pj2/lib/overview.html

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<P>
Parallel Java 2 (PJ2) is
an API and middleware for parallel programming in 100% Java
on multicore parallel computers,
cluster parallel computers,
hybrid multicore cluster parallel computers,
and GPU accelerated parallel computers.
PJ2 also includes a lightweight map-reduce framework.
PJ2 was developed by Professor Alan Kaminsky
in the Department of Computer Science
at the Rochester Institute of Technology.

<P>
I am happy to answer general questions about the Parallel Java 2 Library,
receive bug reports,
and entertain requests for additional features.
Please contact me by email at
ark<FONT SIZE="1" COLOR="#FFFFFF">&shy;</FONT>&#64;<FONT SIZE="1" COLOR="#FFFFFF">&shy;</FONT>cs.rit.edu.
I regret that I am unable to provide technical support,
specific installation instructions for your system,
or advice about configuring your parallel computer hardware.

<P>
<A HREF="#requirements">System Requirements</A>
<BR><A HREF="#installation">Installation</A>
<BR><A HREF="#usage">Usage</A>
<BR><A HREF="#programming">Parallel Programming with PJ2</A>
<BR><A HREF="#license">License</A>
<BR><A HREF="#history">Revision History</A>

<P>
<HR>
<A NAME="requirements"><H2>System Requirements</H2></A>

<P>
PJ2 was developed using
Java Development Kit (JDK) 1.7.
When compiling and running PJ2 programs,
you must use JDK 1.7 or higher.
PJ2 uses features of the Java language and platform
introduced in JDK 1.7
and will not compile with earlier JDK versions.

<P>
<HR>
<A NAME="installation"><H2>Installation</H2></A>

<P>
There are two versions of the PJ2 distribution,
an executable distribution
and a source distribution.

<P>
<B>Executable distribution.</B>
The executable distribution comes in a Java Archive (JAR) file
named <TT>"pj2_<I>YYYYMMDD</I>.jar"</TT>,
where <I>YYYYMMDD</I> are the year, month, and date.
The executable distribution includes the PJ2 class files only.
To install the executable distribution,
simply store the JAR file somewhere.
You may wish to change the file name,
say to <TT>"pj2.jar"</TT>.

<P>
<B>Source distribution.</B>
The source distribution comes in a Java Archive (JAR) file
named <TT>"pj2src_<I>YYYYMMDD</I>.jar"</TT>,
where <I>YYYYMMDD</I> are the year, month, and date.
The source distribution includes the PJ2 class files,
source files, and documentation files (Javadoc).
To install the source distribution,
just unpack the JAR file.
The source distribution expands into a subdirectory
named <TT>"pj2"</TT>.
If you already have a subdirectory of that name
which you want to save,
be sure to unpack the JAR file
in some other directory.
Documentation is stored under the directory
<TT>"pj2/doc"</TT>;
point your HTML browser to that directory.
Java source files and class files
are stored under the directory
<TT>"pj2/lib"</TT>.

<P>
<B>Installation on a multicore computer.</B>
To run PJ2 programs on a single multicore parallel computer,
no further installation is required.

<P>
<B>Installation on a cluster.</B>
To run PJ2 programs on a cluster parallel computer,
on a computing grid, or in the cloud,
in addition to installing the PJ2 JAR file,
you must configure and run certain daemon processes
on the frontend and backend processors of the cluster.
For further information, see package
<A HREF="edu/rit/pj2/tracker/package-summary.html">edu.rit.pj2.tracker</A>.

<P>
<B>Installation for use with GPUs.</B>
PJ2 programs can execute graphics processing unit (GPU) code
using the classes in package
<A HREF="edu/rit/gpu/package-summary.html">edu.rit.gpu</A>;
refer to that package for instructions
on installing PJ2's GPU capability.

<P>
<HR>
<A NAME="usage"><H2>Usage</H2></A>

<P>
<B>Executable distribution.</B>
When compiling and executing Java programs
that use PJ2,
if you have installed the executable distribution,
you must set your classpath
to include the PJ2 JAR file.
Here is an example of a command for the <TT>bash</TT> shell
to set the classpath to the current directory
plus the PJ2 JAR file:

<P>
<TT>export&nbsp;CLASSPATH=.:/home/fac/ark/public_html/pj2.jar</TT>

<P>
Here is an example of a command for the <TT>csh</TT> shell
to set the classpath to the current directory
plus the PJ2 JAR file:

<P>
<TT>setenv&nbsp;CLASSPATH&nbsp;.:/home/fac/ark/public_html/pj2.jar</TT>

<P>
<B>Source distribution.</B>
When compiling and executing Java programs
that use PJ2,
if you have installed the source distribution,
you must set your classpath
to include the top-level directory
under which PJ2's Java class files are stored.

