primitive barrier operation more efficient than
the O(n) implementation given above.
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34
Other Features of Java Threads
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Other Features


This lecture isn’t supposed to cover all the details—for those
you should look at the spec!
But we mention here a few other features you may find
useful.
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36
Join Operations

The Thread API has a family of join() operations. These
implement another simple but useful form of synchronization,
by which the current thread can simply wait for another thread
to terminate, e.g.:
Thread child = new MyThread() ;
child.start() ;
… Do something in current thread …
child.join() ;
// wait for child thread to finish
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Priority and Name

Thread have properties priority and name, which can be
defined by suitable setter methods, before starting the thread,
and accessed by getter methods.
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Sleeping


You can cause a thread to sleep for a fixed interval using the
sleep() methods.
This operation is distinct from and less powerful than wait().
It is not possible for another thread to prematurely wake up a
thread paused using sleep().
– If you want to sleep for a fixed interval, but allow another thread to
wake you beforehand if necessary, use the variants of wait() with
timeouts instead.
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39
Deprecated Thread Methods



There is a family of methods of the Thread class that was originally
supposed to provide external “life-or-death” control over threads.
These were never reliable, and they are now officially “deprecated”. You
should avoid them.
If you have a need to interrupt a running thread, you should explicitly write
the thread it in such a way that it listens for interrupt conditions (see the
next slide).
– If you want to run an arbitrary thread in such a way that it can be externally
killed and cleaned by an external agent, you probably need to fork a separate
process to run it.

The most interesting deprecated methods are:
–
–
–
–
stop()
destroy()
suspend()
resume()
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40
Interrupting Threads


Calling the method interrupt() on a thread instance requests cancellation
of the thread execution.
It does this in an advisory way: the code for the interrupted thread must be
written to explicitly test whether it has been interrupted, e.g.:
public void run() {
while(!interrupted())
… do something …
}


Here interrupted() is a static method of the Thread class which
determines whether the current thread has been interrupted
If the interrupted thread is executing a blocking operation like wait() or
sleep(), the operation may end with an InterruptedException. An
interruptible thread should catch this exception and terminate itself.
Clearly this mechanism depends wholly on suitable implementation of the
thread body. The programmer must decide at the outset whether it is
important that a particular thread be responsive to interrupts—often it
isn’t.
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Thread Groups


There is a mechanism for organizing threads into groups.
This may be useful for imposing security restrictions on
which threads can interrupt other threads, for example.
Check out the API of the ThreadGroup class if you think this
may be important for your application.
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42
Thread-Local Variables


An object from the ThreadLocal class stores an object which
has a different, local value in every thread.
For example, suppose you implemented the MPI messagepassing interface, mapping each MPI process to a Java thread.
You decide that “world communicator” should be a static
variable of the Comm class. But then how do you get the
rank() method to return a different process ID for each
thread, so this kind of thing works?:
int me = Comm.WORLD.rank() ;

One approach would be to store the process ID in the
communicator object in a thread local variable.
– Another approach would be to use a hash map keyed by
Thread.currentThread().

Check the API of the ThreadLocal class for details.
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Volatile Variables

Suppose a the value of a variable must be accessible by multiple threads,
but for some reason you decided you can’t afford the overheads of
synchronized methods or the synchronized statement.
– Presumably effects of race conditions have been proved innocuous.


In general Java does not guarantee that—in the absence of lock operations
to force synchronization of memory—the value of a variable written by a
one thread will be visible to other threads.
But if you declare a field to be volatile:
volatile int myVariable ;

the JVM is supposed to synchronize the value of any thread-local (cached)
copy of the variable with central storage (making it visible to all threads)
every time the variable is updated.
The exact semantics of volatile variables, and the Java memory model in
general, is still controversial, see for example:
“A New Approach to the Semantics of Multithreaded Java”,
Jeremy Manson and William Pugh,
http://www.cs.umd.edu/~pugh/java/memoryModel/
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Thread-based Parallel Applications and
Benchmarks
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Threads on Symmetric Multiprocessors

Most modern implementations of the Java Virtual Machine
will map Java threads into native threads of the underlying
operating system.
– For example these may be POSIX threads.


