If you build your application with intel compilers and -i8, then openmpi must also be built with intel compilers and -i8.
Cheers, Gilles On Sunday, April 24, 2016, Elio Physics <elio-phys...@live.com> wrote: > Well, I changed the compiler from mpif90 to mpiifort with corresponding > flags -i8 -g and recompiled. i am not getting the segmentation fault > problem anymore and the program runs but later stops with no errors (except > that the Fermi energy was not found!) and with some strange empty files > that are produced something like: fortDgcQe3 fortechvF2 fortMaN6a1 > fortnxoYy1 fortvR5F8q. i still feel something is wrong.. Does anybody > know what are these files? > > > Regards > > > ------------------------------ > *From:* users <users-boun...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','users-boun...@open-mpi.org');>> on behalf > of Ralph Castain <r...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','r...@open-mpi.org');>> > *Sent:* Saturday, April 23, 2016 1:38 PM > *To:* Open MPI Users > *Subject:* Re: [OMPI users] MPIRUN SEGMENTATION FAULT > > 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 > <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','users-boun...@open-mpi.org');>> on behalf > of Andy Riebs <andy.ri...@hpe.com > <javascript:_e(%7B%7D,'cvml','andy.ri...@hpe.com');>> > *Sent:* Saturday, April 23, 2016 12:49 PM > *To:* us...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','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> > <javascript:_e(%7B%7D,'cvml','users-boun...@open-mpi.org');> on behalf of > Ralph Castain <r...@open-mpi.org> > <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','users-boun...@open-mpi.org');>> on behalf > of Elio Physics < <javascript:_e(%7B%7D,'cvml','elio-phys...@live.com');> > elio-phys...@live.com > <javascript:_e(%7B%7D,'cvml','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 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 > <javascript:_e(%7B%7D,'cvml','users-boun...@open-mpi.org');>> on behalf > of Ralph Castain < <javascript:_e(%7B%7D,'cvml','r...@open-mpi.org');> > r...@open-mpi.org <javascript:_e(%7B%7D,'cvml','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 < > <javascript:_e(%7B%7D,'cvml','elio-phys...@live.com');> > elio-phys...@live.com > <javascript:_e(%7B%7D,'cvml','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 <javascript:_e(%7B%7D,'cvml','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/2016/04/29000.php> > http://www.open-mpi.org/community/lists/users/2016/04/29000.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> > 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 > > > > > _______________________________________________ > users mailing listus...@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/2016/04/29005.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/2016/04/29007.php > > >
