Comments (11)
a-r-j
commented on May 28, 2024
Hi Jason, sorry to hear you’re having trouble. Could you give me some info on which pytorch3d version and build you’ve installed?
Thanks!
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a-r-j
commented on May 28, 2024
Hi again,
I realise now I’ve not included in the installation step for PyTorch 3D. Silly of me.
I think an uninstall of PyTorch 3D and a pip install pytorch3d should help things along. You can view the relevant docs [here].(https://github.com/facebookresearch/pytorch3d/blob/master/INSTALL.md). I believe if you try to conda install it on mac (which I’m guessing you’re on) it will try to install the CUDA build of PyTorch 3D.
Let me know if this helps.
I’ll update the README asap. Thanks for pointing this out.
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jasonshi10
commented on May 28, 2024
Yes, I'm installing on a Mac (CPU). The pytorch3d version is 0.2.0. I did try to uninstall and re-install pytorch3d and doesn't resolve the issue.
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a-r-j
commented on May 28, 2024
Hmm 0.2.0 should work fine. It looks like a CUDA issue to me. Could you share the output of conda list?
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jasonshi10
commented on May 28, 2024
# Name Version Build Channel
apbs 1.5 h1de35cc_3 schrodinger
appnope 0.1.0 pypi_0 pypi
argon2-cffi 20.1.0 pypi_0 pypi
ase 3.20.1 pypi_0 pypi
async-generator 1.10 pypi_0 pypi
attrs 20.2.0 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
biopandas 0.2.4 pypi_0 pypi
biopython 1.78 py37haf1e3a3_0
blas 1.0 mkl
bleach 3.2.1 pypi_0 pypi
boost 1.68.0 py37h9888f84_1001 conda-forge
boost-cpp 1.68.0 h6f8c590_1000 conda-forge
brotlipy 0.7.0 py37haf1e3a3_1000
bzip2 1.0.8 h1de35cc_0
ca-certificates 2020.6.20 hecda079_0 conda-forge
cairo 1.16.0 h0ab9d94_1001 conda-forge
certifi 2020.6.20 py37hc8dfbb8_0 conda-forge
cffi 1.14.3 py37hed5b41f_0
chardet 3.0.4 py37_1003
cryptography 3.1.1 py37hddc9c9b_0
curl 7.71.1 hb0a8c7a_1
cycler 0.10.0 py37_0
cython 0.29.21 py37hb1e8313_0
dbus 1.13.16 h18a8e69_0
decorator 4.4.2 py_0
defusedxml 0.6.0 pypi_0 pypi
dgl 0.4.3 pypi_0 pypi
dgllife 0.2.5 py37_0 dglteam
dssp 3.0.0 h0a44026_3 salilab
entrypoints 0.3 pypi_0 pypi
expat 2.2.9 hb1e8313_2
fontconfig 2.13.1 h1027ab8_1000 conda-forge
freemol 1.158 py_2 schrodinger
freetype 2.10.2 ha233b18_0
future 0.18.2 pypi_0 pypi
fvcore 0.1.2.post20200926 py_0 conda-forge
gettext 0.19.8.1 hb0f4f8b_2
glew 2.0.0 0 schrodinger
glib 2.65.0 hc5f4afa_0
googledrivedownloader 0.4 pypi_0 pypi
graphein 0.0.1 dev_0 <develop>
h5py 2.10.0 py37h3134771_0
hdf4 4.2.13 h39711bb_2
hdf5 1.10.4 hfa1e0ec_0
icu 58.2 h0a44026_3
idna 2.10 py_0
