Comments (6)
Great, can I confirm your installation works as expected now? Thank you for the comment on the docs - this command has been updated now
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Could you try building the conda environment from this file? Then you should be able to run the pip install
commands from the docs.
You need our forks of both openmmtools and openmm-torch to be compatible with MACE
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Thanks, @jharrymoore . It works with the file mace-openmm.yml
. However, torchvision
and torchaudio
is not included in this .yml file. If I install them via pip install
, pytorch-2.0.1
will be downloaded and installed. But pytorch-2.0.0
is already written in this .yml file. Would you please tell me how to install torchvision
and torchaudio
in such case?
By the way, there is a sklearn
in the file openmmtools/openmm_torch/repex.py
,
from sklearn.random_projection import sample_without_replacement
But I look into this file and find sample_without_replacement
is not used at all. So this line is supposed to be deleted. Otherwise it will lead to errors when I run mace-md
.
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There two ways of installing MACE from documentation or github README, the first is
mamba env create -f mace-openmm.yml
pip install git+https://github.com/ACEsuit/mace.git
which does not require torchvision
or torchaudio
.
The second is
pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 --index-url https://download.pytorch.org/whl/cu118
pip install mace-torch
which requires torchvision
and torchaudio
.
Currently I choose the 1st way to install MACE. It leads to python=3.10.12
, pytorch=2.0.0.post304
. But when I run the mace-md
using
mace-md -f ejm_31.sdf --ml_mol ejm_31.sdf --model_path MACE-OFF23_small.model --output_dir md_test --nl torch --steps 1000 --minimiser ase --dtype float64 --remove_cmm --unwrap
The error is
Traceback (most recent call last):
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/bin/mace-md", line 8, in <module>
sys.exit(main())
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/lib/python3.10/site-packages/openmmtools/scripts/mace_md.py", line 245, in main
system = PureSystem(
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/lib/python3.10/site-packages/openmmtools/openmm_torch/hybrid_md.py", line 953, in __init__
self.create_system(ml_mol=ml_mol, model_path=model_path)
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/lib/python3.10/site-packages/openmmtools/openmm_torch/hybrid_md.py", line 970, in create_system
tmp_model = torch.load(model_path, map_location="cpu")
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/lib/python3.10/site-packages/torch/serialization.py", line 815, in load
return _legacy_load(opened_file, map_location, pickle_module, **pickle_load_args)
File "/public/home/jxzou/software/anaconda3/envs/mace-openmm/lib/python3.10/site-packages/torch/serialization.py", line 1033, in _legacy_load
magic_number = pickle_module.load(f, **pickle_load_args)
_pickle.UnpicklingError: invalid load key, '{'.
@jharrymoore Would you please take a look at this? Thanks!
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I don't believe we depend on torchvision or torch audio packages in mace or through mace-md. Do you need these in your environment for some other reason?
If you are planning on running MD with mace via openmm, you must build the environment via the yaml file, since this ensures the torch binaries from conda forge are compatible with openmm - this is not guaranteed when installing via pip.
On the unpicking error, this normally indicates your model did not download properly, could you inspect the downloaded file and check this looks like a model file (should be several MB in size)
from mace.
Thank you for your quick response. Yes, the torchvision
or torchaudio
is not needed. I was reading here and it says about torchvision
and torchaudio
. Later I use the file mace-openmm.yml
and the installation goes well.
And yes, the file MACE-OFF23_small.model
is incomplete. It was my internet connection problem. This file should be about 7MB.
By the way, it seems that in the documentation --nl torch_nl
should be modified into --nl torch
now.
Best,
Jingxiang
from mace.
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