5.4. Open MPI Java bindings
Open MPI v5.0.5 provides support for Java-based MPI applications.
Warning
The Open MPI Java bindings are provided on a “provisional” basis — i.e., they are not part of the current or proposed MPI standards. Thus, inclusion of Java support is not required by the standard. Continued inclusion of the Java bindings is contingent upon active user interest and continued developer support.
The rest of this document provides step-by-step instructions on building OMPI with Java bindings, and compiling and running Java-based MPI applications. Also, part of the functionality is explained with examples. Further details about the design, implementation and usage of Java bindings in Open MPI can be found in its canonical reference paper 1. The bindings follow a JNI approach, that is, we do not provide a pure Java implementation of MPI primitives, but a thin layer on top of the C implementation. This is the same approach as in mpiJava 2; in fact, mpiJava was taken as a starting point for Open MPI Java bindings, but they were later totally rewritten.
5.4.1. Building the Java bindings
Java support requires that Open MPI be built at least with shared
libraries (i.e., --enable-shared). Note that this is the default
for Open MPI, so you don’t have to explicitly add the option. The Java
bindings will build only if --enable-mpi-java is specified, and a
JDK is found in a typical system default location.
If the JDK is not in a place where we automatically find it, you can specify the location. For example, this is required on the Mac platform as the JDK headers are located in a non-typical location. Two options are available for this purpose:
--with-jdk-bindir=<foo>: the location ofjavacandjavah--with-jdk-headers=<bar>: the directory containingjni.h
Some example configurations are provided in Open MPI configuration
platform files under contrib/platform/hadoop. These examples can
provide a starting point for your own custom configuration.
In summary, therefore, you can configure the system using the following Java-related options:
$ ./configure --with-platform=contrib/platform/hadoop/<your-platform> ...
or:
$ ./configure --enable-mpi-java --with-jdk-bindir=<foo> --with-jdk-headers=<bar> ...
or simply:
$ ./configure --enable-mpi-java ...
if JDK is in a “standard” place that configure can automatically
find.
5.4.2. Building Java MPI applications
The mpijavac wrapper compiler is available for compiling
Java-based MPI applications. It ensures that all required Open MPI
libraries and classpaths are defined. For example:
$ mpijavac Hello.java
You can use the --showme option to see the full command line of
the Java compiler that is invoked:
$ mpijavac Hello.java --showme
/usr/bin/javac -cp /opt/openmpi/lib/mpi.jar Hello.java
Note that if you are specifying a -cp argument on the command line
to pass your application-specific classpaths, Open MPI will extend
that argument to include the mpi.jar:
$ mpijavac -cp /path/to/my/app.jar Hello.java --showme
/usr/bin/javac -cp /path/to/my/app.jar:/opt/openmpi/lib/mpi.jar Hello.java
Similarly, if you have a CLASSPATH environment variable defined,
mpijavac will convert that into a -cp argument and extend it
to include the mpi.jar:
$ export CLASSPATH=/path/to/my/app.jar
$ mpijavac Hello.java --showme
/usr/bin/javac -cp /path/to/my/app.jar:/opt/openmpi/lib/mpi.jar Hello.java
5.4.3. Running Java MPI applications
Once your application has been compiled, you can run it with the
standard mpirun command line:
$ mpirun <options> java <your-java-options> <my-app>
mpirun will detect the java token and ensure that the required
MPI libraries and class paths are defined to support execution. You
therefore do not need to specify the Java library path to the MPI
installation, nor the MPI classpath. Any classpath definitions
required for your application should be specified either on the
command line or via the CLASSPATH environment variable. Note that
the local directory will be added to the classpath if nothing is
specified.
Note
The java executable, all required libraries, and your
application classes must be available on all nodes.
5.4.4. Basic usage of the Java bindings
There is an MPI package that contains all classes of the MPI Java
bindings: Comm, Datatype, Request, etc. These classes have a
direct correspondence with handle types defined by the MPI standard. MPI
primitives are just methods included in these classes. The convention
used for naming Java methods and classes is the usual camel-case
convention, e.g., the equivalent of MPI_File_set_info(fh,info) is
fh.setInfo(info), where fh is an object of the class File.
Apart from classes, the MPI package contains predefined public
attributes under a convenience class MPI. Examples are the
predefined communicator MPI.COMM_WORLD and predefined datatypes such
as MPI.DOUBLE. Also, MPI initialization and finalization are methods
of the MPI class and must be invoked by all MPI Java
applications. The following example illustrates these concepts:
import mpi.*;
class ComputePi {
public static void main(String args[]) throws MPIException {
MPI.Init(args);
int rank = MPI.COMM_WORLD.getRank(),
size = MPI.COMM_WORLD.getSize(),
nint = 100; // Intervals.