<P>
<B>PJ2 GPU programs.</B>
When compiling and executing Java programs
that use PJ2's GPU capability,
you must also set your load library path.
For further information, see package
<A HREF="edu/rit/gpu/package-summary.html">edu.rit.gpu</A>.

<P>
<HR>
<A NAME="programming"><H2>Parallel Programming with PJ2</H2></A>

<OL TYPE=1>
<P><LI>
Install PJ2 as described above.
<P><LI>
Read the documentation for the PJ2 classes. Start with these:
<BR>&mdash; Package <A HREF="edu/rit/pj2/package-summary.html">edu.rit.pj2</A>
<BR>&mdash; PJ2 launcher program, <A HREF="pj2.html"><TT>pj2</TT></A>
<BR>&mdash; Class <A HREF="edu/rit/pj2/Task.html">edu.rit.pj2.Task</A>
<BR>&mdash; Class <A HREF="edu/rit/pj2/Job.html">edu.rit.pj2.Job</A>
<P><LI>
Set the Java classpath as described above.
<P><LI>
Study and run the example programs in package
<A HREF="edu/rit/pj2/example/package-summary.html">edu.rit.pj2.example</A>.
<P><LI>
Write and run your own PJ2 programs!
<P>
Optionally:
<P><LI>
Install the PJ2 GPU capability as described above.
<P><LI>
Read the documentation for the PJ2 GPU capability. Start with these:
<BR>&mdash; Package <A HREF="edu/rit/gpu/package-summary.html">edu.rit.gpu</A>
<BR>&mdash; Class <A HREF="edu/rit/gpu/Gpu.html">edu.rit.gpu.Gpu</A>
<BR>&mdash; Class <A HREF="edu/rit/gpu/Module.html">edu.rit.gpu.Module</A>
<BR>&mdash; Interface <A HREF="edu/rit/gpu/Kernel.html">edu.rit.gpu.Kernel</A>
<P><LI>
Set the load library path as described above.
<P><LI>
Study and run the example programs in package
<A HREF="edu/rit/gpu/example/package-summary.html">edu.rit.gpu.example</A>.
<P><LI>
Write and run your own PJ2 GPU programs!
</OL>

<P>
<HR>
<A NAME="license"><H2>License</H2></A>

<P>
The documentation files,
Java source files,
Java class files,
and C source files
in the Parallel Java 2 Library
("PJ2")
are copyright &copy; 2013&ndash;2016
by Alan Kaminsky.
All rights reserved.
For further information, contact the author, Alan Kaminsky,
at ark<FONT SIZE="1" COLOR="\#FFFFFF">&shy;</FONT>&#64;<FONT SIZE="1" COLOR="\#FFFFFF">&shy;</FONT>cs.rit.edu.
<P>
PJ2 is free software; you can redistribute it and/or modify it under the terms
of the GNU General Public License as published by the Free Software Foundation;
either version 3 of the License, or (at your option) any later version.
<P>
PJ2 is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details.
<P>
A copy of the GNU General Public License
is provided in the file <A HREF="doc-files/gpl.txt"><TT>gpl.txt</TT></A>.
You may also obtain a copy of the GNU General Public License
on the World Wide Web at
<A HREF="http://www.gnu.org/licenses/gpl.html" TARGET="_top">http://www.gnu.org/licenses/gpl.html</A>.

<P>
<HR>
<A NAME="history"><H2>Revision History</H2></A>

<DL COMPACT>

<P><DT>06-Apr-2016
<DD>
In class edu.rit.numeric.BigInteger:
Added bitwise-exclusive-or, bitwise-or,
bitwise-and, and bitwise-and-not methods
that take integer and long integer arguments.
Added packing and unpacking methods
that use big-endian order.
(The existing packing and unpacking methods
still use little-endian order.)

<P><DT>21-Mar-2016
<DD>
In package edu.rit.gpu.example:
Added program KnapsackBnbGpu,
a GPU parallel program
that solves a Knapsack Problem instance
using a branch-and-bound search.

<P><DT>12-Mar-2016
<DD>
In package edu.rit.gpu.example:
Fixed a bug in GPU kernel function KnapsackExhGpu.cu;
the best solution was not updated properly
after evaluating a candidate solution.

