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). >>> >>> -------------------------------------------------------------------------- >>> >>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2015/08/27386.php >>> >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2015/08/27389.php >> > > > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/08/27391.php >
