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faylward / viralrecall

Detection of NCLDV signatures in 'omic data
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Issues with Apple M1 Pro chip? #16

Open ABediSilva opened 2 years ago

ABediSilva commented 2 years ago

Hi there, For context, I'm new to python and shell coding in general. I installed the required packages and directories alongside ViralRecall. As suggested, I tested to see if everything was working using python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f . Sadly, I get the following messages: "Intel MKL FATAL ERROR: This system does not meet the minimum requirements for use of the Intel(R) Math Kernel Library. The processor must support the Intel(R) Supplemental Streaming SIMD Extensions 3 (Intel(R) SSSE3) instructions. The processor must support the Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) instructions. The processor must support the Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions."

I suspect these messages may be due to the fact that I have a new gen MacBook Pro with an Apple M1 Pro chip. Rosetta is installed and working.

Has anyone else had similar issues? Is there perhaps an easy solution that I am not aware of yet?

ABediSilva commented 2 years ago

I found the solution here: https://stackoverflow.com/questions/36659453/intel-mkl-fatal-error-cannot-load-libmkl-avx2-so-or-libmkl-def-so

If using conda then conda install nomkl numpy scipy scikit-learn numexpr should do it if anyone gets this error. This was not necessarily an issue with my Apple silicon but with access (or lack thereof) with Intel's Math Kernel Library within conda. Easy fix.