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Subject: Re: [OMPI users] Segmentation fault with plenty of RAM
From: George Bosilca (bosilca_at_[hidden])
Date: 2010-02-19 09:21:53


I'm puzzled by the fact that the problem might come from the gfortran compiler. I use it daily on my MAC, with LAPACK and BLAS, and so far I didn't has any strange problems. If it can help I use the gfortran precompiler compiler from MAC HPC (

I might have another hint on this. I had similar errors in the past, due to a mismatch between the version of Open MPI used for linking and the one used at runtime. The MAC compiler don't play by the same rules as the normal gcc. The order in which the libraries are linked in your application is slightly different (system libraries have priority). As all 10.5 version Leopard contain a version of Open MPI you have to make sure that the Open MPI library you compile against is the one used at runtime. For this purpose you can use the "otool -L" (similar to ldd on Linux) to see which Open MPI library you linked against (the one you compiler or the one provided by the OS), and then check your $PATH to make sure you use the corresponding executables (mpicc, mpirun and orted).


On Feb 16, 2010, at 22:40 , Christopher O'Brien wrote:

> Trent,
> Thanks for the prompt reply and advice.
> I had made a similar post similar on the Quantum-Espresso help forum and received some helpful advice. It turns out that the problem is not in libSystem.B.dylib (this a Mac system library); The cause of the error was due to using the Mac system LAPACK and BLAS shared libraries. I had to build my own and link to those. It may have to do with using GFORTRAN to compile the program rather than Mac's GCC (which does not have FORTRAN support).
> Oh well, I guess I leaned much more about making programs on BSD today...
> Regards,
> Chris
> On Feb 16, 2010, at 5:23 PM, Trent Creekmore wrote:
>> Christopher,
>> Segmentation faults has nothing to do with amount of memory you have in your
>> system.
>> Rather is has to do with memory access. A segmentation fault occurs as a
>> result of the program trying to access outside the bounds of memory
>> locations that have been set aside for storage at compile time.
>> These are usually caused by programmer error in the code. libSystem.B.dylib
>> could possibly have a bug in it, in which the developers of it either know
>> and about and have fixed it, in the process of fixing it, or need to know
>> about it. You may want to try to get the latest version of it before you
>> look further. Though I am new to OpenMPI myself and really have not had a
>> chance to really dig into it yet, the problem could be elsewhere besides in
>> libSystem.B.dylib.
>> But hopefully someone else here has had similar experience and knows exactly
>> what to do.
>> If you had a shortage of memory, the OS would start doing more and page
>> swaps on the "swap drive" and you would notice this by the system getting
>> painfully slow.
>> Trent
>> -----Original Message-----
>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
>> Behalf Of Christopher O'Brien
>> Sent: Tuesday, February 16, 2010 8:33 AM
>> To: users_at_[hidden]
>> Subject: [OMPI users] Segmentation fault with plenty of RAM
>> To all,
>> I am trying to start work with Quantum Espresso (
>> on my MacBook Pro (running 10.6.2 with 64-bit kernel extensions enabled)
>> using 2GB of ram and an Intel Core2 Duo. Keep in mind that I am not really
>> an expert and I have a very bad track record in compiling applications.
>> I received no errors when compiling the latest versions of FFTW, openmpi,
>> and lapack (which were found by QE's configure program). I ran the basic
>> Openmpi tests included with the distribution, and found no problems. I have
>> modified my path to use the MPI compiler wrappers that I compiled, as Mac's
>> built in openmpi does not have F90/F77 support.
>> Someone reported a similar problem to the error reported below on this forum
>> ( but it may
>> or not be relevant. The problem does not seem to be in one executable of the
>> package ('bands.x') exclusively, but libSystem.B.dylib always seems to be in
>> the middle of things. However, I tracked the memory usage but the example
>> never used more than 40MB.
>> The error message resulting from "example01" follows:
>> running the symmetry analysis for Si bands...[schrodingersdog:00322] ***
>> Process received signal ***
>> [schrodingersdog:00322] Signal: Segmentation fault (11)
>> [schrodingersdog:00322] Signal code: Address not mapped (1)
>> [schrodingersdog:00322] Failing at address: 0x698d3230
>> [schrodingersdog:00322] [ 0] 2 libSystem.B.dylib
>> 0x00007fff87248eaa _sigtramp + 26
>> [schrodingersdog:00322] [ 1] 3 ???
>> 0x00000001013fc080 0x0 + 4315922560
>> [schrodingersdog:00322] [ 2] 4 bands.x
>> 0x000000010003d3ed sym_band_ + 7597
>> [schrodingersdog:00322] [ 3] 5 bands.x
>> 0x00000001000014f5 MAIN__ + 1317
>> [schrodingersdog:00322] [ 4] 6 bands.x
>> 0x0000000100001a01 main + 33
>> [schrodingersdog:00322] [ 5] 7 bands.x
>> 0x0000000100000fa4 start + 52
>> [schrodingersdog:00322] [ 6] 8 ???
>> 0x0000000000000001 0x0 + 1
>> [schrodingersdog:00322] *** End of error message ***
>> ./run_example: line 77: 322 Segmentation fault $BANDS_COMMAND <
>> > si.bands.out
>> done
>> cleaning /Users/ChrisOBrien/tmp... done
>> Thanks in advance,
>> Chris
>> ===================================================================
>> Christopher J. O'Brien
>> cjobrien_at_[hidden]
>> See what I'm citing at
>> Graduate Research Assistant
>> Computational Materials Group
>> Department of Materials Science & Engineering
>> North Carolina State University
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