importlib-metadata 2.0.0 pypi_0 pypi
intel-openmp 2019.4 233
ipykernel 5.3.4 pypi_0 pypi
ipymol 0.5 pypi_0 pypi
ipython 7.18.1 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
ipywidgets 7.5.1 pypi_0 pypi
isodate 0.6.0 pypi_0 pypi
jedi 0.17.2 pypi_0 pypi
jinja2 2.11.2 pypi_0 pypi
joblib 0.16.0 py_0
jpeg 9b he5867d9_2
jsonschema 3.2.0 pypi_0 pypi
jupyter 1.0.0 pypi_0 pypi
jupyter-client 6.1.7 pypi_0 pypi
jupyter-console 6.2.0 pypi_0 pypi
jupyter-core 4.6.3 pypi_0 pypi
jupyterlab-pygments 0.1.1 pypi_0 pypi
kiwisolver 1.2.0 py37h04f5b5a_0
krb5 1.18.2 h75d18d8_0
lab 6.1 pypi_0 pypi
lcms2 2.11 h92f6f08_0
libboost 1.67.0 hebc422b_4
libcurl 7.71.1 h8a08a2b_1
libcxx 10.0.0 1
libedit 3.1.20191231 h1de35cc_1
libffi 3.3 hb1e8313_2
libgfortran 3.0.1 h93005f0_2
libholoplaycore 0.1.0_rc4 0 schrodinger
libiconv 1.16 h1de35cc_0
libnetcdf 4.7.3 he3b6227_0
libopenblas 0.3.10 h0794777_0
libpng 1.6.37 ha441bb4_0
libssh2 1.9.0 ha12b0ac_1
libtiff 4.1.0 hcb84e12_1
libxml2 2.9.10 h3b9e6c8_1
llvm-openmp 10.0.0 h28b9765_0
llvmlite 0.34.0 pypi_0 pypi
lz4-c 1.9.2 hb1e8313_1
markupsafe 1.1.1 pypi_0 pypi
matplotlib 3.3.1 0
matplotlib-base 3.3.1 py37h181983e_0
mengine 1 h1de35cc_1 schrodinger
mistune 0.8.4 pypi_0 pypi
mkl 2019.4 233
mkl-service 2.3.0 py37hfbe908c_0
mkl_fft 1.2.0 py37hc64f4ea_0
mkl_random 1.1.1 py37h959d312_0
mpeg_encode 1 h1de35cc_1 schrodinger
mtz2ccp4_px 1.0 hdc02c5d_3 schrodinger
nbclient 0.5.0 pypi_0 pypi
nbconvert 6.0.6 pypi_0 pypi
nbformat 5.0.7 pypi_0 pypi
ncurses 6.2 h0a44026_1
nest-asyncio 1.4.1 pypi_0 pypi
networkx 2.5 py_0
ninja 1.10.1 py37h879752b_0
notebook 6.1.4 pypi_0 pypi
numba 0.51.2 pypi_0 pypi
numpy 1.19.1 py37h3b9f5b6_0
numpy-base 1.19.1 py37hcfb5961_0
olefile 0.46 py37_0
openssl 1.1.1h haf1e3a3_0 conda-forge
packaging 20.4 pypi_0 pypi
pandas 1.1.1 py37hb1e8313_0
pandocfilters 1.4.2 pypi_0 pypi
parso 0.7.1 pypi_0 pypi
pcre 8.44 hb1e8313_0
pdb2pqr 2.1.2+pymol py_0 schrodinger
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 7.2.0 py37ha54b6ba_0
pip 20.2.2 py37_0
pixman 0.38.0 h1de35cc_0
pmw 2.0.1+3 py_3 schrodinger
portalocker 2.0.0 pypi_0 pypi
prometheus-client 0.8.0 pypi_0 pypi
prompt-toolkit 3.0.7 pypi_0 pypi
ptyprocess 0.6.0 pypi_0 pypi
pycairo 1.19.1 py37h126230b_0
pycparser 2.20 py_2
pygments 2.7.1 pypi_0 pypi
pymol 2.4.1 py37h92f0605_0 schrodinger
pyopenssl 19.1.0 py_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py37h655552a_2
pyrsistent 0.17.3 pypi_0 pypi
pysocks 1.7.1 py37_0
python 3.7.9 h26836e1_0
python-dateutil 2.8.1 py_0
python_abi 3.7 1_cp37m conda-forge
pytorch 1.6.0 py3.7_0 pytorch
pytorch3d 0.2.0 pypi_0 pypi
pytz 2020.1 py_0
pyyaml 5.3.1 pypi_0 pypi
pyzmq 19.0.2 pypi_0 pypi
qt 5.9.7 h468cd18_1
qtconsole 4.7.7 pypi_0 pypi
