gget alphafold "zsh: illegal hardware instruction" on M1

[pachterlab]

gget alphafold "zsh: illegal hardware instruction" on M1

[mcsymbiont]

Hi Laura,

I get it, thanks for trying! I am going to install gget on a linux machine, it does seem M1 specific. (I tried that Terminal app thing already, I had already disabled the "open with rosetta" box.) Thanks again.

[alwhiteh]

Likewise, thanks again!

[lauraluebbert]

Hi Alex,

I don't see an issue with the tensorflow packages you sent. Could you please send me the command you ran? Did you try running gget setup alphafold first?

[mcsymbiont]

Hi Laura,

I get the same error, on a MacBook Pro (14-inch, 2021) running OS 12.4. I have the same tensorflow packages installed as Alex, and I did run gget setup alphafold first:

(base) jpmccutc@BIOD2009 ~ % gget alphafold MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
zsh: illegal hardware instruction  gget alphafold 
(base) jpmccutc@BIOD2009 ~ %

Thanks,

--John

[alwhiteh]

Hi Laura,

I did run gget setup alphafold first. The command I ran was:

gget alphafold MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

In the mean time I also tried installing tensorflow with the M1 mac specific instructions ( https://developer.apple.com/metal/tensorflow-plugin/) and reinstalling gget, but this yields another error:

ERROR: Could not find a version that satisfies the requirement tensorflow-cpu (from alphafold) (from versions: none)
ERROR: No matching distribution found for tensorflow-cpu
Wed Aug 10 12:21:46 2022 ERROR AlphaFold installation failed.

Thanks for your help!

-Alex

[lauraluebbert]

Hi Alex and John,

I am having trouble recreating your error. The package tensorflow should not be required to run gget alphafold (only tensorflow-cpu==2.5.0 is required). Could you please try again in a new environment? This works for me (on MacBook):

conda create -n alphafold python=3.9
conda activate alphafold
pip install -U gget
conda install -c conda-forge openmm=7.5.1
gget setup alphafold
gget alphafold MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTP

[mcsymbiont]

Thanks, Laura. Unfortunately I still get the same error.

[alwhiteh]

Same here. I also tried downgrading tensorflow-cpu to 2.5.0 and got the same result.

[lauraluebbert]

This is difficult for me to debug since I cannot reproduce the error (it seems M1 specific?).

These recommendations might be worth giving a try:
Some people recommend using Python version 3.8.5. (apple/tensorflow_macos#143)

From https://www.pythonfixing.com/2021/11/fixed-illegal-hardware-instruction.html:
Seemed like my terminal app was running in Rosetta. This can be changed by right-clicking on the app -> get info -> disable "open with rosetta".