<P><DT>11-Mar-2016
<DD>
In package edu.rit.gpu.example:
Added program KnapsackExhGpu,
a GPU parallel program
that solves a Knapsack Problem instance
using an exhaustive search.
Added program WalkSackGpu,
a GPU parallel program
that solves a Knapsack Problem instance
using a random walk.
<P>
In class edu.rit.util.Instance:
The <TT>newInstance()</TT> methods
now support arguments of type <TT>int</TT>, <TT>long</TT>, or String
and integer values expressed in binary, octal, decimal, or hexadecimal.

<P><DT>11-Jan-2016
<DD>
In package edu.rit.numeric:
Added class BigInteger.
Removed class BigRational.
Removed method <TT>Statistics.binomialKsTest()</TT>.
<P>
In package edu.rit.numeric.plot:
Fixed bugs in class Plot;
the automatic axis scaling sometimes threw an exception.
<P>
Changed class edu.rit.pj2.Job:
If the <TT>trackerHost</TT> property is set to <TT>"none"</TT>,
the job will not try to connect to the Tracker.
This can also be specified on the <TT>pj2</TT> command line
with the option <TT>tracker=none</TT>.
On some operating systems (notably Windows),
if the Tracker is not running
when a job tries to connect to the Tracker,
the job is delayed
until the connection attempt times out.
Specifying <TT>tracker=none</TT> works around this issue.
On other operating systems (notably Ubuntu Linux),
this issue does not arise,
and <TT>tracker=none</TT> need not be specified.
<P>
In package edu.rit.pjmr.util:
Fixed a bug in class ScatterFiles;
files were not distributed to backend nodes
such that the total file size on each node
was about the same.

<P><DT>11-Aug-2015
<DD>
Added package edu.rit.pjmr.util
with general utility classes and programs for 
Parallel Java Map Reduce (PJMR).
<P>
In package edu.rit.pjmr.example:
Changed the web log analysis programs WebLog01 through WebLog04
to include an optional pattern argument
that limits the analysis
to log entries that match the pattern.
Added programs WebLog05 and MaxTemp01.
<P>
In package edu.rit.pj2.vbl:
Changed classes DoubleVbl.Mean and FloatVbl.Mean:
Added a constructor with a <TT>value</TT> argument;
changed the <TT>accumulate()</TT> method
to return a reference to this shared variable.

<P><DT>21-Jul-2015
<DD>
In package edu.rit.pj2.example:
In classes HamCycClu and HamCycSmp:
Changed the <TT>found</TT> flag to be declared volatile.
In class MineCoinClu3:
Changed the <TT>stop</TT> flag to be declared volatile.

<P><DT>13-Jul-2015
<DD>
In package edu.rit.pjmr:
Fixed a bug in class Combiner;
the <TT>clone()</TT> method was not implemented properly.
This required adding cloning support
to classes edu.rit.util.Set and edu.rit.util.Map.

<P><DT>01-Jul-2015
<DD>
In package edu.rit.pj2.example:
Rewrote programs HamCycSeq, HamCycSmp, and HamCycClu
to simplify the data structures.

<P><DT>26-May-2015
<DD>
In package edu.rit.pj2:
Added classes ObjectParallelForLoop and WorkQueue;
these provide a parallel for loop
that iterates over the work items in a work queue.
Added method <TT>parallelFor(WorkQueue)</TT> to class Task.
Removed class IteratorParallelForLoop;
removed methods <TT>parallelFor(Iterator)</TT>
and <TT>parallelFor(Iterable)</TT> from class Task;
use a work queue instead.
Added class TupleListener
and method <TT>addTupleListener()</TT> in class Task;
these allow reading and taking tuples with a listener pattern.
<P>
In package edu.rit.pj2.example:
Added programs HamCycSeq, HamCycSmp, and HamCycClu
to find a Hamiltonian cycle in a graph;
the latter two use the parallel work queue pattern
on a single multicore node and on a cluster, respectively.
<P>
In package edu.rit.util:
In classes BitSet32, BitSet64, and BitSet:
Added method <TT>randomElement()</TT>.
<P>
In package edu.rit.numeric:
Added class Histogram.
<P>
In package edu.rit.pj2.vbl:
Changed bitset reduction variable classes
BitSetVbl, BitSet32Vbl, and BitSet64Vbl
to be tuples wrapping instances of
classes BitSet, BitSet32, and BitSet64, respectively.
Changed histogram reduction variable class HistogramVbl
to be a tuple wrapping an instance of class Histogram.
<P>
In package edu.rit.pj2.example:
Changed the minimum vertex cover example programs
to use the new bitset classes
and the new bitset reduction variable classes.
Changed the statistical test example programs
to use the new histogram class
and the new histogram reduction variable class.
<P>
In class edu.rit.util.Random:
Added method <TT>nextBigInteger()</TT>.
<P>
In class edu.rit.util.Searching:
Added methods to search just a portion of an array;
added convenience methods
to search an array in ascending order;
added methods to search lists.
<P>
In class edu.rit.util.Sorting:
Added methods to sort just a portion of an array;
added convenience methods
to sort an array into ascending order;
added methods to sort lists.