On multiprocessor architectures with shared memory, these
threads can exploit multiple available processors.
Hence it is possible to do true parallel programming using
Java threads within a single JVM.
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46
Select Application Benchmark Results


We present some results, borrowed from the literature in this
area.
Two codes are described in
“High-Performance Java Codes for Computational Fluid Dynamics”
C. Riley, S. Chatterjee, and R. Biswas,
ACM 2001 Java Grande/ISCOPE


LAURA is a finite-volume flow solver for multiblock,
structured grids.
2D_TAG is a triangular adaptive grid generation tool.
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Parallel Speedup of LAURA Code
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Parallel Speedup of 2D_TAG Code
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Remarks

LAURA speedups are generally fair, and are outstanding with the Jalapeno
JVM on PowerPC (unfortunately this is the only JVM that isn’t freely
available.)
– LAURA is “regular”, and the parallelization strategy needs little or no locking.

2D_TAG results are only reported for PowerPC (presumably worse on
other platforms). This code is very dynamic, very OO, and the naïve
version uses many synchronized methods, hence poor performance.
– The two optimized versions cut down the amount of locking by partitioning
the grid, and only using locks in accesses to edge regions.

As noted earlier, synchronization in Java is quite expensive.
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50
CartaBlanca

CartaBlanca , from Los Alomos National Lab, is a general purpose nonlinear solver environment for physics computations on non-linear grids.
“Parallel Operation of CartaBlanca on Shared and Distributed Memory
Computers”
N. Padial-Collins, W. VanderHeyden, D. Zhang, E. Dendy, D. Livescu.
2002 ACM Java Grande/ISCOPE conference.



It employs an object-oriented component design, and is pure Java.
Parallel versions are based on partitioned meshes, and run either in
multithreaded mode on SMPs, or on networks using a suitable high
performance RMI. Here we are interested in the former case
(multithreaded approach).
Shared memory results are for an 8-processor Intel SMP machine with 900
MHz chips.
– The following results are from a pre-publication version of the paper cited,
and should presumably be taken as indicative only.
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Broken Dam Problem


Two immiscible fluids, side by side.
3D tetrahedral mesh.
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Broken Dam Benchmark Results
Best speedup: 3.65 on 8 processors
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Heat Transfer Problem

Solves transient heat equation on a square domain.
Best speedup: 4.6 on 8 processors
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NAS Parallel Benchmarks


The NAS parallel benchmark suite contains a set of kernel
applications based on CFD codes.
In
Implementation of the NAS Parallel Benchmarks in Java
Michael A. Frumkin, Matthew Schultz, Haoqiang Jin, and Jerry Yan
NAS Technical Report NAS-02-009
the OpenMP versions of the following codes:
–
–
–
–
BT, SP, LU: Simulated CFD applications.
FT: Kernel of a 3-D FFT.
MG: Multigrid solver for 3-D Poisson equation.
CG: Conjugate Gradient method to find eigenvalues of sparse matrix.
were translated to Java using Java threads.
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Timings on IBM p690
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Timings for Origin2000
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Timings for SUN Enterprise10000
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Remarks on NAS Benchmark Results

In this paper the comparisons with Fortran are not flattering to
Java (in fact this was the main conclusion of the authors).
– It seems the SGI Java is particularly slow.
– Generally speaking Java fares much better on Linux or Windows
platforms—not represented here.

Nevertheless, concentrating here on parallel aspects, all cases
show useful or excellent speedup.
– These results are for the largest problem size.
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Special Topic: JOMP
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OpenMP and Java


OpenMP (www.openmp.org) is a well-known standard for parallel
programming on shared-memory computers.
It consists of a series of directives and libraries embedded in a base
language, typically Fortran or C/C++.
– The directives allow definition of parallel regions, executed by a thread-team,
work-sharing directives, which typically define how iterations of a loop are
divided between the thread team, and synchronization features like barriers
and critical regions.


For scientific programming, the OpenMP paradigm can be considerably
more concise and expressive than using generic thread libraries.
Although it doesn’t seem to have been widely taken up, there is an
interesting implementation of OpenMP for Java from Edinburgh Parallel
Computing Center—namely, JOMP.
http://www.epcc.ed.ac.uk/research/jomp/
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JOMP Execution Model


A Java program annotated with JOMP directives is written in
a source file with filename extension .jomp.
This file is fed to the JOMP compiler, which outputs a cryptic
.java file, including calls to a runtime library responsible for
managing Java threads to handle parallel regions, partitioning
work-shared loops, doing barrier synchronizations, etc.
– In the most straightforward case the run-time library is implemented
on top of the standard Java thread library.
– The intermediate .java file is compiled by a standard javac.

One simply executes the resulting class file by, e.g.
java -Djomp.threads=10 MyClass
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JOMP Directives

JOMP directives are syntactically Java comments.
– Note however that OpenMP does not automatically have a property of HPF and
related dialects of Fortran, namely that removing directives leaves a sequential
program with the same semantics.
– In general OpenMP directives will change the behavior and results of a program.
So the fact the directives have the syntax of comments is, arguably, slightly
misleading.
– It is nevertheless possible, and presumably good practice, to write OpenMP
programs in such a way that they do execute the same under a sequential compiler.

