Hi I have disable System_Integrity_Protection to get free surfer working on El Capitan
Knut Jorgen On 30 Oct 2015, at 15:16, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > > There are significant changes in the most recent OSX release El Capitan > and this is one consequence of them > (https://en.wikipedia.org/wiki/OS_X_El_Capitan#System_Integrity_Protection). > We are currently exploring solutions but as of right now, freesurfer is > not fully functional on OS X 10.11 > > > > On 10/30/2015 04:45 AM, Knut Jørgen Bjuland wrote: >> >> Hi >> >> >> When I start freeview form command line on Mac OS X 11.10 it crash with >> this error message. Do I miss a file? >> >> >> >> freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated >> >> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address >> >> Referenced from: >> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> >> dyld: Symbol not found: ___emutls_get_address >> >> Referenced from: >> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> >> [0]PETSC ERROR: Caught signal number 5 TRAP >> >> [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 darwin12. named >> Knuts-MacBook-Pro.local by knutjorgenbjulan Fri Oct 30 09:42:53 2015 >> >> [0]PETSC ERROR: Libraries linked from >> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt >> >> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 >> >> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc >> --with-fc=0 --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 >> >> >> Knut Jørgen Bjuland >> NTNU >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