<P><DT>16-Feb-2015
<DD>
Fixed bugs in the <TT>clone()</TT> methods in several classes;
the methods did not create an instance of the correct class
when an instance of a subclass was cloned.
<P>
Fixed a bug in class edu.rit.util.BitSet;
the private fields were not initialized correctly in all cases.
Thank you to Vaibhav Gandhi for discovering the bug.
<P>
In class edu.rit.numeric.Mathe:
Added the <TT>logBinomProb()</TT>,
<TT>binomProb()</TT>,
and <TT>cumulBinomProb()</TT> methods.

<P><DT>09-Feb-2015
<DD>
In class edu.rit.pj2.vbl.HistogramVbl;
Fixed a bug:
the <TT>clone()</TT> method did not work properly in all cases;
added <TT>prob()</TT>, <TT>expectedCount()</TT>,
and <TT>expectedProb()</TT> methods.

<P><DT>06-Feb-2015
<DD>
In package edu.rit.pj2.vbl:
Added class HistogramVbl and several subclasses.
These provide reduction variable classes
for histograms of various types of data.
<P>
In package edu.rit.util:
Added <TT>searchInterval()</TT> methods to class Searching.

<P><DT>18-Jan-2015
<DD>
In package edu.rit.util:
In classes AList, DList, IntList, and LongList,
added a <TT>removeEachItemIf()</TT> method
that scans the list and optionally removes items.
Added classes and interfaces
Set, MultiSet, LongMultiSet, BitSet, BitSet32, BitSet64,
PairBase, Pair, IntPair, LongPair, IdentityPair,
Map, IdentityMap,
DoubleAction, DoubleActionResult, DoublePredicate, DoubleList,
FloatAction, FloatActionResult, FloatPredicate, FloatList.
<P>
In package edu.rit.io:
Added <TT>writeObjectArray()</TT> and <TT>writeReferenceArray()</TT> methods
to class OutStream.
Added <TT>readObjectArray()</TT> and <TT>readReferenceArray()</TT> methods
to class InStream.
<P>
Added package edu.rit.pj2.tuple
with several tuple subclasses.
The Tuple base class remains in package edu.rit.pj2.
<P>
Added package edu.rit.pj2.vbl.
Moved the reduction variable classes
from package edu.rit.pj2 to package edu.rit.pj2.vbl.
The Vbl interface remains in package edu.rit.pj2.
Added classes BitSetVbl, BitSet32Vbl, BitSet64Vbl.
<P>
Changed classes throughout the Library
to use the above classes.

<P><DT>07-Nov-2014
<DD>
In package edu.rit.pj2:
Added a method to each Vbl subclass
to return the variable's value,
such as <TT>intValue()</TT>, <TT>doubleValue()</TT>, and so on.
In class DoubleVbl.Mean,
eliminated the <TT>mean()</TT> method;
use the <TT>doubleValue()</TT> method instead.
In class FloatVbl.Mean,
eliminated the <TT>mean()</TT> method;
use the <TT>floatValue()</TT> method instead.
<P>
In package edu.rit.pjmr:
Added the <TT>toString()</TT>, <TT>equals()</TT>,
and <TT>hashCode()</TT> methods
to class TextId.
Added the <TT>noMatchIsError()</TT> method
to class TextDirectorySource.

<P><DT>05-Nov-2014
<DD>
In package edu.rit.pjmr:
Redesigned the communication between
the mapper tasks and the reducer task
to include flow control;
this prevents the mapper tasks
from getting too far ahead
of the reducer task.
Changed class Pair to be streamable.
In class Combiner,
added the ability to return custom Pair subclasses
when iterating over the (key, value) pairs;
the intention is to support more efficient streaming of pairs
than the default implementation of streaming in class Pair.
Added class TextDirectorySource.
<P>
In package edu.rit.pjmr.example:
Added program Concordance04.

<P><DT>29-Oct-2014
<DD>
In package edu.rit.gpu.example:
Added class ZombieGpu2
to illustrate the use of C structures in the GPU kernel
and the corresponding Java classes in the main program.

<P><DT>12-Oct-2014
<DD>
In package edu.rit.gpu.example:
Fixed a bug in class ZombieGpu;
the convergence criterion was not implemented correctly.

<P><DT>10-Oct-2014
<DD>
In package edu.rit.gpu.example:
Added the <I>steps</I> argument
to the ZombieGpu program.

