Howard, I have no infinipath hardware, but the infinipath libraries are installed. I tried to run with --mca mtl_psm_priority 0 instead of --mca mtl ^psm but that did not work. without psm mtl, I was unable to reproduce the persistent communication issue, so I concluded there was only one issue here.
do you configure with --disable-dlopen on hopper ? I wonder whether --mca mtl ^psm is effective if dlopen is disabled Cheers, Gilles On Saturday, August 15, 2015, Howard Pritchard <hpprit...@gmail.com> wrote: > Hi Jeff, > > I don't know why Gilles keeps picking on the persistent request problem > and mixing > it up with this user bug. I do think for this user the psm probably is > the problem. > > > They don't have anything to do with each other. > > I can reproduce the persistent request problem on hopper consistently. As > I said > on the telecon last week it has something to do with memory corruption > with the > receive buffer that is associated with the persistent request. > > Howard > > > 2015-08-14 11:21 GMT-06:00 Jeff Squyres (jsquyres) <jsquy...@cisco.com > <javascript:_e(%7B%7D,'cvml','jsquy...@cisco.com');>>: > >> Hmm. Oscar's not around to ask any more, but I'd be greatly surprised if >> he had InfiniPath on his systems where he ran into this segv issue...? >> >> >> > On Aug 14, 2015, at 1:08 PM, Howard Pritchard <hpprit...@gmail.com >> <javascript:_e(%7B%7D,'cvml','hpprit...@gmail.com');>> wrote: >> > >> > Hi Gilles, >> > >> > Good catch! Nate we hadn't been testing on a infinipath system. >> > >> > Howard >> > >> > >> > 2015-08-14 0:20 GMT-06:00 Gilles Gouaillardet <gil...@rist.or.jp >> <javascript:_e(%7B%7D,'cvml','gil...@rist.or.jp');>>: >> > Nate, >> > >> > i could get rid of the problem by not using the psm mtl. >> > the infinipath library (used by the psm mtl) sets some signal handlers >> that conflict with the JVM >> > that can be seen by running >> > mpirun -np 1 java -Xcheck:jni MPITestBroke data/ >> > >> > so instead of running >> > mpirun -np 1 java MPITestBroke data/ >> > please run >> > mpirun --mca mtl ^psm -np 1 java MPITestBroke data/ >> > >> > that solved the issue for me >> > >> > Cheers, >> > >> > Gilles >> > >> > On 8/13/2015 9:19 AM, Nate Chambers wrote: >> >> I appreciate you trying to help! I put the Java and its compiled >> .class file on Dropbox. The directory contains the .java and .class files, >> as well as a data/ directory: >> >> >> >> >> http://www.dropbox.com/sh/pds5c5wecfpb2wk/AAAcz17UTDQErmrUqp2SPjpqa?dl=0 >> >> >> >> You can run it with and without MPI: >> >> >> >> > java MPITestBroke data/ >> >> > mpirun -np 1 java MPITestBroke data/ >> >> >> >> Attached is a text file of what I see when I run it with mpirun and >> your debug flag. Lots of debug lines. >> >> >> >> >> >> Nate >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Aug 12, 2015 at 11:09 AM, Howard Pritchard < >> hpprit...@gmail.com <javascript:_e(%7B%7D,'cvml','hpprit...@gmail.com');>> >> wrote: >> >> Hi Nate, >> >> >> >> Sorry for the delay in getting back to you. >> >> We're somewhat stuck on how to help you, but here are two suggestions. >> >> >> >> Could you add the following to your launch command line >> >> >> >> --mca odls_base_verbose 100 >> >> >> >> so we can see exactly what arguments are being feed to java when >> launching >> >> your app. >> >> >> >> Also, if you could put your MPITestBroke.class file somewhere (like >> google drive) >> >> where we could get it and try to run locally or at NERSC, that might >> help us >> >> narrow down the problem. Better yet, if you have the class or jar >> file for >> >> the entire app plus some data sets, we could try that out as well. >> >> >> >> All the config outputs, etc. you've sent so far indicate a correct >> installation >> >> of open mpi. >> >> >> >> Howard >> >> >> >> >> >> On Aug 6, 2015 1:54 PM, "Nate Chambers" <ncham...@usna.edu >> <javascript:_e(%7B%7D,'cvml','ncham...@usna.edu');>> wrote: >> >> Howard, >> >> >> >> I tried the nightly build openmpi-dev-2223-g731cfe3 and it still >> segfaults as before. I must admit I am new to MPI, so is it possible I'm >> just configuring or running incorrectly? Let me list my steps for you, and >> maybe something will jump out? Also attached is my config.log. >> >> >> >> >> >> CONFIGURE >> >> ./configure --prefix=<install-dir> --enable-mpi-java CC=gcc >> >> >> >> MAKE >> >> make all install >> >> >> >> RUN >> >> <install-dir>/mpirun -np 1 java MPITestBroke twitter/ >> >> >> >> >> >> DEFAULT JAVA AND GCC >> >> >> >> $ java -version >> >> java version "1.7.0_21" >> >> Java(TM) SE Runtime Environment (build 1.7.0_21-b11) >> >> Java HotSpot(TM) 64-Bit Server VM (build 23.21-b01, mixed mode) >> >> >> >> $ gcc --v >> >> Using built-in specs. >> >> Target: x86_64-redhat-linux >> >> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man >> --infodir=/usr/share/info --with-bugurl= >> http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared >> --enable-threads=posix --enable-checking=release --with-system-zlib >> --enable-__cxa_atexit --disable-libunwind-exceptions >> --enable-gnu-unique-object >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada >> --enable-java-awt=gtk --disable-dssi >> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre >> --enable-libgcj-multifile --enable-java-maintainer-mode >> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib >> --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 >> --build=x86_64-redhat-linux >> >> Thread model: posix >> >> gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) >> >> >> >> >> >> >> >> >> >> >> >> On Thu, Aug 6, 2015 at 7:58 AM, Howard Pritchard <hpprit...@gmail.com >> <javascript:_e(%7B%7D,'cvml','hpprit...@gmail.com');>> wrote: >> >> HI Nate, >> >> >> >> We're trying this out on a mac running mavericks and a cray xc >> system. the mac has java 8 >> >> while the cray xc has java 7. >> >> >> >> We could not get the code to run just using the java launch command, >> although we noticed if you add >> >> >> >> catch(NoClassDefFoundError e) { >> >> >> >> System.out.println("Not using MPI its out to lunch for now"); >> >> >> >> } >> >> >> >> as one of the catches after the try for firing up MPI, you can get >> further. >> >> >> >> Instead we tried on the two systems using >> >> >> >> mpirun -np 1 java MPITestBroke tweets repeat.txt >> >> >> >> and, you guessed it, we can't reproduce the error, at least using >> master. >> >> >> >> Would you mind trying to get a copy of nightly master build off of >> >> >> >> http://www.open-mpi.org/nightly/master/ >> >> and install that version and give it a try. >> >> >> >> If that works, then I'd suggest using master (or v2.0) for now. >> >> Howard >> >> >> >> >> >> >> >> >> >> 2015-08-05 14:41 GMT-06:00 Nate Chambers <ncham...@usna.edu >> <javascript:_e(%7B%7D,'cvml','ncham...@usna.edu');>>: >> >> Howard, >> >> >> >> Thanks for looking at all this. Adding System.gc() did not cause it to >> segfault. The segfault still comes much later in the processing. >> >> >> >> I was able to reduce my code to a single test file without other >> dependencies. It is attached. This code simply opens a text file and reads >> its lines, one by one. Once finished, it closes and opens the same file and >> reads the lines again. On my system, it does this about 4 times until the >> segfault fires. Obviously this code makes no sense, but it's based on our >> actual code that reads millions of lines of data and does various >> processing to it. >> >> >> >> Attached is a tweets.tgz file that you can uncompress to have an input >> directory. The text file is just the same line over and over again. Run it >> as: >> >> >> >> java MPITestBroke tweets/ >> >> >> >> >> >> Nate >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Aug 5, 2015 at 8:29 AM, Howard Pritchard <hpprit...@gmail.com >> <javascript:_e(%7B%7D,'cvml','hpprit...@gmail.com');>> wrote: >> >> 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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >> >> >> >> >> >> _______________________________________________ >> >> users mailing list >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27396.php >> >> >> >> >> >> _______________________________________________ >> >> users mailing list >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27399.php >> >> >> >> >> >> _______________________________________________ >> >> users mailing list >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27405.php >> >> >> >> >> >> _______________________________________________ >> >> users mailing list >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27406.php >> >> >> >> _______________________________________________ >> >> users mailing list >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27446.php >> >> >> >> >> >> >> >> _______________________________________________ >> >> users mailing list >> >> >> >> us...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','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/2015/08/27450.php >> > >> > >> > _______________________________________________ >> > users mailing list >> > us...@open-mpi.org <javascript:_e(%7B%7D,'cvml','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/2015/08/27465.php >> > >> > _______________________________________________ >> > users mailing list >> > us...@open-mpi.org <javascript:_e(%7B%7D,'cvml','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/2015/08/27471.php >> >> >> -- >> Jeff Squyres >> jsquy...@cisco.com <javascript:_e(%7B%7D,'cvml','jsquy...@cisco.com');> >> For corporate legal information go to: >> http://www.cisco.com/web/about/doing_business/legal/cri/ >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org <javascript:_e(%7B%7D,'cvml','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/2015/08/27472.php >> > >
