INTEL MKL ERROR on MacOS

[OkonSamuel]

Hi.
I get the following error in travis tests when using Conda on MacOS

INTEL MKL ERROR: dlopen(/Users/travis/.julia/conda/3/lib/libmkl_intel_thread.dylib, 9): Library not loaded: @rpath/libiomp5.dylib

  Referenced from: /Users/travis/.julia/conda/3/lib/libmkl_intel_thread.dylib

  Reason: image not found.

Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.dylib.

I don't get these error on Linux or when i use my local python distribution (That's why am opening an issue here). No error shows if i remove mkl with Conda.rm("mkl")
Any help would be appreciated. Thanks

[stevengj]

Can you give a self-contained example that illustrates the error? What is the test that is failing?

[OkonSamuel]

Thanks @stevengj
Sorry for my choice of words. I should have said errored tests. https://travis-ci.com/github/alan-turing-institute/MLJModels.jl/jobs/339809727#L470. This is as a result of using PYTHON=conda as default python distribution on MacOS(This doesn't error in Linux build)

[OkonSamuel]

Although adding the following code to my tests prevents those errors am still puzzled why it doesn't error in Linux builds.

Conda.add("nomkl")
Conda.add("scikit-learn")
Conda.rm("mkl")

[ppalmes]

add this in your .travis.yml

env:
  - PYTHON=Conda LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.julia/conda/3/lib

the problem is the env variable is not properly set to the right location in MacOS

[ppalmes]

can we have a fix on this in MacOS? for those with conda/python working, this is issue won't bite them. from fresh .julia or new install of conda/pycall, without properly exporting:

export PYTHON=Conda
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.julia/conda/3/lib

in their startup shell, installing conda/python will fail.

[mertsaner]

add this in your .travis.yml

env:
  - PYTHON=Conda LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.julia/conda/3/lib

the problem is the env variable is not properly set to the right location in MacOS

Hi there,
I have the same problem in my Macbook but I did not understand what to do exactly. What is our .traves.yml? My username is mertsaner. So, what is .mertsaner.yml? Could you describe in a detailed way what we need to do solve the problem? Thanks,

[mertsaner]

can we have a fix on this in MacOS? for those with conda/python working, this is issue won't bite them. from fresh .julia or new install of conda/pycall, without properly exporting:

export PYTHON=Conda
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.julia/conda/3/lib

in their startup shell, installing conda/python will fail.

I have tried to write these two to the my shell but it did not worked out

[ppalmes]

you have to do Pkg.build() so that Conda and PyCall will use these new information.

[ppalmes]

export PYTHON=Conda export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.julia/conda/3/lib

in julia prompt:
using Pkg; Pkg.build()

[mertsaner]

Same Error :(

[mertsaner]

It happens when I use Pyplot otherwise it is okay, I use BigSur 11.2.3 on M1 Macbook

[ppalmes]

check on that directory if you have the mkl lib. find it and put it there.

[ppalmes]

you can also remove mkl by using nomkl

Conda.add("nomkl")
Conda.rm("mkl")
pyimport_conda("mkl", "mkl")

[ppalmes]

Same Error :(

make sure you export those commands in the same terminal and run julia and build the packages.

[mertsaner]

Same Error :(

make sure you export those commands in the same terminal and run julia and build the packages.

I tried but, it did not work correctly, something is wrong with Julia but I do not what is

[mertsaner]

Pluto is okay, since even I do not use Pluto, it gives same error within Julia every time, I try to plot something or write Pyplot()

[mertsaner]

like using Pkg, Add PyPlot()

[ppalmes]

did you follow the steps about exporting PYTHON and LD_LIBRARY paths? did you check if MKL lib can be found in the location that the error indicated? please provide more details and more info. if you don’t provide details, we cannot guess too what is the problem.

[ppalmes]

what is your julia version. try running these commands in julia shell to avoid any issues from other packages.

[ppalmes]

did you try the Conda commands suggested above?

[deszoeke]

I had to do some tugging to get GR to compile, after which I got this PyPlot error. The Conda commands worked.