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Bitbol-Lab / ProtMamba-ssm

ProtMamba: a homology-aware but alignment-free protein state space model
https://www.biorxiv.org/content/10.1101/2024.05.24.595730v1
Apache License 2.0
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mamba_ssm code version #3

Closed aksangha closed 4 months ago

aksangha commented 4 months ago

Hi,

As the ProtMamba_ssm/ is missing the mamba_ssm code in the distribution, can you please point me to the right version of mamba_ssm code you used for ProtMamba or add that to the ProtMamba_ssm/?

Thank you

damiano-sg commented 4 months ago

Hi, it's not missing, it's part of the pip requirements on settings.ini It's the original mamba repository and it should be installed when you run pip -e .

aksangha commented 4 months ago

Thanks for the quick reply. Below is the first error I get from running ProtMamba. As you can see there is no layernorm function in mamba_ssm code, infact it is layer_norm. Next it errors with arguments on other mamba_ssm modules/functions. It seems that there are changes in the code that is being installed and that has been used. Traceback (most recent call last): File "/home/ubuntu/scratch/ProtMamba-ssm/ProtMamba_ssm/sample_from_pretrained_model.py", line 4, in from ProtMamba_ssm.modules import * File "/home/ubuntu/scratch/ProtMamba-ssm/ProtMamba_ssm/modules.py", line 19, in from mamba_ssm.ops.triton.layernorm import RMSNorm, layer_norm_fn, rms_norm_fn ModuleNotFoundError: No module named 'mamba_ssm.ops.triton.layernorm'

damiano-sg commented 4 months ago

Oh ok, we didn't specify the version on settings.ini, I fixed it. A quick fix for you would be to downgrade Mamba to the version previous to Mamba2, i.e. 1.1.4