Try pure PGI and pure GCC builds. If only the mixed one fails, then I saw a problem like this in MPICH a few months ago. It appears PGI does not play nice with GCC regarding the C standard library functions. Or at least that's what I concluded. The issue remains unresolved.
Jeff Sent from my iPhone > On Dec 24, 2013, at 5:10 AM, "Jeff Squyres (jsquyres)" <jsquy...@cisco.com> > wrote: > > I'm *very loosely* checking email. :-) > > Agree with what Ralph said: it looks like your program called memalign, and > that ended up segv'ing. That could be an OMPI problem, or it could be an > application problem. Try also configuring OMPI --with-valgrind and running > your app through a memory-checking debugger (although OMPI is not very > valgrind-clean in the 1.6 series :-\ -- you'll get a bunch of false positives > about reads from unallocated and memory being left still-allocated after > MPI_FINALIZE). > > > >> On Dec 23, 2013, at 7:17 PM, Ralph Castain <r...@open-mpi.org> wrote: >> >> I fear that Jeff and Brian are both out for the holiday, Gus, so we are >> unlikely to have much info on this until they return >> >> I'm unaware of any such problems in 1.6.5. It looks like something isn't >> properly aligned in memory - could be an error on our part, but might be in >> the program. You might want to build a debug version and see if that >> segfaults, and then look at the core with gdb to see where it happened. >> >> >>> On Dec 23, 2013, at 3:27 PM, Gus Correa <g...@ldeo.columbia.edu> wrote: >>> >>> Dear OMPI experts >>> >>> I have been using OMPI 1.6.5 built with gcc 4.4.7 and >>> PGI pgfortran 11.10 to successfully compile and run >>> a large climate modeling program (CESM) in several >>> different configurations. >>> >>> However, today I hit a segmentation fault when running a new model >>> configuration. >>> [In the climate modeling jargon, a program is called a "model".] >>> >>> This is somewhat unpleasant because that OMPI build >>> is a central piece of the production CESM model setup available >>> to all users in our two clusters at this point. >>> I have other OMPI 1.6.5 builds, with other compilers, but that one >>> was working very well with CESM, until today. >>> >>> Unless I am misinterpreting it, the error message, >>> reproduced below, seems to indicate the problem >>> happened inside the OMPI library. >>> Or not? >>> >>> Other details: >>> >>> Nodes are AMD Opteron 6376 x86_64, interconnect is Infiniband QDR, >>> OS is stock CentOS 6.4, kernel 2.6.32-358.2.1.el6.x86_64. >>> The program is compiled with the OMPI wrappers (mpicc and mpif90), >>> and somewhat conservative optimization flags: >>> >>> FFLAGS := $(CPPDEFS) -i4 -gopt -Mlist -Mextend -byteswapio >>> -Minform=inform -traceback -O2 -Mvect=nosse -Kieee >>> >>> Is this a known issue? >>> Any clues on how to address it? >>> >>> Thank you for your help, >>> Gus Correa >>> >>> **************** error message ******************* >>> >>> [1,31]<stderr>:[node30:17008] *** Process received signal *** >>> [1,31]<stderr>:[node30:17008] Signal: Segmentation fault (11) >>> [1,31]<stderr>:[node30:17008] Signal code: Address not mapped (1) >>> [1,31]<stderr>:[node30:17008] Failing at address: 0x17 >>> [1,31]<stderr>:[node30:17008] [ 0] /lib64/libpthread.so.0(+0xf500) >>> [0x2b788ef9f500] >>> [1,31]<stderr>:[node30:17008] [ 1] >>> /sw/openmpi/1.6.5/gnu-4.4.7-pgi-11.10/lib/libmpi.so.1(+0x100ee3) >>> [0x2b788e200ee3] >>> [1,31]<stderr>:[node30:17008] [ 2] >>> /sw/openmpi/1.6.5/gnu-4.4.7-pgi-11.10/lib/libmpi.so.1(opal_memory_ptmalloc2_int_malloc+0x111) >>> [0x2b788e203771] >>> [1,31]<stderr>:[node30:17008] [ 3] >>> /sw/openmpi/1.6.5/gnu-4.4.7-pgi-11.10/lib/libmpi.so.1(opal_memory_ptmalloc2_int_memalign+0x97) >>> [0x2b788e2046d7] >>> [1,31]<stderr>:[node30:17008] [ 4] >>> /sw/openmpi/1.6.5/gnu-4.4.7-pgi-11.10/lib/libmpi.so.1(opal_memory_ptmalloc2_memalign+0x8b) >>> [0x2b788e2052ab] >>> [1,31]<stderr>:[node30:17008] [ 5] ./ccsm.exe(pgf90_auto_alloc+0x73) >>> [0xe2c4c3] >>> [1,31]<stderr>:[node30:17008] *** End of error message *** >>> -------------------------------------------------------------------------- >>> mpiexec noticed that process rank 31 with PID 17008 on node node30 exited >>> on signal 11 (Segmentation fault). >>> -------------------------------------------------------------------------- >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > 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 > http://www.open-mpi.org/mailman/listinfo.cgi/users
