Open amelie-iska opened 7 months ago
Hi @amelie-iska,
So this exception is about wrong version of rdkit. One solution is as follow:
conda search rdkit -c rdkit
. Here is what I got (my current runnable env, not the one from Nvidia):
rdkit 2014.03.1 np18py27_3 rdkit
rdkit 2014.09.1 np19py26_1 rdkit
rdkit 2014.09.1 np19py27_1 rdkit
...
...
...
rdkit 2020.03.3.0 py37hc20afe1_1 rdkit
rdkit 2020.09.1.0 py36hd50e099_1 rdkit
rdkit 2020.09.1.0 py37hd50e099_1 rdkit
2020.09.1.0
.@amelie-iska I had the same issue. Changing most conda installs to pip installs fixed this for me. This is the docker file that worked:
FROM nvcr.io/nvidia/pytorch:22.01-py3 as base
#create a new new user
RUN useradd -ms /bin/bash shengchaol
# #change to this user
# USER shengchaol
#set working directory
WORKDIR /home/shengchaol
RUN chmod -R 777 /home/shengchaol
RUN chmod -R 777 /usr/bin
RUN chmod -R 777 /bin
RUN chmod -R 777 /usr/local
RUN chmod -R 777 /opt/conda
RUN conda install -y python=3.7
RUN pip install rdkit
RUN conda install -y -c conda-forge -c pytorch pytorch=1.9.1
RUN conda install -y -c pyg -c conda-forge pyg
RUN pip install requests
RUN pip install tqdm
RUN pip install matplotlib
RUN pip install spacy
# for SciBert
RUN pip install boto3
RUN pip install transformers
# for MoleculeNet
RUN pip install ogb
# install pysmilesutils
RUN python -m pip install git+https://github.com/MolecularAI/pysmilesutils.git
RUN pip install deepspeed
# install Megatron
RUN cd /tmp && git clone https://github.com/MolecularAI/MolBART.git --branch megatron-molbart-with-zinc && cd /tmp/MolBART/megatron_molbart/Megatron-LM-v1.1.5-3D_parallelism && pip install .
# install apex
RUN cd /tmp && git clone https://github.com/chao1224/apex.git
RUN cd /tmp/apex/ && pip install -v --disable-pip-version-check --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./
#expose port for Jupyter
EXPOSE 8888
Thanks @kosonocky any chance you've had any luck with ProteinDT (the other CLIP based model by @chao1224) as well?
Issue: Docker fails at installing rdkit. Attempted Workarounds: Tried removing the version of rdkit, also tried using
pip install rdkit
.