External Email - Use Caution
Adding more details provided by my user:
The crash only happens when loading surface files, either via the -f flag from
the CLI or directly through the GUI. Could this be an issue with the surface
files or the manner in which they are created?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of TRISTAN J PAUTSCH
<freesurfer-boun...@nmr.mgh.harvard.edu>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution
Greetings all, I'll try to keep this succinct.
I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I
used the stable 6.0/CentOS 6 download, in addition to the dev version of
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview
launches fine and stays open when launched alone, however attempting to open a
volume (either through the GUI or directly via the CLI) causes a crash and the
following error about 5-8 seconds after launching (brain images begin to
populate, then crash):
---
[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 xxxxxxx by xxxxxxx Tue Aug 20
13:44:15 2019
[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)
---
I've seen a number of other posts on the mailing list about this, but all of
them I could find either end abruptly without a solution or with an unanswered
request for more info.
Happy to provide any additional information or anything that may aid in the
resolution of this issue.
Thanks everyone,
~T
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