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pengxingang / Pocket2Mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
MIT License
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GPU not used when running sample_for_pdb.py #31

Open xy127 opened 1 year ago

xy127 commented 1 year ago

Hello,

Thank you for sharing your code! I found GPU was not used after executing sample_for_pdb.py image

The first two lines of log show:
[2023-07-31 17:13:34,403::sample::INFO] Namespace(bbox_size=23.0, center=[32.0, 28.0, 36.0], config='./configs/sample_for_pdb.yml', device='cuda', outdir='./outputs', pdb_path='./example/4yhj.pdb')
[2023-07-31 17:13:34,403::sample::INFO] {'model': {'checkpoint': './ckpt/pretrained_Pocket2Mol.pt'}, 'sample': {'seed': 2020, 'num_samples': 100, 'beam_size': 300, 'max_steps': 50, 'threshold': {'focal_threshold': 0.5, 'pos_threshold': 0.25, 'element_threshold': 0.3, 'hasatom_threshold': 0.6, 'bond_threshold': 0.4}}}
...

Since it takes forever long to use the first choice, I installed manually following the instruction. And below is my conda list:

_libgcc_mutex             0.1                 conda_forge    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
absl-py                   1.4.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
aiohttp                   3.8.5            py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
attrs                     23.1.0             pyh71513ae_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
beautifulsoup4            4.12.2                   pypi_0    pypi
biopython                 1.81             py38h1de0b5d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blas                      1.0                         mkl    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
blinker                   1.6.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost                     1.74.0           py38h2b96118_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost-cpp                 1.74.0               h6cacc03_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
brotlipy                  0.7.0           py38h0a891b7_1005    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2                     1.0.8                h7f98852_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
c-ares                    1.19.1               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates           2023.7.22            hbcca054_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cachetools                5.3.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cairo                     1.16.0            ha00ac49_1009    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi                   2023.7.22                pypi_0    pypi
cffi                      1.15.1           py38h4a40e3a_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
click                     8.1.6           unix_pyh707e725_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
cryptography              41.0.2           py38hcdda232_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cudatoolkit               11.3.1              hb98b00a_12    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
easydict                  1.10                     pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig                2.14.1               hef1e5e3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
fonts-conda-ecosystem     1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-forge         1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype                  2.10.4               hca18f0e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
frozenlist                1.4.0            py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gdown                     4.7.1                    pypi_0    pypi
gettext                   0.21.1               h27087fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
giflib                    5.2.1                h0b41bf4_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
google-auth               2.22.0             pyh1a96a4e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
google-auth-oauthlib      1.0.0              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
googledrivedownloader     0.4                      pypi_0    pypi
greenlet                  2.0.2            py38h17151c0_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
grpcio                    1.56.2           py38h94a1851_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu                       69.1                 h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
idna                      3.4                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
importlib-metadata        6.8.0              pyha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
intel-openmp              2023.1.0         hdb19cb5_46305    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
isodate                   0.6.1                    pypi_0    pypi
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.3.1                    pypi_0    pypi
jpeg                      9e                   h0b41bf4_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
kiwisolver                1.4.4            py38h43d8883_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lcms2                     2.15                 hfd0df8a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lerc                      4.0.0                h27087fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libabseil                 20230125.3      cxx17_h59595ed_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libblas                   3.9.0           1_h86c2bf4_netlib    conda-forge
libcblas                  3.9.0           5_h92ddd45_netlib    conda-forge
libdeflate                1.17                 h5eee18b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libffi                    3.4.2                h7f98852_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 13.1.0               he5830b7_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libglib                   2.76.4               hebfc3b9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.1.0               he5830b7_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgrpc                   1.56.2               h3905398_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.17                 h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblapack                 3.9.0           5_h92ddd45_netlib    conda-forge
libnsl                    2.0.0                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng                    1.6.39               h753d276_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libprotobuf               4.23.3               hd1fb520_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsqlite                 3.42.0               h2797004_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.5.0                h6adf6a1_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid                   2.38.1               h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuv                     1.44.2               hd590300_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp                   1.2.4                h1daa5a0_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp-base              1.2.4                h5eee18b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libxcb                    1.15                 h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2                   2.9.14               haae042b_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzlib                   1.2.13               hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lmdb                      1.4.1                    pypi_0    pypi