<P><DT>19-Sep-2014
<DD>
Fixed a bug in class edu.rit.pj2.Backend;
the standard output and standard error streams
were not flushed to the console
properly in all cases.
Thank you to Umang Gala for discovering the bug.

<P><DT>22-Jul-2014
<DD>
Changed class edu.rit.http.HttpServer.
The HTTP server now processes each incoming socket connection
in a separate thread obtained from an internal thread pool.
If the HTTP server encounters an I/O error
while trying to read an HTTP request message
from an incoming socket connection,
the HTTP server now closes the connection without processing anything.
These changes help defend against malicious behavior
on the part of clients.
<P>
Fixed a bug in class edu.rit.pj2.tracker.Tracker;
if there was a problem with an incoming socket connection
to the Tracker's HTTP server,
the Tracker could freeze,
causing heartbeats to fail and jobs to terminate.
Also, changed the Tracker's summary web page URL
to <TT>http://<I>host</I>:<I>port</I>/summary</TT>;
consequently, the Tracker will not respond with status information
if a client requests the default home page;
this is to fend off web crawlers.

<P><DT>21-Jul-2014
<DD>
Fixed a bug in class edu.rit.util.Heartbeat;
the methods were not properly synchronized.

<P><DT>08-Jul-2014
<DD>
In class edu.rit.pj2.TaskSpec:
Changed the <TT>args()</TT> method
to append arguments to the task's command line argument array,
instead of replacing the task's command line argument array.
<P>
In package edu.rit.pj2.example:
Fixed a bug in class MineCoinClu3;
the StopTuple class did not override
the <TT>writeOut()</TT> and <TT>readIn()</TT> methods.
Changed the continuous cellular automaton programs
and the Mandelbrot Set programs
to turn on world read and write permissions
for the output files.
Changed the ZombieClu program
to simplify the tuple subclasses.

<P><DT>02-Jul-2014
<DD>
In package edu.rit.io:
Changed classes Color, ColorArray, Gray, and GrayArray
to be streamable instead of serializable.
Added the <TT>copy()</TT> method to classes ColorArray and GrayArray.
<P>
In package edu.rit.pj2:
Added documentation to class Tuple
emphasizing that tuple objects
are assumed to be immutable.
Changed class Job;
when putting multiple copies of a tuple into tuple space,
the job puts multiple references to the tuple
rather than multiple clones of the tuple;
this is safe because tuples are assumed to be immutable.
Changed the tuple space implementation in class TupleSpace;
eliminated separate lists of tuples
for each tuple subclass.
<P>
In package edu.rit.pj2.tracker:
Changed class Proxy
to turn on the <TT>TCP_NODELAY</TT> option
for all socket connections;
this allows interprocess messages to be sent more quickly
and reduces the running time
of tightly coupled cluster parallel programs.
<P>
In package edu.rit.pj2.example:
Added a <TT><I>steps</I></TT> command line argument
to the ZombieSeq, ZombieSmp, and ZombieClu programs.
Added class CCACell.
Changed the CCASeq, CCASmp, and CCAClu programs
to use class CCACell.
Added class MandelbrotClu.

<P><DT>20-Jun-2014
<DD>
In package edu.rit.pj2:
Fixed bugs in classes WorkerIntParallelForLoop
and WorkerLongParallelForLoop;
properties set on the parallel for loop object
did not override properties of the enclosing task.
<P>
In package edu.rit.pj2.example:
Added program MinVerCovDist.
<P>
In package edu.rit.numeric:
Added several methods to class Mathe.
Added class NormalFit.

<P><DT>17-Jun-2014
<DD>
Fixed a bug in class edu.rit.pj2.tracker.JobReceiver;
insufficient buffer space was allocated
to receive a "write standard stream" message.
<P>
In package edu.rit.pj2.example:
Tweaked programs MinVerCovSeq and MinVerCovSmp.
Added programs MinVerCovSeq2, MinVerCovSmp2,
MinVerCovSeq3, and MinVerCovSmp3.
These solve the minimum vertex cover problem
in various ways.

