Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it
crash?
thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can
always restore it by renaming the temporary file (wm.mgz~) but it obviously
doen't save any changes.
I've tried different computers (same FS version) and on some it works and on
some the same problem occurs. I just tried it on the 6.0.0beta version and it
saved like a charm. I would rather, however, keep editing my data with the same
version.
Here is the error message I get in the terminal:
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30
17:22:55 2015
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)
Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn
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