double h = 1.0/(double)nint, sum = 0.0;
for (int i=rank+1; i<=nint; i+=size) {
double x = h * ((double)i - 0.5);
sum += (4.0 / (1.0 + x * x));
}
double sBuf[] = { h * sum },
rBuf[] = new double[1];
MPI.COMM_WORLD.reduce(sBuf, rBuf, 1, MPI.DOUBLE, MPI.SUM, 0);
if (rank == 0) {
System.out.println("PI: " + rBuf[0]);
}
MPI.Finalize();
}
}
5.4.5. Exception handling
The Java bindings in Open MPI support exception handling. By default,
errors are fatal, but this behavior can be changed. The Java API will
throw exceptions if the MPI.ERRORS_RETURN error handler is set:
MPI.COMM_WORLD.setErrhandler(MPI.ERRORS_RETURN);
If you add this statement to your program, it will show the line where it breaks, instead of just crashing in case of an error. Error-handling code can be separated from main application code by means of try-catch blocks, for instance:
try
{
File file = new File(MPI.COMM_SELF, "filename", MPI.MODE_RDONLY);
}
catch(MPIException ex)
{
System.err.println("Error Message: "+ ex.getMessage());
System.err.println(" Error Class: "+ ex.getErrorClass());
ex.printStackTrace();
System.exit(-1);
}
5.4.6. How to specify buffers
In MPI primitives that require a buffer (either send or receive), the Java API admits a Java array. Since Java arrays can be relocated by the Java runtime environment, the MPI Java bindings need to make a copy of the contents of the array to a temporary buffer, then pass the pointer to this buffer to the underlying C implementation. From the practical point of view, this implies an overhead associated to all buffers that are represented by Java arrays. The overhead is small for small buffers but increases for large arrays.
There is a pool of temporary buffers with a default capacity of 64K. If a temporary buffer of 64K or less is needed, then the buffer will be obtained from the pool. But if the buffer is larger, then it will be necessary to allocate the buffer and free it later.
The default capacity of pool buffers can be modified with an Open MPI MCA parameter:
$ mpirun --mca ompi_mpi_java_eager SIZE ...
The value of SIZE can be:
N: An integer number of bytesNk: An integer number (suffixed withk) of kilobytesNm: An integer number (suffixed withm) of megabytes
An alternative is to use “direct buffers” provided by standard classes
available in the Java SDK such as ByteBuffer. For convenience,
Open MPI provides a few static methods new[Type]Buffer in the
MPI class to create direct buffers for a number of basic
datatypes. Elements of the direct buffer can be accessed with methods
put() and get(), and the number of elements in the buffer can
be obtained with the method capacity(). This example illustrates
its use:
int myself = MPI.COMM_WORLD.getRank();
int tasks = MPI.COMM_WORLD.getSize();
IntBuffer in = MPI.newIntBuffer(MAXLEN * tasks),
out = MPI.newIntBuffer(MAXLEN);
for (int i = 0; i < MAXLEN; i++)
out.put(i, myself); // fill the buffer with the rank
Request request = MPI.COMM_WORLD.iAllGather(
out, MAXLEN, MPI.INT, in, MAXLEN, MPI.INT);
request.waitFor();
request.free();
for (int i = 0; i < tasks; i++) {
for (int k = 0; k < MAXLEN; k++) {
if (in.get(k + i * MAXLEN) != i)
throw new AssertionError("Unexpected value");
}
}
Direct buffers are available for: BYTE, CHAR, SHORT,
INT, LONG, FLOAT, and DOUBLE.
Note
There is no direct buffer for booleans.
Direct buffers are not a replacement for arrays, because they have higher allocation and deallocation costs than arrays. In some cases arrays will be a better choice. You can easily convert a buffer into an array and vice versa.
Important
All non-blocking methods must use direct buffers. Only blocking methods can choose between arrays and direct buffers.
The above example also illustrates that it is necessary to call the
free() method on objects whose class implements the Freeable
interface. Otherwise, a memory leak will occur.
5.4.7. Specifying offsets in buffers
In a C program, it is common to specify an offset in a array with
&array[i] or array+i to send data starting from a given
position in the array. The equivalent form in the Java bindings is to
slice() the buffer to start at an offset. Making a slice() on
a buffer is only necessary, when the offset is not zero. Slices work
for both arrays and direct buffers.
import static mpi.MPI.slice;
// ...
int numbers[] = new int[SIZE];
// ...
MPI.COMM_WORLD.send(slice(numbers, offset), count, MPI.INT, 1, 0);
5.4.8. Supported APIs
Complete MPI-3.1 coverage is provided in the Open MPI Java bindings, with a few exceptions:
The bindings for the
MPI_Neighbor_alltoallwandMPI_Ineighbor_alltoallwfunctions are not implemented.Also excluded are functions that incorporate the concepts of explicit virtual memory addressing, such as
MPI_Win_shared_query.
5.4.9. Known issues
There exist issues with the Omnipath (PSM2) interconnect involving Java. The problems definitely exist in PSM2 v10.2; we have not tested previous versions.
As of November 2016, there is not yet a PSM2 release that completely fixes the issue.
The following mpirun command options will disable PSM2:
shell$ mpirun ... --mca mtl ^psm2 java ...your-java-options... your-app-class
5.4.10. Questions? Problems?
The Java API documentation is generated at build time in
$prefix/share/doc/openmpi/javadoc.
Additionally, this Cisco blog post has quite a bit of information about the Open MPI Java bindings.
If you have any problems, or find any bugs, please feel free to report them to Open MPI user’s mailing list.
Footnotes