RosettaCommons / RosettaCommons/RFdiffusion

Not working with CUDA 11.1

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Description

I installed CUDA 11.1 but doesn't work. Does any one know why...
The python version is 3.9.18
CUDA version is 11.1
Pytorch version i tried both 1.9.1 and 2.1.2.

When i tried the design_unconditional.sh, i got the following errors:
(SE3nv) xtni@T640:~/tools/RFdiffusion/examples$ ./design_unconditional.sh
Traceback (most recent call last):
File "/home/xtni/tools/RFdiffusion/examples/../scripts/run_inference.py", line 25, in
from rfdiffusion.inference import utils as iu
File "/home/xtni/tools/RFdiffusion/rfdiffusion/inference/utils.py", line 6, in
from rfdiffusion.diffusion import get_beta_schedule
File "/home/xtni/tools/RFdiffusion/rfdiffusion/diffusion.py", line 12, in
from rfdiffusion.util_module import ComputeAllAtomCoords
File "/home/xtni/tools/RFdiffusion/rfdiffusion/util_module.py", line 7, in
import dgl
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/init.py", line 16, in
from .backend import load_backend, backend_name
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/backend/init.py", line 109, in
load_backend(get_preferred_backend())
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/backend/init.py", line 43, in load_backend
from .._ffi.base import load_tensor_adapter # imports DGL C library
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/_ffi/base.py", line 45, in
_LIB, _LIB_NAME, _DIR_NAME = _load_lib()
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/_ffi/base.py", line 35, in _load_lib
lib = ctypes.CDLL(lib_path[0])
File "/opt/miniconda3/envs/SE3nv/lib/python3.9/ctypes/init.py", line 382, in init
self._handle = _dlopen(self._name, mode)
OSError: /opt/miniconda3/envs/SE3nv/lib/python3.9/site-packages/dgl/../../../libcublas.so.11: undefined symbol: free_gemm_select, version libcublasLt.so.11

Here is my conda environment:
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /opt/miniconda3/envs/SE3nv/conda-meta/decorator-5.1.1-pyhd3eb1b0_0.json. Please remove this file manually (you may need to reboot to free file handles)

packages in environment at /opt/miniconda3/envs/SE3nv:

