Was the subject folder that fails ever uploaded? If not please upload and let me know when it's ready and I'll take a look. If it was already uploaded try reuploading as that area get cleared up occasionally.
> On Mar 1, 2017, at 5:17 PM, Mira Michelle Raman <mra...@stanford.edu> wrote: > > 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 > 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> 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 >> Phone: 401-421-9440 >> Fax: 401-453-3578 >> >> >> >>> On Feb 17, 2017, at 12:00 PM, 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> >>> 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 >>> Message-ID: <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> >>>> Phone: 401-421-9440 >>>> Fax: 401-453-3578 >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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