Hi Tristan, Would it be possible to send us the files and the command-line you run?
Best, Ruopeng > On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH <[email protected]> wrote: > > 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: [email protected] > <[email protected]> on behalf of TRISTAN J PAUTSCH > <[email protected]> > Sent: Tuesday, August 20, 2019 2:35 PM > To: [email protected] <[email protected]> > 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 > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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