I don’t see any way this could be compilation related - I suspect there is simply some error in the program (e.g., forgetting to initialize some memory region).
> On Apr 23, 2016, at 8:03 AM, Elio Physics <elio-phys...@live.com> wrote: > > Hello Andy, > > the program is not mine. I have got it from a group upon request. It might be > program related because I run other codes such as quantum espresso and work > perfectly fine although it is the cluster people who compiled it. Since I > have compiled the program I am having problems with, I am thinking that it > might be "compilation" related. This is why i wanted some experts' opinion on > this > > > > From: users <users-boun...@open-mpi.org <mailto:users-boun...@open-mpi.org>> > on behalf of Andy Riebs <andy.ri...@hpe.com <mailto:andy.ri...@hpe.com>> > Sent: Saturday, April 23, 2016 12:49 PM > To: us...@open-mpi.org <mailto:us...@open-mpi.org> > Subject: Re: [OMPI users] MPIRUN SEGMENTATION FAULT > > The challenge for the MPI experts here (of which I am NOT one!) is that the > problem appears to be in your program; MPI is simply reporting that your > program failed. If you got the program from someone else, you will need to > solicit their help. If you wrote it, well, it is never a bad time to learn to > use gdb! > > Best regards > Andy > > On 04/23/2016 10:41 AM, Elio Physics wrote: >> I am not really an expert with gdb. What is the core file? and how to use >> gdb? I have got three files as an output when the executable is used. One is >> the actual output which stops and the other two are error files (from which >> I knew about the segmentation fault). >> >> >> thanks >> >> >> From: users <users-boun...@open-mpi.org> <mailto:users-boun...@open-mpi.org> >> on behalf of Ralph Castain <r...@open-mpi.org> <mailto:r...@open-mpi.org> >> Sent: Saturday, April 23, 2016 11:39 AM >> To: Open MPI Users >> Subject: Re: [OMPI users] MPIRUN SEGMENTATION FAULT >> >> valgrind isn’t going to help here - there are multiple reasons why your >> application could be segfaulting. Take a look at the core file with gdb and >> find out where it is failing. >> >>> On Apr 22, 2016, at 10:20 PM, Elio Physics <elio-phys...@live.com >>> <mailto:elio-phys...@live.com>> wrote: >>> >>> One more thing i forgot to mention in my previous e-mail. In the output >>> file I get the following message: >>> >>> >>> 2 total processes killed (some possibly by mpirun during cleanup) >>> >>> Thanks >>> >>> >>> >>> From: users <users-boun...@open-mpi.org >>> <mailto:users-boun...@open-mpi.org>> on behalf of Elio Physics < >>> <mailto:elio-phys...@live.com>elio-phys...@live.com >>> <mailto:elio-phys...@live.com>> >>> Sent: Saturday, April 23, 2016 3:07 AM >>> To: Open MPI Users >>> Subject: Re: [OMPI users] MPIRUN SEGMENTATION FAULT >>> >>> I have used valgrind and this is what i got: >>> >>> valgrind mpirun ~/Elie/SPRKKR/bin/kkrscf6.3MPI Fe_SCF.inp > >>> scf-51551.jlborges.fisica.ufmg.br.out >>> ==8135== Memcheck, a memory error detector >>> ==8135== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. >>> ==8135== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info >>> ==8135== Command: mpirun /home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI >>> Fe_SCF.inp >>> ==8135== >>> -------------------------------------------------------------------------- >>> mpirun noticed that process rank 0 with PID 8147 on node >>> jlborges.fisica.ufmg.br <http://jlborges.fisica.ufmg.br/> exited on signal >>> 11 (Segmentation fault). >>> -------------------------------------------------------------------------- >>> ==8135== >>> ==8135== HEAP SUMMARY: >>> ==8135== in use at exit: 485,683 bytes in 1,899 blocks >>> ==8135== total heap usage: 7,723 allocs, 5,824 frees, 12,185,660 bytes >>> allocated >>> ==8135== >>> ==8135== LEAK SUMMARY: >>> ==8135== definitely lost: 34,944 bytes in 34 blocks >>> ==8135== indirectly lost: 26,613 bytes in 58 blocks >>> ==8135== possibly lost: 0 bytes in 0 blocks >>> ==8135== still reachable: 424,126 bytes in 1,807 blocks >>> ==8135== suppressed: 0 bytes in 0 blocks >>> ==8135== Rerun with --leak-check=full to see details of leaked memory >>> ==8135== >>> ==8135== For counts of detected and suppressed errors, rerun with: -v >>> ==8135== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 6 from 6) >>> >>> What does that supposed to mean? >>> >>> Regards >>> From: users <users-boun...