qtpy 1.9.0 pypi_0 pypi
rdflib 5.0.0 pypi_0 pypi
rdkit 2018.09.3 py37haff9cca_0 conda-forge
readline 8.0 h1de35cc_0
requests 2.24.0 py_0
rigimol 1.3 2 schrodinger
scikit-learn 0.23.2 py37h959d312_0
scipy 1.5.2 py37h912ce22_0
seaborn 0.11.0 py_0
send2trash 1.5.0 pypi_0 pypi
setuptools 49.6.0 py37_1
simplejson 3.17.2 pypi_0 pypi
sip 4.19.8 py37h0a44026_0
six 1.15.0 py_0
sqlite 3.33.0 hffcf06c_0
tabulate 0.8.7 pyh9f0ad1d_0 conda-forge
termcolor 1.1.0 pypi_0 pypi
terminado 0.9.1 pypi_0 pypi
testpath 0.4.4 pypi_0 pypi
threadpoolctl 2.1.0 pyh5ca1d4c_0
ticc 0.1.4 pypi_0 pypi
tk 8.6.10 hb0a8c7a_0
torch-cluster 1.5.7 pypi_0 pypi
torch-geometric 1.6.1 pypi_0 pypi
torch-scatter 2.0.5 pypi_0 pypi
torch-sparse 0.6.7 pypi_0 pypi
torch-spline-conv 1.2.0 pypi_0 pypi
torchvision 0.7.0 py37_cpu pytorch
tornado 6.0.4 py37h1de35cc_1
tqdm 4.46.0 pypi_0 pypi
traitlets 5.0.4 pypi_0 pypi
txt2tags 3.7 pypi_0 pypi
urllib3 1.25.10 py_0
vmd-python 3.0.6 py37hcc20023_2 conda-forge
wcwidth 0.2.5 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
wheel 0.35.1 py_0
widgetsnbextension 3.5.1 pypi_0 pypi
xz 5.2.5 h1de35cc_0
yacs 0.1.8 pypi_0 pypi
yaml 0.2.5 haf1e3a3_0 conda-forge
zipp 3.2.0 pypi_0 pypi
zlib 1.2.11 h1de35cc_3
zstd 1.4.5 h41d2c2f_0
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a-r-j
commented on May 28, 2024
Hi Jason,
Hopefully you've seen the response on your PyTorch 3D issue facebookresearch/pytorch3d#377
Copying the response here for reference:
Note that this issue and what I write here is mac specific.
pytorch3d has to be built for a particular version of pytorch. You are getting this error because of a mismatch between the > version with which pytorch3d has been built and the version of pytorch (or one of them) you have in your environment.
If you are using the package from pypi (i.e. pip install pytorch3d) then there is only one right version of pytorch. The packages from latest version of pytorch3d (0.2.5) match the latest version of pytorch (1.6.0). The packages from version 0.2.0 of pytorch3d use pytorch 1.5.0.
Please let me know if this works & I can close this issue.
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jasonshi10
commented on May 28, 2024
Hi Arian,
I used torch 1.5.0 and pytorch3d 0.2.0 and the import error has been resolved. Thank you!
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Arielbs
commented on May 28, 2024
Hi, I believe I have the same issue, I followed the steps above (macOS as well with no CUDA), torch 1.5.0 and torch3d 0.2.0 (I've also tried 1.6.0 and 0.2.5 with the same result) but I get the same error: RDKit is not installed, which is required for utils related to cheminformatics. Any chance I missing anything?