In JOMP the typical syntax of a construct is:
//omp directive
Java-statement
where the Java-statement is most often a compound statement, like a for
statement, or a block in braces, { }.
 Other JOMP directives stand alone, and are not associated with a following Java
block (e.g. the barrier directive).
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JOMP Directives: parallel

The parallel construct has basic form:
//omp parallel
Java-statement



The effect is to “create a thread team”. The original thread
becomes master of the team. Master and all other team
members execute the Java-statement, which will nearly always
be some compound statement.
There is an implicit barrier synchronization at the end of the
parallel region.
There are various optional clauses, e.g.:
//omp parallel shared(vars1) private(vars2) …
Java-statement
Here vars1, vars2 are lists of variable names. These clauses
control whether the specified variables are shared or private to
threads within the parallel region.
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JOMP Directives: for

The for construct has basic form:
//omp for
for(integer-type var = expr ; test-var ; incr-var)
Java-statement



A for construct must appear nested (lexically or “dynamically”) inside a
parallel construct—the iterations are divided amongst the active thread team.
The form of the enclosed Java for statement is restricted so that the number of
iterations can be computed before the loop starts (it must be basically
equivalent to a traditional FORTRAN DO loop).
There is an implicit barrier synchronization at the end of the for construct; this
can be disabled by using the nowait clause:
//omp for nowait …
Java-for-statement

The way the iterations are partitioned can be controlled by a schedule clause:
//omp for schedule(mode, chunk-size) …
Java-for-statement
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JOMP Directives: master, critical, barrier

The master construct has the form:
//omp master
Java-statement

This appears inside a parallel construct. The Java-statement is only executed
by the master thread.
The critical construct has the form:
//omp critical [name]
Java-statement

This appears inside a parallel construct, and defines a critical region. The
optional name specifies a lock (if omitted, the default lock is used).
The barrier directive has the form:
//omp barrier
This appears inside a parallel construct. It is treated like an executable
statement and specifies a barrier synchronization at the point it appears in the
program.
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Other Features


There are various other directives and clauses in OpenMP and
JOMP that we didn’t cover, but we gave a flavor.
It is up to the programmer to ensure that all threads in a thread
team encounter work-sharing constructs, and other constructs
that imply barrier synchronization, in the same order.
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An Example


We describe an example from the JOMP release, a CFD code
taken from the JOMP version of the Java Grande Benchmark
suite.
The code Tunnel (presumably short for “Java Wind Tunnel”),
in the JG JOMP benchmarks folder section3/euler/, solves the
Euler equations for 2-dimensional inviscid flow.
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The Euler Equations (in one slide)

Euler equations are a family of conservation equations for (in 2D) 4 quantities:
matter (or mass), 2 components of momentum, total energy:
Flow variables (f, g) related to dependent variables U by:
ρ = density, (u, v) = velocity, E = energy, H = enthalpy.
With equations of state, can easily compute (f, g) as a function of U.
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Finite Volume Discretization

A finite volume approach: divide space into a series of
quadrilaterals, and integrate over a single cell using Gauss’
theorem:
where Ω is cell volume and:
Note U and (f, g) are defined in the centers of the cells. The
face values of (f, g) are computed as averages between
neighboring cells. So R(U) ends up involving values from
neighboring cells.
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Runge Kutta Integration


Now we have a large set of coupled ordinary differential
equations that can be integrated by, e.g., a Runge-Kutta
scheme. In the variant used here a single integration step
is a sequence of four stages each of the form:
where the αs are small constants.
We skipped over some important details (e.g. boundary
conditions, artificial damping) but the equations above
summarize the core algorithm implemented by the Tunnel
program.
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Organization

So the program Tunnel involves a sequence of steps like:
1. Calculate p, H from current U components (using equations of state
for fluid).
2. Calculate f from U, p, H.
3. Calculate g from U, p, H.
4. Calculate R from (f, g).
5. Update U.


