sdvae
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Hanjun-Dai
Assertion Error
I've set up everything according to the instructions, except with more recent packages (I don't think this has much of an effect though?).
When running the 2d molecular visualization, I get an assertion error on line 264 of attribute_tree_decoder.py: https://github.com/Hanjun-Dai/sdvae/blob/bd26ea949c496419634fd2cf4802fc8e19a9194c/mol_vae/mol_decoder/attribute_tree_decoder.py#L264 This is because cap_remain is equal to 0 but it should be >0.
I'm not sure why this happens at all, the only thing I can think of is package versions but I don't know why that would cause this error. My package list is below:
# packages in environment at /home/vinay/miniconda3/envs/sdvae:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
argparse 1.4.0 pypi_0 pypi
blas 1.0 mkl
boost 1.74.0 py38h2b96118_5 conda-forge
boost-cpp 1.74.0 h6cacc03_7 conda-forge
bottleneck 1.3.7 py38ha9d4c09_0
brotli 1.0.9 h5eee18b_8
brotli-bin 1.0.9 h5eee18b_8
bzip2 1.0.8 h5eee18b_6
ca-certificates 2024.9.24 h06a4308_0
cairo 1.16.0 hb05425b_5
click 8.1.7 pypi_0 pypi
contourpy 1.1.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
expat 2.6.3 h6a678d5_0
filelock 3.13.1 pypi_0 pypi
fontconfig 2.14.1 h52c9d5c_1
fonttools 4.55.0 pypi_0 pypi
freetype 2.10.4 h5ab3b9f_0
fsspec 2024.2.0 pypi_0 pypi
future 1.0.0 pypi_0 pypi
glib 2.78.4 h6a678d5_0
glib-tools 2.78.4 h6a678d5_0
greenlet 3.0.1 py38h6a678d5_0
h5py 3.11.0 pypi_0 pypi
icu 69.1 h9c3ff4c_0 conda-forge
importlib-resources 6.4.5 pypi_0 pypi
importlib_resources 6.4.0 py38h06a4308_0
intel-openmp 2023.1.0 hdb19cb5_46306
jinja2 3.1.3 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jpeg 9e h5eee18b_3
kiwisolver 1.4.7 pypi_0 pypi
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.40 h12ee557_0
lerc 3.0 h295c915_0
libbrotlicommon 1.0.9 h5eee18b_8
libbrotlidec 1.0.9 h5eee18b_8
libbrotlienc 1.0.9 h5eee18b_8
libdeflate 1.17 h5eee18b_1
libffi 3.4.4 h6a678d5_1
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libglib 2.78.4 hdc74915_0
libgomp 14.2.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libpng 1.6.39 h5eee18b_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.5.1 h6a678d5_0
libuuid 1.41.5 h5eee18b_0
libwebp-base 1.3.2 h5eee18b_1
libxcb 1.15 h7f8727e_0
libxml2 2.9.14 haae042b_4 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lz4-c 1.9.4 h6a678d5_1
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.7.5 pypi_0 pypi
matplotlib-base 3.7.2 py38h1128e8f_0
mkl 2023.1.0 h213fc3f_46344
mkl-service 2.4.0 py38h5eee18b_1
mkl_fft 1.3.8 py38h5eee18b_0
mkl_random 1.2.4 py38hdb19cb5_0
mpmath 1.3.0 pypi_0 pypi
ncurses 6.4 h6a678d5_0
networkx 3.0 pypi_0 pypi
nltk 3.9.1 pypi_0 pypi
numexpr 2.8.4 py38hc78ab66_1
numpy 1.24.1 pypi_0 pypi
numpy-base 1.24.3 py38h060ed82_1
nvidia-cublas-cu12 12.4.2.65 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.4.99 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.4.99 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.4.99 pypi_0 pypi