Thanks
Name Version Build Channel
apbs 1.5 h1de35cc_3 schrodinger
appnope 0.1.0 pypi_0 pypi
ase 3.20.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
biopandas 0.2.4 pypi_0 pypi
biopython 1.78 py37h60d8a13_1 conda-forge
blas 2.21 mkl conda-forge
boost 1.68.0 py37h9888f84_1001 conda-forge
boost-cpp 1.68.0 h6f8c590_1000 conda-forge
brotlipy 0.7.0 py37h395d20d_1001 conda-forge
bzip2 1.0.8 haf1e3a3_3 conda-forge
c-ares 1.17.1 hc929b4f_0 conda-forge
ca-certificates 2020.11.8 h033912b_0 conda-forge
cached-property 1.5.2 pypi_0 pypi
cairo 1.16.0 h0ab9d94_1001 conda-forge
certifi 2020.11.8 py37hf985489_0 conda-forge
cffi 1.14.3 py37h446cb54_1 conda-forge
chardet 3.0.4 py37h2987424_1008 conda-forge
cryptography 3.2.1 py37h3b7a55b_0 conda-forge
curl 7.71.1 hcb81553_8 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.21 py37h08f6e3d_1 conda-forge
dbus 1.13.6 h0c50699_1 conda-forge
decorator 4.4.2 py_0 conda-forge
dgl 0.4.3 pypi_0 pypi
dgllife 0.2.6 py37_0 dglteam
dssp 3.0.0 h0a44026_3 salilab
expat 2.2.9 hb1e8313_2 conda-forge
fontconfig 2.13.1 h1027ab8_1000 conda-forge
freemol 1.158 py_2 schrodinger
freetype 2.10.4 h3f75d11_0 conda-forge
future 0.18.2 pypi_0 pypi
fvcore 0.1.2.post20201122 pypi_0 pypi
gettext 0.19.8.1 haf92f58_1004 conda-forge
glew 2.0.0 0 schrodinger
glib 2.66.3 h519c658_0 conda-forge
googledrivedownloader 0.4 pypi_0 pypi
graphein 0.0.1 dev_0
h5py 3.1.0 nompi_py37h6dbf366_100 conda-forge
hdf4 4.2.13 h84186c3_1003 conda-forge
hdf5 1.10.6 nompi_h2ccf146_1110 conda-forge
icu 58.2 h0a44026_1000 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
ipymol 0.5 pypi_0 pypi
ipython 7.19.0 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
isodate 0.6.0 pypi_0 pypi
jedi 0.17.2 pypi_0 pypi
jinja2 2.11.2 pypi_0 pypi
joblib 0.17.0 py_0 conda-forge
jpeg 9d hbcb3906_0 conda-forge
kiwisolver 1.3.1 py37h8ec247f_0 conda-forge
krb5 1.17.2 h60d9502_0 conda-forge
lcms2 2.11 h11f7e16_1 conda-forge
libblas 3.8.0 21_mkl conda-forge
libboost 1.67.0 hebc422b_4
libcblas 3.8.0 21_mkl conda-forge
libcurl 7.71.1 h9bf37e3_8 conda-forge
libcxx 11.0.0 h439d374_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.2.1 hb1e8313_1007 conda-forge
libgfortran 5.0.0 h7cc5361_13 conda-forge
libgfortran5 9.3.0 h7cc5361_13 conda-forge
libglib 2.66.3 h2575888_0 conda-forge
libholoplaycore 0.1.0_rc4 0 schrodinger
libiconv 1.16 haf1e3a3_0 conda-forge
liblapack 3.8.0 21_mkl conda-forge
liblapacke 3.8.0 21_mkl conda-forge
libnetcdf 4.7.4 nompi_h4844aed_106 conda-forge
libnghttp2 1.41.0 h7580e61_2 conda-forge
libopenblas 0.3.12 openmp_h54245bb_1 conda-forge
libpng 1.6.37 h7cec526_2 conda-forge
libssh2 1.9.0 h8a08a2b_5 conda-forge
libtiff 4.1.0 hca7d577_6 conda-forge
libwebp-base 1.1.0 hbcb3906_3 conda-forge
libxml2 2.9.9 hd80cff7_2 conda-forge
llvm-openmp 11.0.0 h73239a0_1 conda-forge
llvmlite 0.34.0 pypi_0 pypi
lz4-c 1.9.2 hb1e8313_3 conda-forge
markupsafe 1.1.1 pypi_0 pypi
matplotlib 3.3.3 py37hf985489_0 conda-forge
matplotlib-base 3.3.3 py37hdacc966_0 conda-forge
mengine 1 h1de35cc_1 schrodinger
mkl 2020.4 h08c4f10_301 conda-forge
mpeg_encode 1 h1de35cc_1 schrodinger
mtz2ccp4_px 1.0 hdc02c5d_3 schrodinger
ncurses 6.2 h2e338ed_4 conda-forge
