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#Signal[0]PETSC 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 > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH > Sent: Tuesday, November 04, 2014 11:59 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] freeview fault: PETSC Error ... > > you can try downloading our nightly 'dev' build of freeview, from here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > or here's a quicker way (this is a one-line command... wget <file>): > > wget > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin> > 86_64/freeview.bin<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin> > > and copy it to $FREESURFER_HOME/bin > then > chmod a+x $FREESURFER_HOME/bin/freeview.bin > > N. > > > On Tue, 2014-11-04 at 12:35 +0000, Krieger, Donald N. wrote: > > I recently downloaded and installed > > freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . > > > > I had been running this version previously but had to reload > > everything due to a disk crash. > > > > > > > > recon-all –all goes to completion with no errors. > > > > freeview starts up fine but fails on loading a volume file with the > > PETC error listed below. > > > > I found several references to this error in the archive but no > > resolution for my problem. > > > > Any thoughts would be welcome – thanks. > > > > > > > > [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.ht > > ml#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 BTRC-Server01 by > > kriegerd Tue Nov 4 06:55:17 2014 > > > > [0]PETSC ERROR: Libraries linked > > from > > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p1 > > 3/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 > > > > > > > > Regards, > > > > > > > > Don > > > > > > > > Signature0001 > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > University ofPittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail.
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