Parallelizing in JOMP is very straightforward.
The operations above are called from the method called
doIteration(). A simplified, schematic form is given on the
next slide.
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Main Driver
void doIteration() {
int i, j ;
//omp parallel private(i, j)
{
…
calculateStateVar(pg1, tg1, ug1) ;
calculateF(pg1, tg1, ug1) ;
calculateG(pg1, tg1, ug1) ;
calculateR()
//omp for
for(i = 1; j < imax ; i++)
for(j = 1 ; j < jmax ; ++j) {
ug1[i][j].a = ug[i][j].a – 0.5*deltat/a[i][j]*(r[i][j].a – d[i][j].a) ;
ug1[i][j].b = ug[i][j].b – 0.5*deltat/a[i][j]*(r[i][j].b – d[i][j].b) ;
ug1[i][j].c = ug[i][j].c – 0.5*deltat/a[i][j]*(r[i][j].c – d[i][j].c) ;
ug1[i][j].d = ug[i][j].d – 0.5*deltat/a[i][j]*(r[i][j].d – d[i][j].d) ;
}
… Three other similar stages
}
…
}
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Remarks





The arrays ug, ug1 hold states of the four components of U
(in fields a, b, c, d of their elements).
The arrays pg, and tg are pressure and temperature. The array
a is cell volume.
The array d holds artificial viscosity, which we didn’t discuss.
We have shown one work-sharing construct within this
method—a for construct.
Much of the real work is in the routines calculateR(), etc,
which are called inside the parallel construct.
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Calculation of R
private void calculateR() {
double temp;
int j;
//omp for
for (int i = 1; i < imax; i++)
for (j = 1; j < jmax; ++j) {
…Set fields of r[i][j] to zero…
/* East Face */
temp = 0.5 * (ynode[i][j] - ynode[i][j-1]);
r[i][j].a += temp*(f[i][j].a + f[i+1][j].a);
r[i][j].b += temp*(f[i][j].b + f[i+1][j].b);
r[i][j].c += temp*(f[i][j].c + f[i+1][j].c);
r[i][j].d += temp*(f[i][j].d + f[i+1][j].d);
temp = - 0.5*(xnode[i][j] - xnode[i][j-1]);
r[i][j].a += temp * (g[i][j].a+g[i+1][j].a);
r[i][j].b += temp * (g[i][j].b+g[i+1][j].b);
r[i][j].c += temp * (g[i][j].c+g[i+1][j].c);
r[i][j].d += temp * (g[i][j].d+g[i+1][j].d);
…Add similar contributions of N, S, W faces…
}
}
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Remarks

This is the practical implementation of the mathematical definition
of R given on the earlier slide about discretization.
– We average cell-centered flow values because they are formally evaluated
on the faces of the cell.
– The arrays xnode, ynode contain coordinates of the vertices of the grid.

The for directive here is not in the lexical scope of a parallel
construct. It is called an orphaned directive.
– It is in the dynamic scope of a parallel construct—i.e. this method is called
from the body of a parallel construct.

Those of us conditioned by distributed-memory, domaindecompositions tend to think of the accesses to neighbors as
communications. Of course this is wrong here. There is no fixed
association between array elements and threads.
– Note, on the other hand, there is an implicit thread synchronization
associated with the barrier finishing every for construct (by default).
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76
General Observations on JOMP


In the example we borrowed, parallelization of code was very
easy compared with most other approaches.
The automatic work-sharing of the for construct is very
convenient.
– One limitation is that it only naturally applies to the outer loop of a
multidimensional loop nest—doesn’t generally support
multidimensional blocking.


It relies on a good implementation of the OpenMP
synchronization primitives. Not obvious a priori that the
frequent, implicit barriers will translate efficiently to standard
Java thread operations.
Lack of implementations:
– Sources of the prototype JOMP compiler, etc are not available at the
EPCC Web site? Will anybody use the software if it’s non-standard
and closed source??
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77
Suggested Exercises
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1. Java Thread Synchronization


Following the pattern of the Semaphore class, complete the
implementation of a queue with a get() operation that blocks
when the queue is empty, using wait() and notify().
Extend this to implement send() and recv() primitives for
communicating between threads by message-passing.
– Try implementing other features of the MPI standard for
communication between threads, e.g. synchronous mode sends (where
both sender and receive block until both are ready to communicate).
Avoid “busy-waiting” or polling solutions.
– Define an MPI_Comm_Rank-like function using a ThreadLocal
variable.
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2. Experiment with JOMP

Download and install the JOMP software from
http://www.epcc.ed.ac.uk/research/jomp/
(This just involves downloading a .jar file and adding it to


your CLASSPATH.)
You may also want to download the JOMP version of the Java
Grande benchmarks from the same location.
Implement your favorite parallel algorithm in Java using the
JOMP implementation of OpenMP.
– Do you encounter any implementation limits of the compiler or
runtime?
– Do you get parallel speedup on multiprocessor machines?
– Tell us your results!
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80
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