<P><DT>06-Jun-2014
<DD>
In class edu.rit.pj2.Task:
Changed the names of the
<TT>initialNodeName()</TT>,
<TT>initialCores()</TT>,
and <TT>initialGpus()</TT> methods to
<TT>nodeNameRequired()</TT>,
<TT>coresRequired()</TT>,
and <TT>gpusRequired()</TT>, respectively.
Added the ability to specify
that a task requires all the GPU accelerators on the node.
<P>
In package edu.rit.io:
Added class ThreadedOutputStream,
which automatically synchronizes multiple threads
writing to an underlying output stream.
<P>
In package edu.rit.pj2:
Changed class Job and class Task
to use a ThreadedOutputStream
when printing to <TT>System.out</TT> and <TT>System.err</TT>.
The printouts actually appear on the console when
the job or task terminates; to make the printouts appear earlier, call
<TT>System.out.flush()</TT> or <TT>System.err.flush()</TT>.
Eliminated the no-longer-needed class Print.
<P>
In package edu.rit.gpu:
Added the ability to work with C struct data types;
see classes Struct, GpuStructVbl, and GpuStructArray.
In package edu.rit.gpu.example:
Added program Powers to illustrate the use of C struct data types
in Java GPU parallel programs.
<P>
In package edu.rit.pj2.example:
Added programs RandomGraph, MinVerCovSeq, and MinVerCovSmp,
which find a minimum vertex cover of a graph via exhaustive search.

<P><DT>13-Apr-2014
<DD>
In package edu.rit.gpu:
Added class GpuMatrix and subclasses
to provide matrix variables (two-dimensional arrays)
on the GPU.
In package edu.rit.gpu.example:
Added classes OuterProductGpu and OuterProductSeq.
<P>
In package edu.rit.util:
Added class PriorityQueue.
In package edu.rit.sim:
Changed classes Event and Simulation
to use class PriorityQueue.

<P><DT>25-Mar-2014
<DD>
Added GPU support in package edu.rit.gpu.
Added GPU example programs in package edu.rit.gpu.example.
Added GPU unit test programs in package edu.rit.gpu.test.
<P>
Added protected static methods to class edu.rit.pj2.Task
that can optionally be overridden
to specify the initial
<TT>threads</TT>, <TT>schedule</TT>, <TT>chunk</TT>,
<TT>nodeName</TT>, <TT>cores</TT>, and/or <TT>gpus</TT> properties
for all instances of the Task subclass.
<P>
In class edu.rit.pj2.tracker.Tracker:
Added support for allocating GPU devices to tasks.
As a consequence, 
the message format is now incompatible
with earlier versions of the Library.

<P><DT>14-Mar-2014
<DD>
In package edu.rit.pjmr:
Fixed bugs that caused deserialization errors
when PJMR jobs were run on a cluster.
<P>
In class edu.rit.numeric.Mathe:
Added the <TT>log2()</TT> method.

<P><DT>04-Feb-2014
<DD>
Added the <TT>jvmFlags</TT> property to the <TT>pj2</TT> program.
Added the <TT>jvmFlags()</TT> method to class edu.rit.pj2.Job.
Added class edu.rit.numeric.Mathe.

<P><DT>28-Jan-2014
<DD>
In class edu.rit.pj2.Job:
Two methods are now named <TT>masterSchedule()</TT>
and <TT>masterChunk()</TT>
rather than <TT>workerSchedule()</TT>
and <TT>workerChunk()</TT>.
<P>
In class pj2:
Two command line options are now named <TT>masterSchedule</TT>
and <TT>masterChunk</TT>
rather than <TT>workerSchedule</TT>
and <TT>workerChunk</TT>.

