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Subject: Re: [OMPI users] Segmentation fault on OMPI 1.6.5 built with gcc 4.4.7 and PGI pgfortran 11.10
From: Jeff Hammond (jeff.science_at_[hidden])
Date: 2013-12-24 10:17:30


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)" <jsquyres_at_[hidden]> 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 <rhc_at_[hidden]> 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 <gus_at_[hidden]> 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).
>>> --------------------------------------------------------------------------
>>>
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>>
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>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
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