Hi guys
I figured out what the problem was: my code uses the HDF(5) library, and the
version I had installed was compiled with parallel I/O support and linked to
OMPI 2.1.1. In the end I was only linking my code with OMPI 3.0.0, but
something in there got confused and it led to the crash.
Recompiling HDF5 with OMPI 3.0.0 fixed the whole thing.
Sorry about bothering you with this,
Thanks again for your help,
Ricardo
> Message: 1
> Date: Tue, 12 Dec 2017 20:00:25 +0000
> From: "Jeff Squyres (jsquyres)" <jsquy...@cisco.com>
>
> I am unable to reproduce your error with Open MPI v3.0.0 on the latest stable
> MacOS High Sierra.
>
> Given that you're failing in MPI_INIT, it feels like the application
> shouldn't matter. But regardless, can you test with the trivial Fortran test
> programs in the examples/ directory in the Open MPI tarball?
>
>
>
>> On Dec 11, 2017, at 11:21 PM, r...@open-mpi.org wrote:
>>
>> FWIW: I just cloned the v3.0.x branch to get the latest 3.0.1 release
>> candidate, built and ran it on Mac OSX High Sierra. Everything built and ran
>> fine for both C and Fortran codes.
>>
>> You might want to test the same - could be this was already fixed.
>>
>>> On Dec 11, 2017, at 12:43 PM, Ricardo Parreira de Azambuja Fonseca
>>> <ricardo.fons...@ist.utl.pt> wrote:
>>>
>>> Hi guys
>>>
>>> I?m having problems with a Fortran based code that I develop with OpenMPI
>>> 3.0.0 on Mac OS X. The problem shows itself with both gfortran and intel
>>> ifort compilers, and it runs perfectly with version 2.1.2 (and earlier
>>> versions).
>>>
>>> Launching the code, even without using mpiexec, causes a segfault when my
>>> code calls mpi_init()
>>>
>>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> reference.
>>>
>>> Backtrace for this error:
>>> #0 0x1107a41fc
>>> (?)
>>> #10 0x10f86eff1
>>> Segmentation fault: 11
>>>
>>> Recompiling OpenMPI with ?enable-debug, and launching the code through lldb
>>> gives:
>>>
>>> (lldb) run
>>> Process 65169 launched: '../source/build/osiris.e' (x86_64)
>>> Process 65169 stopped
>>> * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS
>>> (code=1, address=0x48)
>>> frame #0: 0x0000000100fbe79a
>>> libmpi.40.dylib`ompi_hook_base_mpi_init_top_post_opal(argc=0,
>>> argv=0x0000000000000000, requested=0, provided=0x00007ffeefbfe290) at
>>> hook_base.c:278
>>> 275
>>> 276 void ompi_hook_base_mpi_init_top_post_opal(int argc, char
>>> **argv, int requested, int *provided)
>>> 277 {
>>> -> 278 HOOK_CALL_COMMON( mpi_init_top_post_opal, argc, argv,
>>> requested, provided);
>>> 279 }
>>> 280
>>> 281 void ompi_hook_base_mpi_init_bottom(int argc, char **argv, int
>>> requested, int *provided)
>>> Target 0: (osiris.e) stopped.
>>> (lldb) bt
>>> * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS
>>> (code=1, address=0x48)
>>> * frame #0: 0x0000000100fbe79a
>>> libmpi.40.dylib`ompi_hook_base_mpi_init_top_post_opal(argc=0,
>>> argv=0x0000000000000000, requested=0, provided=0x00007ffeefbfe290) at
>>> hook_base.c:278
>>> frame #1: 0x0000000100dce0ff libmpi.40.dylib`ompi_mpi_init(argc=0,
>>> argv=0x0000000000000000, requested=0, provided=0x00007ffeefbfe290) at
>>> ompi_mpi_init.c:486
>>> frame #2: 0x0000000100eb3f38
>>> libmpi.40.dylib`PMPI_Init(argc=0x00007ffeefbfe2d0, argv=0x00007ffeefbfe2c8)
>>> at pinit.c:66
>>> frame #3: 0x0000000100cceb0b
>>> libmpi_mpifh.40.dylib`ompi_init_f(ierr=0x00007ffeefbfe9f8) at init_f.c:84
>>> frame #4: 0x0000000100ccead5
>>> libmpi_mpifh.40.dylib`mpi_init_(ierr=0x00007ffeefbfe9f8) at init_f.c:65
>>> frame #5: 0x0000000100004e5a osiris.e`__m_system_MOD_system_init at
>>> os-sys-multi.f03:323
>>> frame #6: 0x000000010036edb5 osiris.e`MAIN__ at os-main.f03:36
>>> frame #7: 0x000000010039eff2 osiris.e`main at memory.h:19
>>> frame #8: 0x00007fff6ee7d115 libdyld.dylib`start + 1
>>>
>>> Any thoughts?
>>>
>>> Thanks in advance,
>>> Ricardo
>>>
>>> ?
>>> Ricardo Fonseca
>>>
>>> Full Professor | Professor Catedr?tico
>>> GoLP - Grupo de Lasers e Plasmas
>>> Instituto de Plasmas e Fus?o Nuclear
>>> Instituto Superior T?cnico
>>> Av. Rovisco Pais
>>> 1049-001 Lisboa
>>> Portugal
>>>
>>> tel: +351 21 8419202
>>> web: http://epp.tecnico.ulisboa.pt/
>>> _______________________________________________
>>> users mailing list
>>> users@lists.open-mpi.org
>>> https://lists.open-mpi.org/mailman/listinfo/users
>>
>> _______________________________________________
>> users mailing list
>> users@lists.open-mpi.org
>> https://lists.open-mpi.org/mailman/listinfo/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
—
Ricardo Fonseca
Full Professor | Professor Catedrático
GoLP - Grupo de Lasers e Plasmas
Instituto de Plasmas e Fusão Nuclear
Instituto Superior Técnico
Av. Rovisco Pais
1049-001 Lisboa
Portugal
tel: +351 21 8419202
web: http://epp.tecnico.ulisboa.pt/
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