Name Version Build Channel

_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
antlr4-python3-runtime 4.9.3 pypi_0 pypi
asttokens 2.0.5 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
backcall 0.2.0 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
blas 1.0 mkl https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
brotli-python 1.0.9 py39h6a678d5_7 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ca-certificates 2023.12.12 h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
certifi 2023.11.17 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cffi 1.16.0 py39h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
charset-normalizer 2.0.4 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
click 8.1.7 pypi_0 pypi
comm 0.1.2 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
configparser 6.0.0 pypi_0 pypi
cryptography 41.0.7 py39hdda0065_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cudatoolkit 11.1.1 hb139c0e_12 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
debugpy 1.6.7 py39h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
decorator 5.1.0 pypi_0 pypi
dgl-cuda11.1 0.9.1post1 py39_0 dglteam
dllogger 1.0.0 pypi_0 pypi
docker-pycreds 0.4.0 pypi_0 pypi
e3nn 0.3.3 pypi_0 pypi
exceptiongroup 1.0.4 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
executing 0.8.3 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
freetype 2.12.1 h4a9f257_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
future 0.18.3 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
giflib 5.2.1 h5eee18b_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gitdb 4.0.11 pypi_0 pypi
gitpython 3.1.40 pypi_0 pypi
hydra-core 1.3.2 pypi_0 pypi
idna 3.4 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
importlib-metadata 6.0.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
importlib_metadata 6.0.0 hd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
intel-openmp 2021.4.0 h06a4308_3561 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ipykernel 6.25.0 py39h2f386ee_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ipython 8.15.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jedi 0.18.1 py39h06a4308_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jpeg 9e h5eee18b_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jupyter_client 8.6.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
jupyter_core 5.5.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
lcms2 2.12 h3be6417_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ld_impl_linux-64 2.38 h1181459_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
lerc 3.0 h295c915_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libblas 3.9.0 12_linux64_mkl https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libdeflate 1.17 h5eee18b_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libffi 3.4.4 h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgcc-ng 13.2.0 h807b86a_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng 11.2.0 h00389a5_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgfortran5 11.2.0 h1234567_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgomp 13.2.0 h807b86a_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng 1.6.39 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libprotobuf 3.18.3 h6239696_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsodium 1.0.18 h7b6447c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libstdcxx-ng 13.2.0 h7e041cc_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff 4.5.1 h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libwebp 1.3.2 h11a3e52_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libwebp-base 1.3.2 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libzlib 1.2.13 hd590300_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lz4-c 1.9.4 h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
matplotlib-inline 0.1.6 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl 2021.4.0 h06a4308_640 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl-service 2.4.0 py39h7f8727e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_fft 1.3.1 py39hd3c417c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_random 1.2.2 py39h51133e4_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mpmath 1.3.0 pypi_0 pypi
ncurses 6.4 h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
nest-asyncio 1.5.6 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
networkx 3.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ninja 1.10.2 h06a4308_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ninja-base 1.10.2 hd09550d_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy 1.24.3 py39h14f4228_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy-base 1.24.3 py39h31eccc5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
omegaconf 2.3.0 pypi_0 pypi
openjpeg 2.4.0 h3ad879b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
openssl 3.0.12 h7f8727e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
opt-einsum 3.3.0 pypi_0 pypi
opt-einsum-fx 0.1.4 pypi_0 pypi
packaging 23.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
parso 0.8.3 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pathtools 0.1.2 pypi_0 pypi
pexpect 4.8.0 pyhd3eb1b0_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pickleshare 0.7.5 pyhd3eb1b0_1003 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pillow 10.0.1 py39ha6cbd5a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pip 23.3.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
platformdirs 3.10.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pooch 1.7.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
promise 2.3 pypi_0 pypi
prompt-toolkit 3.0.36 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
protobuf 4.25.1 pypi_0 pypi
psutil 5.9.0 py39h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ptyprocess 0.7.0 pyhd3eb1b0_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pure_eval 0.2.2 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pycparser 2.21 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pygments 2.15.1 py39h06a4308_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pynvml 11.0.0 pypi_0 pypi
pyopenssl 23.2.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pyrsistent 0.20.0 pypi_0 pypi
pysocks 1.7.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python 3.9.18 h955ad1f_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-dateutil 2.8.2 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python_abi 3.9 2_cp39 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytorch 1.9.1 cpu_py39hc5866cc_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyyaml 6.0.1 pypi_0 pypi
pyzmq 25.1.0 py39h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
readline 8.2 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
requests 2.31.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
rfdiffusion 1.1.0 dev_0
scipy 1.10.1 py39h14f4228_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sentry-sdk 1.39.1 pypi_0 pypi
setuptools 68.2.2 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
shortuuid 1.0.11 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sleef 3.5.1 h9b69904_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
smmap 5.0.1 pypi_0 pypi
sqlite 3.41.2 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
stack_data 0.2.0 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
subprocess32 3.5.4 pypi_0 pypi
sympy 1.12 pypi_0 pypi
tk 8.6.12 h1ccaba5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
torchaudio 0.9.1 py39 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch
torchvision 0.15.2 cpu_py39h83e0c9b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tornado 6.3.3 py39h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tqdm 4.65.0 py39hb070fc8_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
traitlets 5.7.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
typing_extensions 4.7.1 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tzdata 2023c h04d1e81_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
urllib3 1.26.18 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
wandb 0.12.0 pypi_0 pypi
wcwidth 0.2.5 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
wheel 0.41.2 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xz 5.4.5 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zeromq 4.3.4 h2531618_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zipp 3.11.0 py39h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zlib 1.2.13 hd590300_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstd 1.5.5 hc292b87_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

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First steps

  1. Read the whole issue, then the project's contributing guide.
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  3. Fork the repository and make your change on a branch.
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Research direction

Reproduce examples/design_unconditional.sh and trace the import chain through scripts/run_inference.py, rfdiffusion/inference/utils.py, rfdiffusion/diffusion.py, and rfdiffusion/util_module.py. Investigate the DGL load failure for libcublas.so.11 and its free_gemm_select/libcublasLt.so.11 symbol, using the listed Python, CUDA, PyTorch, and dgl versions. Done means identifying a supported dependency combination or documenting the incompatibility and its reproduction conditions.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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