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Subject: Re: [OMPI users] Segmentation fault with plenty of RAM
From: Trent Creekmore (mtcreekmore_at_[hidden])
Date: 2010-02-16 17:23:42


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 (www.quantum_espresso.org)
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
(http://www.open-mpi.org/community/lists/users/2008/08/6348.php) 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.in > si.bands.out
done
cleaning /Users/ChrisOBrien/tmp... done

Thanks in advance,
Chris

===================================================================
Christopher J. O'Brien
cjobrien_at_[hidden]
http://www4.ncsu.edu/~cjobrien/index.html
See what I'm citing at http://www.citeulike.org/cjo123

Graduate Research Assistant
Computational Materials Group
Department of Materials Science & Engineering
North Carolina State University
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