<P><DT>26-Jan-2014
<DD>
I made numerous changes to
the Parallel Java 2 Library
based on my experience teaching and working with it
during RIT's fall 2013 semester.
The major changes are summarized below.
<P>
Added class edu.rit.numeric.Int96.
Removed classes edu.rit.util.Range and edu.rit.util.LongRange;
these were replaced by classes
edu.rit.pj2.Chunk and edu.rit.pj2.LongChunk.
<P>
For multicore parallel programming in package edu.rit.pj2:
Added the "proportional" enumeral to enum Schedule.
Added classes Chunk, LongChunk,
DoubleVbl.Mean, and FloatVbl.Mean.
Rewrote the parallel for loop classes
to partition the loop iterations
using the new Int96 class
instead of java.math.BigInteger.
To avert false sharing
between different threads' thread-local variables,
added hidden padding fields to class LoopBody,
all the Vbl subclasses,
and classes edu.rit.crypto.RC4,
edu.rit.crypto.SHA256,
and edu.rit.util.Random.
<P>
For cluster parallel programming in package edu.rit.pj2:
The syntax for specifying rules in a job was simplified.
The default number of cores a task requires
is now all cores on the node, rather than one core.
There are now methods for specifying
the <TT>nodeName</TT>, <TT>cores</TT>, <TT>gpus</TT>,
<TT>workers</TT>, <TT>workerSchedule</TT>, and <TT>workerChunk</TT> properties
of tasks and jobs,
and those properties can now be specified
on the <TT>pj2</TT> command line;
see classes Job, Rule, TaskSpec, and Task for further information.
In a task launched by an on-demand rule,
the methods for getting the matching tuples
that caused the rule to fire
are now <TT>matchingTupleCount()</TT> and <TT>getMatchingTuple()</TT>.
In a task launched by a start rule or a finish rule,
there are no matching tuples;
the task can still take or read tuples
by calling <TT>takeTuple()</TT>, <TT>tryToTakeTuple()</TT>,
<TT>readTuple()</TT>, or <TT>tryToReadTuple()</TT>.
Added methods for master-worker cluster parallel for loops;
see <TT>Job.masterFor()</TT> and <TT>Task.workerFor()</TT>.
<P>
In package edu.rit.io:
Removed classes DataInputStream, DataOutputStream, and SerializedObject.
Added classes/interfaces Streamable, InStream, and OutStream.
These implement a lightweight binary I/O and object I/O capability
as a replacement for Java Object Serialization.
Updated classes throughout the Parallel Java 2 Library
to use the new Streamable capability.
As a consequence, 
the message format is now incompatible
with earlier versions of the Library.
<P>
Class edu.rit.pj2.Tuple now implements interface Streamable.
As a consequence,
all subclasses of class Tuple
now must include a no-argument constructor
and must override the <TT>writeOut()</TT> and <TT>readIn()</TT> methods
to write and read the tuple's fields.
If this is not done,
tuples will not transfer between processes correctly.
<P>
In package edu.rit.pj2.example:
Added programs ZombieSeq, ZombieSmp, and ZombieClu.
<P>
In the unnamed package:
Removed programs StrongPlot and WeakPlot;
these were replaced by program ScalePlot.

<P><DT>02-Dec-2013
<DD>
In package edu.rit.pj2.tracker:
Fixed a bug in class Tracker;
the Tracker would die if it received incorrect data
after accepting a socket connection.

<P><DT>21-Nov-2013
<DD>
In package edu.rit.pjmr:
Changed the reducer task
to optionally sort the (key, value) pairs
before reducing them;
this is specified by the <TT>comesBefore()</TT> method
of class Customizer.
Changed the example PJMR map-reduce programs
in package edu.rit.pjmr.example
to use the new capability.

<P><DT>20-Nov-2013
<DD>
Fixed several bugs in package edu.rit.pjmr.
Added more example PJMR map-reduce programs
in package edu.rit.pjmr.example.

<P><DT>19-Nov-2013
<DD>
Added the Parallel Java Map Reduce Framework (PJMR),
a simple parallel map-reduce framework
built on top of Parallel Java 2,
in package edu.rit.pjmr.
Added example PJMR map-reduce programs
in package edu.rit.pjmr.example.
<P>
In package edu.rit.pj2:
The parallel for loop body classes were refactored.
Class Loop is the body for an integer parallel for loop;
class LongLoop is the body for a long integer parallel for loop;
class ObjectLoop is the body for an iterator parallel for loop;
these all extend a common LoopBody base class.
This change improves the compile time type safety
of the loop body classes
and eliminates a bug
where the iterator parallel for loop body's <TT>run()</TT> method
could not be overridden properly.
However,
this requires changing programs
with long integer parallel for loops
to use class LongLoop instead of class Loop,
and changing programs
with iterator parallel for loops
to use class ObjectLoop instead of class Loop.
Also,
made the <TT>threadLocal()</TT> method a generic method;
this eliminates the need to downcast the return value.
<P>
In package edu.rit.pj2:
Changed all the shared variable classes
to extend class Tuple
and to define the <TT>toString()</TT> method.
Added class StringVbl.
Added the <TT>parallelDo(int,Section)</TT> method
to class Task;
this executes a number of copies of the same section in parallel.
<P>
In package edu.rit.io:
Added class SerializedObject.
In package edu.rit.pj2.tracker:
Changed the backend, job, launcher, and tracker sender and receiver classes
to use DataInputStream and DataOutputStream with class SerializedObject,
rather than ObjectInputStream and ObjectOutputStream.
This fixed an intermittent bug
where an end-of-file was encountered
in the middle of a message.
However,
the message format is now incompatible
with earlier versions of the Library.

<P><DT>29-Oct-2013
<DD>
Fixed a bug in class edu.rit.pj2.tracker.JobSender;
the methods were not all properly synchronized.

<P><DT>24-Oct-2013
<DD>
Fixed a bug in class edu.rit.pj2.TupleSpace;
removal of tuples did not work properly
if the same tuple object was put into tuple space multiple times
(which is allowed).
Thank you to Pankaj Deshmukh for discovering the bug.

