Hi Nate, Sorry for the delay in getting back. Thanks for the sanity check. You may have a point about the args string to MPI.init - there's nothing the Open MPI is needing from this but that is a difference with your use case - your app has an argument.
Would you mind adding a System.gc() call immediately after MPI.init call and see if the gc blows up with a segfault? Also, may be interesting to add the -verbose:jni to your command line. We'll do some experiments here with the init string arg. Is your app open source where we could download it and try to reproduce the problem locally? thanks, Howard 2015-08-04 18:52 GMT-06:00 Nate Chambers <ncham...@usna.edu>: > Sanity checks pass. Both Hello and Ring.java run correctly with the > expected program's output. > > Does MPI.init(args) expect anything from those command-line args? > > > Nate > > > On Tue, Aug 4, 2015 at 12:26 PM, Howard Pritchard <hpprit...@gmail.com> > wrote: > >> 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 >>> >> >> >> _______________________________________________ >> 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/2015/08/27392.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/2015/08/27393.php >
