HI, I had reported this issue a while ago and have been trying to track it down because it seems to be popping up in strange places on our El Capitan and Sierra machines.
So I initially encountered the error dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib when trying to run with the -parallel flag for the same subject who finished fine through the traditional pipeline. I have since encountered it when running mri_deface and mri_info. The good news about that is they are really quick to run, unlike having to run the whole pipeline. Here is an example, and it is repeatable on my machine for multiple input images (so hopefully the developers can reproduce) I can do something as simple as mri_info cert01.nii from the command line as it works as usual. I then put the same command in a very simple script (I tried bash and tsch) #! /bin/bash -f # mri_info cert01.nii and it fails with dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I then switch to Freesurfer 5.3 and run the same little script and it spits out the usual info. Hopefully this can help in tracking down the problem, and creating a Sierra compatible build, because we can't roll any of our newly ordered machines back to Yosemite anymore. Sincerely, Mira ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K <zkauf...@nmr.mgh.harvard.edu> Sent: Monday, February 20, 2017 9:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding Hello Jared, Would it be possible to tar up the subject directory and upload it to our server so I can take a look? https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange FtpFileExchange - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange> surfer.nmr.mgh.harvard.edu top. Uploading Data. If you have been asked to send the FreeSurfer team a file, you can either send it via FTP or File Drop. Instructions for both are below. -Zeke On Feb 20, 2017, at 2:47 PM, Jared Saletin <jared_sale...@brown.edu<mailto:jared_sale...@brown.edu>> wrote: Dear Zeke, Thanks for your reply. I can verify that recon-all completes without error on a single thread, but crashes on parallel. I thought it may be hippocampus-subfield specific, but the same pattern remerges regardless of the subfield reconstruction. Is there something in newer OS X that broke the libraries? Thanks! Jared — Jared M. Saletin, PhD Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906 Email: jared_sale...@brown.edu<mailto:jared_sale...@brown.edu> Phone: 401-421-9440 Fax: 401-453-3578 On Feb 17, 2017, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Message: 30 Date: Fri, 17 Feb 2017 10:21:03 -0500 From: Z K <zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <c4e0438e-3a66-2e2e-038c-887ea392a...@nmr.mgh.harvard.edu<mailto:c4e0438e-3a66-2e2e-038c-887ea392a...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Hello Jared, Curious... Can you try processing this particular subject with a single thread and see what happens? If the problem persists let me know and I will take a look at the subject. -Zeke On 02/17/2017 08:28 AM, Jared Saletin wrote: Hi Freesurfer gurus: I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with an error in mris_smooth. It looks like a library issue. A prior post had the same issue and indicated uninstalling the whole distribution and re-installing 6.0.0 fresh (as opposed to installing over 5.3). I receive the same error however (pasted below). Does anyone have any thoughts? Thanks! Jared #@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017 /Users/jared/Desktop/fMRITest/test/scripts \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n Waiting for PID 11130 of (11130 11133) to complete... /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort trap: 6 exec $JOB >> $LOG 2>&1 Waiting for PID 11133 of (11130 11133) to complete... /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort trap: 6 exec $JOB >> $LOG 2>&1 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib PIDs (11130 11133) completed and logs appended. Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64 recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017 ? Jared M. Saletin, PhD Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906 Email: jared_sale...@brown.edu<mailto:jared_sale...@brown.edu> <mailto:jared_sale...@brown.edu> Phone: 401-421-9440 Fax: 401-453-3578 _______________________________________________ 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
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