error while importing design-bench

[erfanhamdi]

Hello

I installed the design-bench package the way you mentioned that didn't require MuJoCo and every thing goes fine until when I am trying to import design-bench I get this error.

Exception has occurred: ValueError
Can't find a vocabulary file at path '/Users/venus/miniconda3/envs/mbo/lib/python3.11/site-packages/design_bench_data/smiles_vocab.txt'. To load the vocabulary from a Google pretrained model use `tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)`
  File "/Users/venus/miniconda3/envs/design_bench_conda/lib/python3.11/site-packages/design_bench_data/test.py", line 2, in <module>
    import design_bench
ValueError: Can't find a vocabulary file at path '/Users/venus/miniconda3/envs/mbo/lib/python3.11/site-packages/design_bench_data/smiles_vocab.txt'. To load the vocabulary from a Google pretrained model use `tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)

Is there anything that I am missing? like downloading other files?

[christopher-beckham]

What version of transformers are you using? I'm assuming maybe it's a version mismatch since the error mentions BertTokenizer.

When I set up design bench I try (as much as I can) to use the dependencies listed in design-baselines:

https://github.com/brandontrabucco/design-baselines/blob/master/requirements.txt

[harish2sista]

Hi!
I'm facing the same issue. I have strictly installed all the package versions from requirements.txt. But the issue still persists. Does anyone have any other recommendations?

[christopher-beckham]

@harish2sista can you list the error that you get? Is it the same as the original poster's error message?

In my own experience setting this up there are some very specific version requirements for some of the packages, and it's not guaranteed to work out of the box when you install from requirements.txt. There were certain packages that I had to install with pip install <module>==version --no-deps so that it didn't pull in newer version numbers for other dependencies (i.e. emphasis on --no-deps).

You can check my own working requirements.txt here: https://gist.github.com/christopher-beckham/d1b319e84ae359e671b67e5fa7c663da

For example if you suspect the issue is with the transformers module you can try the version from my requirements.txt file:

pip install transformers==3.5.1 --no-deps

However you may also have to do the same thing for any extra dependencies of transformers.

[harish2sista]

@christopher-beckham Thanks for the swift response. The error message I received is

File "/home/<user_name>/miniconda3/envs/design-baselines/lib/python3.7/site-packages/transformers/tokenization_bert.py", line 196, in __init__ "model use 'tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)'".format(vocab_file) ValueError: Can't find a vocabulary file at path '/home/<user_name>/miniconda3/envs/design-baselines/lib/python3.7/site-packages/design_bench_data/smiles_vocab.txt'. To load the vocabulary from a Google pretrained model use 'tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)'
//replaced my <user_name>

And thank you for sending your requirements.txt file. Are you using python >= 3.8? because the conda env create -f design-baselines/environment.yml code installs python3.7. I received Python version incompatibility issue with your file.

[harish2sista]

Also, after investigation I found that the /home/<user_name>/miniconda3/envs/design-baselines/lib/python3.7/site-packages/design_bench_data directory is empty. I don't know if this has anything to do with the root library.

[christopher-beckham]

I am using Python 3.8 yes. If you could try with that it would be good.

I never tried Python 3.7 but my first attempt at the environment was with 3.9 and I didn't get it to work. For 3.9 there were certain modules (wheels) which were compiled for 3.8 but not 3.9, and so I had to downgrade because of pip complaining it couldn't find anything. Again, this seems to be a consequence of the fact that Design Bench requires some older library versions.

I am currently working on a fork which fixes some of these issues and is much more forgiving with dependencies. If you think it might help you, I could try work on it a bit more this weekend and make it public. Thanks.

[harish2sista]

@christopher-beckham Thank you very much!! That would be really helpful!
In the meantime, I will try the installation with Python 3.8. I'll let you know if I come across any new issues.
I'm very excited about your repo! I'm looking forward to it.

[harish2sista]

Hi, which Mujoco-py version are you using?

[christopher-beckham]

I'm using the latest version I got from the Github. Here are some instructions I wrote for myself, your mileage may vary:

design-baselines appears to be using version mujoco-py==2.0.2.3, but I had trouble trying to install this. I could only install a slightly newer version by following one of the replies in openai/mujoco-py#773 which suggests to do the following:

• (1) Add a compiler directive compiler_directives={'legacy_implicit_noexcept': True} to the line 239 of mujoco_py/builder.py
• (2) Update Cython to the latest version (use pip install / upgrade or whatever)
• (3) Then pip install . inside the repo to install.

This worked for me so long as I exported my LD_LIBRARY_PATH to be the following (note that the compilation log will tell you if something is missing in this path which you need to add):

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<path to mujoco>/mujoco210/bin:/usr/lib/nvidia

The last issue involved something to do with some missing libs which need to be installed. While this can be easily done with root privileges and apt-get, you can also install them with conda by following openai/mujoco-py#627 (comment)

conda install -c conda-forge glew
conda install -c conda-forge mesalib
conda install -c menpo glfw3
export CPATH=$CONDA_PREFIX/include
pip install patchelf

[seminumber]

I'm facing the same issue. If I'm correct, it seems that the file on the web 'https://storage.googleapis.com/design-bench/smiles_vocab.txt' is missing. It is defined in morgan_fingerprint_features.py:67 and onward:

vocab_file = DiskResource(
    os.path.join(DATA_DIR, 'smiles_vocab.txt'),
    download_method="direct",
    download_target=f'{SERVER_URL}/smiles_vocab.txt')

This code seems to cache a file on the web, the link to the file seems broken now.

[harish2sista]

Hi @seminumber, Thanks for bringing this up. I did more deep research following this solution. It seems the entire design-bench server is not working!

@brandontrabucco, could you please help us resolve this issue?

[christopher-beckham]

Hmm this is concerning. I have smiles_vocab locally, maybe I can upload it somewhere for now for you. I could maybe modify the code on my fork so that it will just pull the file from my Google Drive.

(For context, I am working on my own fork which will not import everything at once. Dataset specific imports should only happen when those datasets get created. Right now in order to import design_bench you need to have satisfied every dataset's dependencies.)

[harish2sista]

@christopher-beckham, Thank you for the help! Could you please post the link to the smiles_vocab file after you upload it?

Looking forward to your fork; thank you!

[christopher-beckham]

You can get the data here: https://drive.google.com/drive/folders/1tmbFImzhkivZUjHeh434D7V7mrxTBu1H?usp=drive_link

I don't know if it has all the data, because I only imported certain things like the RL environments.

Extract the contents to <path to design bench repo>/design-bench/design_bench_data.

I could look at my fork and maybe specify an alternative which downloads it from my gdrive.

[christopher-beckham]

Brandon is currently on vacation but I did recently inform him about this so hopefully it will be an easy fix from his end. Unfortunately I am suffering from this issue myself since my design_bench_data directory doesn't contain everything, only the stuff for Ant/Kitty/Superconductor.