Installation issues and a test run

[ryao-mdanderson]

Dear ResGen author:

I attempted to install pytorch, cuda version as you suggested in both miniforge3 and miniconda3, hit issues that packages will be upgrade or downgrade.

Use miniforge3 installation as an example:
(resgen) [ryao@gdragon001 ~]$ conda list

packages in environment at /rsrch3/home/itops/ryao/miniforge3/envs/resgen:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
aiohappyeyeballs 2.3.5 pyhd8ed1ab_0 conda-forge
aiohttp 3.10.3 py38h2019614_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
biopython 1.83 py38h01eb140_0 conda-forge
blas 2.123 blis conda-forge
blas-devel 3.9.0 23_linux64_blis conda-forge
blis 0.9.0 h4ab18f5_2 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py38h17151c0_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cairo 1.18.0 hebfffa5_3 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.17.0 py38heb5c249_0 conda-forge
chardet 5.2.0 py38h578d9bd_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.1.1 py38h7f3f72f_1 conda-forge
cuda-version 11.6 hca96458_3 conda-forge
cudatoolkit 11.6.2 hfc3e2af_13 conda-forge
cudnn 8.9.7.29 hbc23b4c_3 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
easydict 1.9 py_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.53.1 py38h2019614_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
frozenlist 1.4.1 py38h01eb140_0 conda-forge
fsspec 2024.6.1 pyhff2d567_0 conda-forge
greenlet 3.0.3 py38h17151c0_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py38h7f3f72f_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 23_linux64_blis conda-forge
libboost 1.84.0 h0ccab89_5 conda-forge
libboost-python 1.84.0 py38haa4b4a7_5 conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 23_linux64_blis conda-forge
libdeflate 1.21 h4bc722e_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libglib 2.80.3 h315aac3_2 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
libhwloc 2.11.1 default_hecaa2ac_1000 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 6_ha36c22a_netlib conda-forge
liblapacke 3.9.0 6_ha36c22a_netlib conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.4 h482b261_0 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
librdkit 2024.03.5 h79cfef2_3 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libtiff 4.6.0 h46a8edc_4 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.48.0 hd590300_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.16 hd590300_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
llvm-openmp 18.1.8 hf5423f3_0 conda-forge
magma 2.5.4 hc72dce7_4 conda-forge
markupsafe 2.1.5 py38h01eb140_0 conda-forge
matplotlib-base 3.7.3 py38h58ed7fa_0 conda-forge
mkl 2022.2.1 h6508926_16999 conda-forge
mkl-devel 2022.2.1 ha957f24_16999 conda-forge
mkl-include 2022.2.1 ha957f24_16999 conda-forge
multidict 6.0.5 py38h01eb140_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nccl 2.22.3.1 hee583db_1 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
ninja 1.12.1 h297d8ca_0 conda-forge
numpy 1.24.4 py38h59b608b_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4bc722e_2 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 py38h01efb38_1 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
pillow 10.4.0 py38h2bc05a7_0 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
pooch 1.8.2 pyhd8ed1ab_0 conda-forge
psutil 6.0.0 py38hfb59056_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycairo 1.26.1 py38he403b34_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyg 2.5.2 py38_torch_1.12.0_cu116 pyg
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.19 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-lmdb 1.5.1 py38h79ccf07_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.8 4_cp38 conda-forge
pytorch 1.12.1 cuda112py38hd94e077_201 conda-forge
pytorch-mutex 1.0 cuda pytorch
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py38h2019614_0 conda-forge
rdkit 2024.03.5 py38h890d753_3 conda-forge
readline 8.2 h8228510_1 conda-forge
reportlab 4.2.2 py38hfb59056_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
scikit-learn 1.3.2 py38ha25d942_2 conda-forge
scipy 1.10.1 py38h59b608b_3 conda-forge
setuptools 72.1.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.6.1 h3400bea_1 conda-forge
sqlalchemy 2.0.32 py38h2019614_0 conda-forge
tbb 2021.12.0 h434a139_3 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
unicodedata2 15.1.0 py38h01eb140_0 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py38h01eb140_0 conda-forge
zipp 3.19.2 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zstandard 0.23.0 py38h62bed22_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
(resgen) [ryao@gdragon001 ~]$

To run an example, hit the message:
(resgen) [ryao@edragon037 ResGen]$ python gen.py --pdf_file ./examples/4iiy.pdb --sdf_file ./examples/4iiy_ligand.sdf --outdir ./examples/
Traceback (most recent call last):
File "gen.py", line 19, in
from utils.feats.protein import get_protein_feature_v2
File "/rsrch3/home/itops/ryao/ResGen/utils/feats/init.py", line 2, in
from .protein import parse_PDB_v2
File "/rsrch3/home/itops/ryao/ResGen/utils/feats/protein.py", line 8, in
import torch_cluster
ModuleNotFoundError: No module named 'torch_cluster'

I have spent hours working on this without a solution, please advise. If there is a container version of Resgen with all the dependencies, that will be great.

Regards,
Rong Yao

[HaotianZhangAI4Science]

I think the most challenging part of environment configuration is the PyG. Please first install PyG, torch, and RDKit! I think I have provided a conda-pack file that can be used directly after unzipping. Please give it a try!