Hello Nate,

As a sanity check of your installation, could you try to compile the
examples/*.java codes using the mpijavac you've installed and see that
those run correctly?
I'd be just interested in the Hello.java and Ring.java?

Howard







2015-08-04 14:34 GMT-06:00 Nate Chambers <ncham...@usna.edu>:

> Sure, I reran the configure with CC=gcc and then make install. I think
> that's the proper way to do it. Attached is my config log. The behavior
> when running our code appears to be the same. The output is the same error
> I pasted in my email above. It occurs when calling MPI.init().
>
> I'm not great at debugging this sort of stuff, but happy to try things out
> if you need me to.
>
> Nate
>
>
> On Tue, Aug 4, 2015 at 5:09 AM, Howard Pritchard <hpprit...@gmail.com>
> wrote:
>
>> Hello Nate,
>>
>> As a first step to addressing this, could you please try using gcc rather
>> than the Intel compilers to build Open MPI?
>>
>> We've been doing a lot of work recently on the java bindings, etc. but
>> have never tried using any compilers other
>> than gcc when working with the java bindings.
>>
>> Thanks,
>>
>> Howard
>>
>>
>> 2015-08-03 17:36 GMT-06:00 Nate Chambers <ncham...@usna.edu>:
>>
>>> We've been struggling with this error for a while, so hoping someone
>>> more knowledgeable can help!
>>>
>>> Our java MPI code exits with a segfault during its normal operation, *but
>>> the segfault occurs before our code ever uses MPI functionality like
>>> sending/receiving. *We've removed all message calls and any use of
>>> MPI.COMM_WORLD from the code. The segfault occurs if we call MPI.init(args)
>>> in our code, and does not if we comment that line out. Further vexing us,
>>> the crash doesn't happen at the point of the MPI.init call, but later on in
>>> the program. I don't have an easy-to-run example here because our non-MPI
>>> code is so large and complicated. We have run simpler test programs with
>>> MPI and the segfault does not occur.
>>>
>>> We have isolated the line where the segfault occurs. However, if we
>>> comment that out, the program will run longer, but then randomly (but
>>> deterministically) segfault later on in the code. Does anyone have tips on
>>> how to debug this? We have tried several flags with mpirun, but no good
>>> clues.
>>>
>>> We have also tried several MPI versions, including stable 1.8.7 and the
>>> most recent 1.8.8rc1
>>>
>>>
>>> ATTACHED
>>> - config.log from installation
>>> - output from `ompi_info -all`
>>>
>>>
>>> OUTPUT FROM RUNNING
>>>
>>> > mpirun -np 2 java -mx4g FeaturizeDay datadir/ days.txt
>>> ...
>>> some normal output from our code
>>> ...
>>>
>>> --------------------------------------------------------------------------
>>> mpirun noticed that process rank 0 with PID 29646 on node r9n69 exited
>>> on signal 11 (Segmentation fault).
>>>
>>> --------------------------------------------------------------------------
>>>
>>>
>>>
>>>
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>>
>>
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