@open-mpi.org >>> <mailto:users-boun...@open-mpi.org>> on behalf of Ralph Castain < >>> <mailto:r...@open-mpi.org>r...@open-mpi.org <mailto:r...@open-mpi.org>> >>> Sent: Saturday, April 23, 2016 1:36:50 AM >>> To: Open MPI Users >>> Subject: Re: [OMPI users] MPIRUN SEGMENTATION FAULT >>> >>> All I can say is that your program segfault’d during execution - you might >>> want to look at the core file using a debugger like gdb to see why it >>> failed. >>> >>> >>>> On Apr 22, 2016, at 8:32 PM, Elio Physics < >>>> <mailto:elio-phys...@live.com>elio-phys...@live.com >>>> <mailto:elio-phys...@live.com>> wrote: >>>> >>>> Dear all, >>>> >>>> I have successfully compiled a code where the executable have been >>>> produced. However when I started using the executable with mpirun, the >>>> code stopped with the following error: >>>> >>>> "mpirun noticed that process rank 0 with PID 570 on node compute-1-9.local >>>> exited on signal 11 (Segmentation fault)." >>>> >>>> What is that error due to? and How can i solve it? >>>> >>>> I will post the make.inc compilation file: >>>> >>>> BUILD_TYPE ?= >>>> #BUILD_TYPE := debug >>>> >>>> VERSION = 6.3 >>>> >>>> ifeq ($(BUILD_TYPE), debug) >>>> VERSION := $(VERSION)$(BUILD_TYPE) >>>> endif >>>> >>>> BIN =~/Elie/SPRKKR/bin >>>> #BIN=~/bin >>>> #BIN=/tmp/$(USER) >>>> >>>> LIB = -L/opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64 >>>> -L/opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64 >>>> -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 >>>> -lmkl_core -lmkl_sequential -lmkl_blacs_i >>>> ntelmpi_ilp64 -lpthread -lm -ldl >>>> >>>> #Include mpif.h >>>> INCLUDE = -I/opt/intel/mkl/include/intel64/ilp64 >>>> -I/opt/intel/mkl/lib/include >>>> >>>> #FFLAGS >>>> FFLAGS = -O2 >>>> >>>> FC = mpif90 -c $(FFLAGS) $(INCLUDE) >>>> LINK = mpif90 $(FFLAGS) $(INCLUDE) >>>> >>>> MPI=MPI >>>> >>>> Thanks in advance >>>> >>>> Elio >>>> University of Rondonia, brazil >>>> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>> Subscription: >>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users>http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>> Link to this post: >>>> <http://www.open-mpi.org/community/lists/users/2016/04/29000.php>http://www.open-mpi.org/community/lists/users/2016/04/29000.php >>>> <http://www.open-mpi.org/community/lists/users/2016/04/29000.php> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>> Subscription: >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users>http://www.open-mpi.org/mailman/listinfo.cgi/users >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>> Link to this post: >>> <http://www.open-mpi.org/community/lists/users/2016/04/29003.php>http://www.open-mpi.org/community/lists/users/2016/04/29003.php >>> <http://www.open-mpi.org/community/lists/users/2016/04/29003.php> >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org <mailto:us...@open-mpi.org> >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/04/29005.php >> <http://www.open-mpi.org/community/lists/users/2016/04/29005.php> > _______________________________________________ > users mailing list > us...@open-mpi.org <mailto:us...@open-mpi.org> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > <http://www.open-mpi.org/mailman/listinfo.cgi/users> > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/04/29007.php > <http://www.open-mpi.org/community/lists/users/2016/04/29007.php>