networkx 2.5 py_0 conda-forge
ninja 1.10.1 h445f430_2 conda-forge
numba 0.51.2 pypi_0 pypi
numpy 1.19.4 py37h9ebeaaa_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openssl 1.1.1h haf1e3a3_0 conda-forge
pandas 1.1.4 py37h9b0e0a3_0 conda-forge
parso 0.7.1 pypi_0 pypi
patsy 0.5.1 py_0 conda-forge
pcre 8.44 hb1e8313_0 conda-forge
pdb2pqr 2.1.2+pymol py_0 schrodinger
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 8.0.1 py37h09f51b7_0 conda-forge
pip 20.2.4 py_0 conda-forge
pixman 0.38.0 h01d97ff_1003 conda-forge
pmw 2.0.1+3 py_3 schrodinger
portalocker 2.0.0 pypi_0 pypi
prompt-toolkit 3.0.8 pypi_0 pypi
ptyprocess 0.6.0 pypi_0 pypi
pycairo 1.20.0 py37ha7df449_1 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.7.2 pypi_0 pypi
pymol 2.4.1 py37h92f0605_0 schrodinger
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.9.2 py37h2a560b1_4 conda-forge
pysocks 1.7.1 py37h2987424_2 conda-forge
python 3.7.8 h837cb1c_2_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 1_cp37m conda-forge
pytorch 1.5.0 py3.7_0 pytorch
pytorch3d 0.2.0 pypi_0 pypi
pytz 2020.4 pyhd8ed1ab_0 conda-forge
pyyaml 5.3.1 pypi_0 pypi
qt 5.9.7 h93ee506_2 conda-forge
rdflib 5.0.0 pypi_0 pypi
rdkit 2018.09.3 py37haff9cca_0 conda-forge
readline 8.0 h0678c8f_2 conda-forge
requests 2.25.0 pyhd3deb0d_0 conda-forge
rigimol 1.3 2 schrodinger
scikit-learn 0.23.2 py37ha0250bc_3 conda-forge
scipy 1.5.3 py37h821cff1_0 conda-forge
seaborn 0.11.0 h694c41f_1 conda-forge
seaborn-base 0.11.0 pyhd8ed1ab_1 conda-forge
setuptools 49.6.0 py37h2987424_2 conda-forge
sip 4.19.8 py37h0a44026_0
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.33.0 h960bd1c_1 conda-forge
statsmodels 0.12.1 py37h8ba3199_1 conda-forge
tabulate 0.8.7 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
ticc 0.1.4 pypi_0 pypi
tk 8.6.10 hb0a8c7a_1 conda-forge
torch-cluster 1.5.7 pypi_0 pypi
torch-geometric 1.6.1 pypi_0 pypi
torch-scatter 2.0.5 pypi_0 pypi
torch-sparse 0.6.7 pypi_0 pypi
torch-spline-conv 1.2.0 pypi_0 pypi
torchvision 0.6.0 py37_cpu pytorch
tornado 6.1 py37h4b544eb_0 conda-forge
tqdm 4.46.0 pypi_0 pypi
traitlets 5.0.5 pypi_0 pypi
urllib3 1.26.2 pypi_0 pypi
vmd-python 3.0.6 py37h992095b_5 conda-forge
wcwidth 0.2.5 pypi_0 pypi
wheel 0.35.1 pyh9f0ad1d_0 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
yacs 0.1.8 pypi_0 pypi
zlib 1.2.11 h7795811_1010 conda-forge
zstd 1.4.5 h289c70a_2 conda-forge
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a-r-j
commented on May 28, 2024
Hi @Arielbs that looks to be DGL/DGL-LifeSci related rather than PyTorch3d related. I think this thread may be useful: awslabs/dgl-lifesci#107
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Arielbs
commented on May 28, 2024
Thank you Arian,
I found that I need explicitly import torch prior fo graphein functionalities for the rdkit to be recognized, it works now.
Ariel
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a-r-j
commented on May 28, 2024
Great! Thanks for pointing that out, that's good to know. I hope Graphein proves useful. Please do let me know if you come across any issues or missing functionality that would be useful.
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