<P><DT>06-Oct-2013
<DD>
In the <TT>pj2</TT> program,
added the <TT>timelimit</TT> parameter.
In class edu.rit.pj2.Job,
added the <TT>timeLimit()</TT> method.

<P><DT>05-Oct-2013
<DD>
In class edu.rit.pj2.Debug:
Added the <TT>makespan</TT> debug printout.
<P>
In package edu.rit.pj2.example:
Changed class PiClu to a hybrid parallel program.
Added classes BCAClu, BCASmp, and TotientClu.
<P>
In class edu.rit.pj2.Tracker:
Added the time each job has spent waiting or running
on the Tracker's web interface summary page.

<P><DT>19-Sep-2013
<DD>
In class edu.rit.pj2.Loop:
Made the <TT>threadLocal()</TT> method a generic method;
this eliminates the need to downcast the return value.
Thank you to Matthew Fluet for suggesting this change.
<P>
In package edu.rit.pj2.example:
Added class MineCoinClu3.

<P><DT>13-Sep-2013
<DD>
In class edu.rit.pj2.Task:
Changed the names of the methods that take tuples out of tuple space;
they are now called <TT>takeTuple()</TT> and <TT>tryToTakeTuple()</TT>.
Added methods that read tuples without taking them out of tuple space;
they are called <TT>readTuple()</TT> and <TT>tryToReadTuple()</TT>.
<P>
In package edu.rit.pj2:
Changed class Vbl to an interface.
Eliminated class ObjectVbl;
to do parallel reduction on an object,
write a class that implements interface Vbl.
This change eliminates a layer of indirection
and simplifies programs involving parallel reduction on objects.

<P><DT>02-Sep-2013
<DD>
In package edu.rit.pj2:
Fixed a bug in class Job;
tuple take requests were not processed properly
in all cases.
Fixed a bug in class Tuple;
a null field was not printed properly.

<P><DT>30-Aug-2013
<DD>
In package edu.rit.pj2:
In class Task:
Added the non-blocking <TT>tryToGetTuple()</TT> method.
<P>
In package edu.rit.util:
In class Packing:
Added methods to pack and unpack
short integers to integers,
short integers to long integers,
and integers to long integers.

<P><DT>12-Aug-2013
<DD>
In class edu.rit.draw.item.Arrow:
Added the ability to specify the arrow width.
<P>
In package edu.rit.crypto:
Added classes/interfaces CipherInputStream, CipherOutputStream,
RC4, and StreamCipher.
<P>
In package edu.rit.pj2:
In class Job:
Fixed a bug;
printouts on the standard output or standard error
from tasks in other nodes
were not synchronized properly.
In class Task:
Changed the <TT>putTuple(int,Tuple)</TT> method;
the number of copies is now the first argument.
<P>
In package edu.rit.swing:
Added a "PNG Setup" dialog to class DisplayableFrame
that lets the user specify scale factor and resolution
when saving a PNG file.
As a consequence,
the View program (in the unnamed package)
now writes PNG files
with a user-selectable scale factor and resolution.

<P><DT>19-Jul-2013
<DD>
In package edu.rit.util:
Added classes/interfaces
LongAction,
LongActionResult,
LongList,
and LongPredicate.
<P>
In package edu.rit.image:
Added the ability
to specify the physical pixel dimensions
in the PNG image writer classes.
<P>
In class edu.rit.swing.DisplayableIO:
Added the ability
to specify the physical pixel dimensions
in the PNG image writing methods.
As a consequence,
the View program (in the unnamed package)
now writes PNG files
at a resolution of 300&times;300 pixels per inch.
<P>
Added package edu.rit.crypto
with classes/interfaces
HashFunction
and SHA256.
<P>
In package edu.rit.pj2:
Added class TerminateException.
Code in a job or task must not call <TT>System.exit()</TT>;
rather, it should throw a TerminateException
or another runtime exception
to terminate the program.
<P>
In package edu.rit.pj2.example:
Changed the Totient programs to use class LongList.
Changed the MineCoin programs to use class SHA256.
Changed all the programs to exit by throwing an IllegalArgumentException
if the command line arguments are bad.
<P>
In package edu.rit.pj2.tracker:
Changed class Launcher;
the command that launches the JVM
can now include arguments after the command name.

<P><DT>12-Jul-2013
<DD>
The initial version of PJ2 was released.
This version supports tightly coupled multicore parallel programming
(class <A HREF="edu/rit/pj2/Task.html">edu.rit.pj2.Task</A>)
and loosely coupled cluster parallel programming
(class <A HREF="edu/rit/pj2/Job.html">edu.rit.pj2.Job</A>).

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