nvidia-cudnn-cu12 9.1.0.70 pypi_0 pypi
nvidia-cufft-cu12 11.2.0.44 pypi_0 pypi
nvidia-curand-cu12 10.3.5.119 pypi_0 pypi
nvidia-cusolver-cu12 11.6.0.99 pypi_0 pypi
nvidia-cusparse-cu12 12.3.0.142 pypi_0 pypi
nvidia-nccl-cu12 2.20.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.4.99 pypi_0 pypi
nvidia-nvtx-cu12 12.4.99 pypi_0 pypi
openjpeg 2.5.2 he7f1fd0_0
openssl 3.0.15 h5eee18b_0
packaging 24.2 pypi_0 pypi
pandas 2.0.3 py38h1128e8f_0
pcre2 10.42 hebb0a14_1
pillow 10.2.0 pypi_0 pypi
pip 24.2 py38h06a4308_0
pixman 0.40.0 h7f8727e_1
progressbar 2.5 pypi_0 pypi
pycairo 1.23.0 py38hd1222b9_0
pyparsing 3.1.4 pypi_0 pypi
python 3.8.20 he870216_0
python-dateutil 2.9.0post0 py38h06a4308_2
python-tzdata 2023.3 pyhd3eb1b0_0
python_abi 3.8 2_cp38 conda-forge
pytz 2024.2 pypi_0 pypi
rdkit 2022.03.2 py38ha829ea6_0 conda-forge
readline 8.2 h5eee18b_0
regex 2024.11.6 pypi_0 pypi
reportlab 3.6.13 py38h5eee18b_0
scikit-learn 1.3.2 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
setuptools 75.1.0 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlalchemy 2.0.34 py38h00e1ef3_0
sqlite 3.45.3 h5eee18b_0
sympy 1.13.1 pypi_0 pypi
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 3.5.0 pypi_0 pypi
tk 8.6.14 h39e8969_0
torch 2.4.0+cu124 pypi_0 pypi
torchaudio 2.4.0+cu124 pypi_0 pypi
torchvision 0.19.0+cu124 pypi_0 pypi
tqdm 4.67.0 pypi_0 pypi
triton 3.0.0 pypi_0 pypi
typing-extensions 4.9.0 pypi_0 pypi
typing_extensions 4.11.0 py38h06a4308_0
tzdata 2024.2 pypi_0 pypi
unicodedata2 15.1.0 py38h5eee18b_0
wheel 0.44.0 py38h06a4308_0
xz 5.4.6 h5eee18b_1
zipp 3.20.2 py38h06a4308_0
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 hc292b87_0
Package Version
------------------------ ------------ PIP PACKAGES
Bottleneck 1.3.7
click 8.1.7
contourpy 1.0.5
cycler 0.11.0
filelock 3.13.1
fonttools 4.51.0
fsspec 2024.2.0
future 1.0.0
greenlet 3.0.1
h5py 3.11.0
importlib_resources 6.4.0
Jinja2 3.1.3
joblib 1.4.2
kiwisolver 1.4.4
MarkupSafe 2.1.5
matplotlib 3.7.2
mkl-fft 1.3.8
mkl-random 1.2.4
mkl-service 2.4.0
mpmath 1.3.0
networkx 3.0
nltk 3.9.1
numexpr 2.8.4
numpy 1.24.1
nvidia-cublas-cu12 12.4.2.65
nvidia-cuda-cupti-cu12 12.4.99
nvidia-cuda-nvrtc-cu12 12.4.99
nvidia-cuda-runtime-cu12 12.4.99
nvidia-cudnn-cu12 9.1.0.70
nvidia-cufft-cu12 11.2.0.44
nvidia-curand-cu12 10.3.5.119
nvidia-cusolver-cu12 11.6.0.99
nvidia-cusparse-cu12 12.3.0.142
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.4.99
nvidia-nvtx-cu12 12.4.99
packaging 24.1
pandas 2.0.3
pillow 10.2.0
pip 24.2
progressbar 2.5
pycairo 1.23.0
pyparsing 3.0.9
python-dateutil 2.9.0.post0
pytz 2024.1
regex 2024.11.6
reportlab 3.6.13
scikit-learn 1.3.2
scipy 1.10.1
setuptools 75.1.0
six 1.16.0
SQLAlchemy 2.0.34
sympy 1.13.1
threadpoolctl 3.5.0
torch 2.4.0+cu124
torchaudio 2.4.0+cu124
torchvision 0.19.0+cu124
tqdm 4.67.0
triton 3.0.0
typing_extensions 4.11.0
tzdata 2023.3
unicodedata2 15.1.0
wheel 0.44.0
zipp 3.20.2
Any help is appreciated!!
