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Subject: Re: [OMPI users] MPI Java Bindings on Mac OSX
From: Jeff Squyres (jsquyres) (jsquyres_at_[hidden])
Date: 2013-01-10 10:25:23


With respect to Java support: frankly, Ralph and I have been somewhat surprised by the level of interest for Java+MPI! We wanted Java for some other reasons, but didn't really expect *too* much interest from the community.

Unfortunately, the Java package we imported into Open MPI is both a bit dated and is known to be buggy in a few cases. I'd really like to replace it with:

- interfaces that are closer to a 1:1 mapping to the MPI C bindings
- a full set of MPI interfaces

Is this something that you'd be able to help with, perchance? Neither Ralph nor I are Java experts, and we're a bit pressed for resources -- anyone who can help here would be greatly appreciated.

See http://www.open-mpi.org/community/lists/devel/2013/01/11915.php.

On Jan 3, 2013, at 5:12 PM, Chuck Yahoo <chuckmosher_at_[hidden]> wrote:

> It's nice to see that this mail list has a lot of activity !
>
> Thanks for the tips, I haven't used modules in quite a few years, having been spoiled by Java ;-)
>
> Takes me back to the good old days, spending 10x more time configuring than coding !
>
> Chuck
>
> On Jan 3, 2013, at 1:05 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>
>> FWIW: I test it regularly on Mountain Lion, without problem. We know that some of the bindings aren't quite right, particularly on some of the collectives, but send/recv is fine
>>
>>
>> On Jan 3, 2013, at 10:09 AM, "Beatty, Daniel D CIV NAVAIR, 474300D" <daniel.beatty_at_[hidden]> wrote:
>>
>>> Greetings Chuck,
>>> I tend to agree with Doug. It hope to be able to test soon OpenMPI under Lion/Mountain Lion. If someone has already done so, especially with Java, that could be quite handy.
>>>
>>> V/R,
>>>
>>> Daniel Beatty, Ph.D.
>>> Computer Scientist, Detonation Sciences Branch
>>> Code 474300D
>>> 1 Administration Circle M/S 1109
>>> China Lake, CA 93555
>>> daniel.beatty_at_[hidden]
>>> (LandLine) (760)939-7097
>>> (iPhone) (806)438-6620
>>>
>>>
>>>
>>>
>>> On 1/3/13 9:49 AM, "Ralph Castain" <rhc_at_[hidden]> wrote:
>>>
>>> Hi Doug
>>>
>>> What modules software do you use on the Mac? Would be nice to know :-)
>>>
>>>
>>> On Jan 3, 2013, at 8:34 AM, Doug Reeder <dlr1_at_[hidden]> wrote:
>>>
>>> Chuck,
>>>
>>> In step 4 you might want to consider the following
>>>
>>> --prefix=/usr/local/openmpi-1.7rc5
>>>
>>> and use the modules software to select which version of openmpi to use. I have to have multiple versions of openmpi available on my macs and this approach has worked well for me.
>>>
>>> Doug Reeder
>>> On Jan 3, 2013, at 9:22 AM, Chuck Mosher wrote:
>>>
>>> Hi,
>>>
>>> I've been trying to get a working version of the MPI java bindings on Mac OSX (10.6.8 with Java 1.6.0_37).
>>>
>>> I ran into a number of issues along the way that I thought I would record here for others who might be foolish enough to try the same ;-)
>>>
>>> The issues I had to spend time with were:
>>>
>>> 1. Installing a C compiler that can run from the command line
>>> 2. Finding and installing an appropriate Java JDK for my OS version
>>> 3. Building and installing OpenMPI for the first time on a Mac
>>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed already on my Mac
>>> 5. Figuring out syntax for using the mpirun command line to run java
>>> 6. Odd behavior when trying to use "localhost" or the output from `hostname` on the command line or in a hostfile
>>>
>>> Resolution for each of these in order:
>>>
>>> 1. Installing a C compiler for the command line
>>> Found a good resource here:
>>> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion <http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion>
>>> The solution is to install XCode, then enable command line compilers from the XCode console.
>>>
>>> 2. Finding and installing an appropriate Java JDK for my OS version
>>> Used this resource to eventually figure out what to do:
>>> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X <http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X>
>>> It didn't exactly match my setup, but had enough clues.
>>> The solution is to first find your java version (java -version, 1.6.0_37 in my case) and then match that version number to the Apple Java update version (11 in my case).
>>> The key document is:
>>> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
>>> Which is a table relating java version numbers to the appropriate "Java for Mac OS X xx.x Update xx".
>>> Once you know the update number, you can download the JDK installer from
>>> https://developer.apple.com/downloads/index.action
>>> where you of course have to have an Apple developer ID to access.
