Re: [Freesurfer] freeview fault: PETSC Error ... PERSISTENT - Freesurfer

10 Nov 2014

      Hi Nick,
I downloaded the most recent version of freeview.bin using wget as you suggested and ran it on two different machines.
It appeared to load a volume file fully whereas before it was crashing when showing it had loaded only 1%.
But it still crashes after that with the message below my signature.
I tried a few different .mgz files including the original one with the same result.  Both the machines on which I ran it have 8 GBytes of RAM.  Any other thoughts would be welcome.
Regards,
Don
[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#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find m
emory 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 donHome1TB by kriegerd Mon Nov 10 13:48:15 2014
[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-sha
red=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
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-----Original Message-----
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From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-
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bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH
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Sent: Tuesday, November 04, 2014 11:59 PM
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To: Freesurfer support list
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Subject: Re: [Freesurfer] freeview fault: PETSC Error ...
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you can try downloading our nightly 'dev' build of freeview, from here:
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https://surfer.nmr.mgh.harvard.edu/fswiki/Download
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or here's a quicker way (this is a one-line command... wget <file>):
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wget
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ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_xftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin
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86_64/freeview.binftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin
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and copy it to $FREESURFER_HOME/bin
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then
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chmod a+x $FREESURFER_HOME/bin/freeview.bin
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N.
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On Tue, 2014-11-04 at 12:35 +0000, Krieger, Donald N. wrote:
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I recently downloaded and installed
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freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .
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I had been running this version previously but had to reload
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everything due to a disk crash.
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recon-all –all goes to completion with no errors.
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freeview starts up fine but fails on loading a volume file with the
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PETC error listed below.
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I found several references to this error in the archive but no
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resolution for my problem.
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Any thoughts would be welcome – thanks.
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[0]PETSC ERROR:
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--
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[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
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probably memory access out of range
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[0]PETSC ERROR: Try option -start_in_debugger or
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-on_error_attach_debugger
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[0]PETSC ERROR: or see
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http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.ht
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ml#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man
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libgmalloc on Apple to find memory corruption errors
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[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
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and run
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[0]PETSC ERROR: to get more information on the crash.
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[0]PETSC ERROR: --------------------- Error Message
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[0]PETSC ERROR: Signal received!
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[0]PETSC ERROR:
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--
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[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
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17:29:26 CDT 2008 HG revision:
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4466c6289a0922df26e20626fd4a0b4dd03c8124
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[0]PETSC ERROR: See docs/changes/index.html for recent updates.
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[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
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[0]PETSC ERROR: See docs/index.html for manual pages.
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[0]PETSC ERROR:
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--
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[0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by
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kriegerd Tue Nov  4 06:55:17 2014
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[0]PETSC ERROR: Libraries linked
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from
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/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p1
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3/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
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[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
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[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
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--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1
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--with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0
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COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
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[0]PETSC ERROR:
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--
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[0]PETSC ERROR: User provided function() line 0 in unknown directory
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unknown file
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[unset]: aborting job:
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application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
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Regards,
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Don
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Signature0001
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Don Krieger, Ph.D.
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Department of Neurological Surgery
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University ofPittsburgh
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(412)648-9654 Office
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(412)521-4431 Cell/Text
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