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#Sig... 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
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#Sig... 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
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 zkaufman@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#Sig... 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
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freesurfer@nmr.mgh.harvard.edu
-
Knut Jørgen Bjuland -
Z K