Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
I second the problem found in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the System Integrity Protection issue, I installed my freesurfer folder in a local "Documents" folder instead of in Applications and that seemed to allow me to keep System Integrity Protection enabled while running FreeSurfer commands.
Last night I ran recon-all on the same subject simultaneously, one using the -parallel tag and the other without it. This morning I see that only the one with the -parallel tag exited with errors and it seems to be this same "lazy symbol" error (see attached for recon-all error log).
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
I can try running with System Integrity Protection off to see if that will make the -parallel tag work... any other thoughts?
Thanks, Daniela
I could be wrong, but I dont think it has anything to do with the installation location. Can you upload your subject folder so I can take a look?
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On 03/03/2017 09:11 AM, Daniela wrote:
I second the problem found in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the System Integrity Protection issue, I installed my freesurfer folder in a local "Documents" folder instead of in Applications and that seemed to allow me to keep System Integrity Protection enabled while running FreeSurfer commands.
Last night I ran recon-all on the same subject simultaneously, one using the -parallel tag and the other without it. This morning I see that only the one with the -parallel tag exited with errors and it seems to be this same "lazy symbol" error (see attached for recon-all error log).
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
I can try running with System Integrity Protection off to see if that will make the -parallel tag work... any other thoughts?
Thanks, Daniela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Daniela,
Ive been looking into this error, and although I am unable to replicate it on my Mac, I do have what might be a potential solution. Could you please source freesurfer, then run the following command.
$> sudo -E fs_update
Then retry the subject with the parallel flag. Please let me know how it goes if you end up trying again. Thanks.
-Zeke
I second the problem found in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the System Integrity Protection issue, I installed my freesurfer folder in a local "Documents" folder instead of in Applications and that seemed to allow me to keep System Integrity Protection enabled while running FreeSurfer commands.
Last night I ran recon-all on the same subject simultaneously, one using the -parallel tag and the other without it. This morning I see that only the one with the -parallel tag exited with errors and it seems to be this same "lazy symbol" error (see attached for recon-all error log).
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
I can try running with System Integrity Protection off to see if that will make the -parallel tag work... any other thoughts?
Thanks, Daniela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
Sorry for the late reply. I did try re-running it and it did work this time! Thank you.
Daniela
On Mon, Mar 6, 2017 at 12:15 AM, zkaufman@nmr.mgh.harvard.edu wrote:
Hello Daniela,
Ive been looking into this error, and although I am unable to replicate it on my Mac, I do have what might be a potential solution. Could you please source freesurfer, then run the following command.
$> sudo -E fs_update
Then retry the subject with the parallel flag. Please let me know how it goes if you end up trying again. Thanks.
-Zeke
I second the problem found in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the System Integrity Protection issue, I installed my freesurfer folder in a local "Documents" folder instead of in Applications and that seemed to allow me to keep System Integrity Protection enabled while running FreeSurfer commands.
Last night I ran recon-all on the same subject simultaneously, one using the -parallel tag and the other without it. This morning I see that only the one with the -parallel tag exited with errors and it seems to be this same "lazy symbol" error (see attached for recon-all error log).
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
I can try running with System Integrity Protection off to see if that will make the -parallel tag work... any other thoughts?
Thanks, Daniela _______________________________________________ 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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