markdown                  3.4.4              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
markupsafe                2.1.3            py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
matplotlib-base           3.4.3            py38hf4fb855_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mkl                       2023.1.0         h6d00ec8_46342    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl-service               2.4.0            py38h5eee18b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_fft                   1.3.6            py38h417a72b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_random                1.2.2            py38h417a72b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
multidict                 6.0.4            py38h1de0b5d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses                   6.4                  hcb278e6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
numpy                     1.24.4                   pypi_0    pypi
numpy-base                1.24.3           py38h060ed82_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
oauthlib                  3.2.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl                   3.1.1                hd590300_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    2.0.3            py38h01efb38_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre2                     10.40                hc3806b6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pillow                    9.4.0            py38h6a678d5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pip                       23.2.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pixman                    0.40.0               h36c2ea0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
platformdirs              3.9.1              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
protobuf                  4.23.3           py38h830738e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
psutil                    5.9.5                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyasn1                    0.4.8                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyasn1-modules            0.2.7                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pycairo                   1.24.0           py38h1a1917b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pycparser                 2.21               pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyg                       2.0.4           py38_torch_1.10.0_cu113    pyg
pyjwt                     2.8.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyopenssl                 23.2.0             pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pysocks                   1.7.1              pyha2e5f31_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python                    3.8.17          he550d4f_0_cpython    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-louvain            0.16               pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi                3.8                      3_cp38    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytorch                   1.10.1          py3.8_cuda11.3_cudnn8.2.0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch
pytorch-cluster           1.6.0           py38_torch_1.10.0_cu113    pyg
pytorch-mutex             1.0                        cuda    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch
pytorch-scatter           2.0.9           py38_torch_1.10.0_cu113    pyg
pytorch-sparse            0.6.13          py38_torch_1.10.0_cu113    pyg
pytorch-spline-conv       1.2.1           py38_torch_1.10.0_cu113    pyg
pytz                      2023.3             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyyaml                    6.0.1                    pypi_0    pypi
rdflib                    6.3.2                    pypi_0    pypi
rdkit                     2022.03.5        py38ha829ea6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
re2                       2023.03.02           h8c504da_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline                  8.2                  h8228510_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
reportlab                 3.6.12           py38h5eee18b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
requests                  2.31.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
rocm-smi                  5.6.0                h59595ed_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
rsa                       4.9                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
scikit-learn              1.3.0            py38hc099248_0    conda-forge
scipy                     1.10.1           py38h59b608b_3    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
six                       1.16.0             pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
soupsieve                 2.4.1                    pypi_0    pypi
sqlalchemy                2.0.19           py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tbb                       2021.8.0             hdb19cb5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tensorboard               2.13.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tensorboard-data-server   0.7.0            py38h3d167d9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tk                        8.6.12               h27826a3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tornado                   6.3.2            py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
typing-extensions         4.7.1                hd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
typing_extensions         4.7.1              pyha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
urllib3                   2.0.4                    pypi_0    pypi
werkzeug                  2.3.6              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
wheel                     0.41.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libice               1.1.1                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libsm                1.2.4                h7391055_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxau               1.0.11               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxrender           0.9.11               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xproto               7.0.31            h7f98852_1007    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.6                h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
yacs                      0.1.8              pyhd8ed1ab_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yarl                      1.9.2            py38h01eb140_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zipp                      3.16.2             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib                      1.2.13               hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.2                hfc55251_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
explorer1212 commented 6 months ago

Hello, @xy127 . May I know the sampling time when you run the sample.py? I found that this file just uses the cpu to sample, and I tried to change the device to cuda, but the speed is also low, about 50min~1h. Thank you!