>>> Enter "java" in the search bar on the left and find the matching java update, and you're good to go.
>>>
>>> 3. Building and installing OpenMPI for the first time on a Mac
>>> After the usual false starts with a new installation on a new OS, I managed to get a working build of openmpi-1.7rc5 with Java bindings.
>>> I could only find the java bindings in the 1.7 pre-release.
>>> I used the defaults as much as possible.
>>>
>>> After downloading from:
>>> http://www.open-mpi.org/software/ompi/v1.7/
>>> and unarchiving to Downloads, open a Terminal window.
>>>
>>> cd Downloads/openmpi-1.7rc5
>>> ./configure --enable-java --prefix=/usr/local
>>> make all
>>> sudo make install
>>>
>>> Verify that you can run the commands and examples:
>>>
>>> chuck-> /usr/local/bin/mpirun -version
>>> mpirun (Open MPI) 1.7rc5
>>>
>>> chuck-> cd examples
>>> chuck-> make
>>> chuck-> /usr/local/bin/mpirun -np 2 hello_c
>>> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI chuck_at_chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>>> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI chuck_at_chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>>>
>>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed already on my Mac
>>> OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
>>> So, if you accidentally type:
>>>
>>> chuck-> mpirun -np 2 hello_c
>>> --------------------------------------------------------------------------
>>> A requested component was not found, or was unable to be opened
>>> ...
>>>
>>> you picked up the wrong "mpirun" and you will get a bunch of error output complaining about sockets or mis-matched shared library versions.
>>>
>>> I dealt with this moving the existing OpenMPI related commands to a subdirectory, and then created symbolic links from /usr/local/bin to /usr/bin for the commands I needed.
>>>
>>> 5. Figuring out syntax for using the mpirun command line to run java
>>> First be sure you can run Java
>>>
>>> chuck-> /usr/bin/java -version
>>> java version "1.6.0_37"
>>> Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
>>> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
>>>
>>> Then be sure you can run your java class from the command line as well. To figure this out I created a couple of simple java files in a temp directory:
>>>
>>> chuck-> cd ~/tmp
>>> chuck-> mkdir classes
>>> chuck -> cat HelloWorld.java
>>>
>>> public class HelloWorld {
>>> public static void main(String[] args) {
>>> System.out.println("Hello World, from Java !");
>>> }
>>> }
>>>
>>> chuck-> javac -d classes HelloWorld.java
>>> chuck-> java -cp ./classes HelloWorld
>>>
>>> Hello World, from Java !
>>>
>>> No sense going further until you can get the code above to run.
>>> If you have that working, then you can try the MPI version of HelloWorld:
>>>
>>> chuck-> cat HelloWorldMPI.java
>>>
>>> import mpi.*;
>>> class HelloWorldMPI {
>>> public static void main(String[] args) throws MPIException {
>>> MPI.Init(args);
>>> System.out.println("Hello world from rank " +
>>> MPI.COMM_WORLD.Rank() + " of " +
>>> MPI.COMM_WORLD.Size() );
>>> MPI.Finalize();
>>> }
>>> }
>>>
>>> chuck-> /usr/local/bin/mpijavac -d classes HelloWorldMPI.java
>>> /usr/local/bin/mpirun -np 2 /usr/bin/java -cp ./classes HelloWorldMPI
>>>
>>> Hello world from rank 0 of 2
>>> Hello world from rank 1 of 2
>>>
>>> And you're ready to go !
>>> Except for one last thing ...
>>>
>>> 6. Odd behavior when trying to use "localhost" or the output from `hostname` on the command line or in a hostfile
>>> You will note in the examples above no host names, hostifle, or appfile was used.
>>> I found that trying to use "-host localhost" or "-hostfile hostfile" which contained "localhost" would not work:
>>>
>>> mpirun -host localhost -np 2 ...
>>>
>>> in the examples above would not work, returning:
>>>
>>> chuck$ /usr/local/bin/mpirun -host localhost -np 2 /usr/bin/java -cp ./classes HelloWorldMPI
>>> --------------------------------------------------------------------------
>>> All nodes which are allocated for this job are already filled.
>>> --------------------------------------------------------------------------
>>>
>>> I posted this in a previous e-mail to this list, and it looks like a bug.
>>> You can get around it by using the output from `hostname -s` which provides a trimmed name:
>>>
>>> chuck-> /usr/local/bin/mpirun -host `hostname -s` -np 2 /usr/bin/java -cp ./classes HelloWorldMPI
>>> Hello world from rank 0 of 2
>>> Hello world from rank 1 of 2
>>>
>>> You will also need to use this name in any hostfiles or appfiles as well until the bug is fixed.
>>>
>>> Thanks to all for this great product !
>>>
>>> Chuck Mosher for JavaSeis.org <http://javaseis.org/>
>>>
>>>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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