Invalid Mex-files using 2018a Xcode 9.2

Hi,

While trying to run Matlab 2018a code using "BM3D" downloaded from from http://www.cs.tut.fi/~foi/GCF-BM3D/ (the file is http://www.cs.tut.fi/~foi/GCF-BM3D/BM3D.zip I'm getting this errors.

tried almost every solution suggested on Matlab Answers Community with no success.

I'm using Xcode 9.2.

   Invalid MEX-file '/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64': dlopen(/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64,
  6): Library not loaded: @loader_path/libmat.dylib
    Referenced from: /Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64
    Reason: image not found.

Error in BM3D (line 342)
y_hat = bm3d_thr(z, hadper_trans_single_den, Nstep, N1, N2, lambda_thr2D,...

[Yul Kim]

Hi, I'm having the exact same problem. Did you solve this by any chance? Thanks!

[Eric Elharer]

Hi,

By saying "I'm having the exact same problem" do you mean with BM3d?

if so, i wrote to Prof. Foi, who is associate Professor of Signal Processing at Tampere University of Technology, Finland, that developed the BM3D algorithm.

He was kind enough to send me a beta version that solves the problem with detailed instructions.

if you are interested send me an email and i will forward you the instructions and software.

[e-mail]

[Jaakko Lehtinen]

Same here..

Does anyone happen to recall the last known good version of Matlab for BM3D? In a little bit of a pinch for getting comparison results done, so could well install an older version just for that.

[Walter Roberson]

Jaakko Lehtinen which Mac OS version are you using? I suspect that is more relevant than the MATLAB version for this purpose.

[Walter Roberson]

The original poster mentioned XCode 9.2, which is for MacOS 10.12.6+ onward, which is for Sierra; High Sierra needs XCode 9.3 or later.

MacOS Sierra was the release where Apple starting getting serious with System Integrity Protection, which turns off recognition of DYLD_DYNAMIC_PATH in some cases. This wasn't a MATLAB issue; it was an Apple issue. Individual programs could adapt to the Apple restriction, but the most obvious adaptation is to static link libraries instead of using DLL. For third-party packages such as BM3D, that would involve a change to BM3D rather than a change to MATLAB.

[Eric Elharer]

Hi I received a beta version for Bm3d which solves this problem If interested I will forward the file with the instructions

[Wen Ying]

hi I meet the same problem, and i use matlab2018a and xcode11.2.1 macos 10.14.6.

i did not find the function the solve this issue.

could you send me the beta version for bm3d？

[Amal Hafiane Mokadem]

hi please can you send me the beta version for Bm3d if you still have it

Answer 1

[Walter Roberson]

Sierra and High Sierra ignore DYLD_DYNAMIC_PATH in some cases, for security reasons. It is only intended to apply to some executables, but likely it is interfering.

https://github.com/nteract/nteract/issues/1523

tl;dr -- put copies of the library in /usr/lib

[Eric Elharer]

Hi, could you please be more specific about the steps to be done

[Walter Roberson]

sudo cp /Applications/MATLAB_R2018a.app//bin/maci64/libmat.dylib /usr/lib

[Eric Elharer]

Hi, cp: /usr/lib/libmat.dylib: Operation not permitted I read there is a way to release this lock shell I try thIs before ?

[Eric Elharer]

The steps to release protection are described on thus web: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

[Walter Roberson]

Sorry, I do not know.

[Eric Elharer]

Any other idea to solve my problem? If not, thanks for your time and try to help

[Eric Elharer]

Hi,

I've followed http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ and managed to perform your advised solution -

sudo cp /Applications/MATLAB_R2018a.app//bin/maci64/libmat.dylib /usr/lib

now although the error massege starts with invalid mex I file it is a bit different and concludes

Symbole not found
Invalid MEX-file '/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64': dlopen(/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64,
6): *Symbol not found*: _mxCreateNumericArray_700
  Referenced from: /Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64.

Error in BM3D (line 342)
y_hat = bm3d_thr(z, hadper_trans_single_den, Nstep, N1, N2, lambda_thr2D,...

Error in Poisson_denoising_Anscombe_exact_unbiased_inverse_fastprof (line 39)
    [dummy D]=BM3D(1,transformed,transformed_sigma*255,'lc');  % denoise assuming additive white Gaussian noise

Error in ReconsCarSignalHospB3DMCompToNLSPCAP4IPOnEIsNoiseElectrons (line 142)
            [y_hat, PSNR_y_hat, NMISE_y_hat] = Poisson_denoising_Anscombe_exact_unbiased_inverse_fastprof(ImageA,ImageB); %%B3DM and Anscombe transform

[Yilin Lin]

I am facing the exact same issue - please let me know when you get it to work! Thanks a lot.

[Zhihong Pan]

stuck at the same error on MacOS, any updates on this?

[Eric Elharer]

Hi Send me a gmail address mail and I'll share with u a folder with all the information and software updates that helped me Hope it would work for u 2 [e-mail]