ModuleNotFoundError: No module named 'torch.utils._import_utils' #1
Description
Hi,
First of all, thankyou for making RF2-Lite available. I'm very excited to try using it to screen for PPIs!
I've followed all three steps in the installation guide in the README (that all ran smoothly). However, I'm getting some errors when running the predict_complex.py script.
From inside the networks directory, I ran the command python predict_complex.py -msa ../example/1318230at2759_735423at2759_i90.a3m -out ~/RF2-lite_test -L1 100 and I got this error
Traceback (most recent call last):
File "/home/grig0076/GitHubs/RF2-Lite/networks/predict_complex.py", line 8, in <module>
from RoseTTAFoldModel import RoseTTAFoldModule
File "/home/grig0076/GitHubs/RF2-Lite/networks/RoseTTAFoldModel.py", line 3, in <module>
from Embeddings import MSA_emb, Extra_emb, Templ_emb, Recycling
File "/home/grig0076/GitHubs/RF2-Lite/networks/Embeddings.py", line 6, in <module>
from util_module import Dropout, get_clones, create_custom_forward, rbf, init_lecun_normal
File "/home/grig0076/GitHubs/RF2-Lite/networks/util_module.py", line 7, in <module>
import dgl
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/__init__.py", line 16, in <module>
from . import (
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/dataloading/__init__.py", line 13, in <module>
from .dataloader import *
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 27, in <module>
from ..distributed import DistGraph
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/distributed/__init__.py", line 5, in <module>
from .dist_graph import DistGraph, DistGraphServer, edge_split, node_split
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/distributed/dist_graph.py", line 11, in <module>
from .. import backend as F, graphbolt as gb, heterograph_index
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/graphbolt/__init__.py", line 8, in <module>
from .base import *
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/graphbolt/base.py", line 8, in <module>
from torchdata.datapipes.iter import IterDataPipe
ModuleNotFoundError: No module named 'torchdata'
So I went and installed torchvision (conda install torchvision) and torchdata (pip install torchdata). I'm now, getting this error here:
Traceback (most recent call last):
File "/home/grig0076/GitHubs/RF2-Lite/networks/predict_complex.py", line 8, in <module>
from RoseTTAFoldModel import RoseTTAFoldModule
File "/home/grig0076/GitHubs/RF2-Lite/networks/RoseTTAFoldModel.py", line 3, in <module>
from Embeddings import MSA_emb, Extra_emb, Templ_emb, Recycling
File "/home/grig0076/GitHubs/RF2-Lite/networks/Embeddings.py", line 6, in <module>
from util_module import Dropout, get_clones, create_custom_forward, rbf, init_lecun_normal
File "/home/grig0076/GitHubs/RF2-Lite/networks/util_module.py", line 7, in <module>
import dgl
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/__init__.py", line 16, in <module>
from . import (
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/dataloading/__init__.py", line 13, in <module>
from .dataloader import *
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 27, in <module>
from ..distributed import DistGraph
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/distributed/__init__.py", line 5, in <module>
from .dist_graph import DistGraph, DistGraphServer, edge_split, node_split
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/distributed/dist_graph.py", line 11, in <module>
from .. import backend as F, graphbolt as gb, heterograph_index
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/graphbolt/__init__.py", line 8, in <module>
from .base import *
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/dgl/graphbolt/base.py", line 8, in <module>
from torchdata.datapipes.iter import IterDataPipe
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/torchdata/datapipes/__init__.py", line 11, in <module>
from . import iter, map, utils
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/torchdata/datapipes/iter/__init__.py", line 79, in <module>
from torchdata.datapipes.iter.util.cacheholder import (
File "/home/grig0076/miniconda3/envs/RF2Lite_torch/lib/python3.10/site-packages/torchdata/datapipes/iter/util/cacheholder.py", line 24, in <module>
from torch.utils._import_utils import dill_available
ModuleNotFoundError: No module named 'torch.utils._import_utils'
Which seems a little odd to me since the correct version of torch should have been installed when I set up the conda environment using the yaml file. Are there other torch dependencies that I could potentially me missing? This is what by conda environment is looking like.
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
aiohappyeyeballs 2.4.0 py310h06a4308_0
aiohttp 3.10.5 py310h5eee18b_0
aiosignal 1.2.0 pyhd3eb1b0_0
async-timeout 4.0.3 py310h06a4308_0
attrs 23.1.0 py310h06a4308_0
blas 1.0 mkl
brotli-python 1.0.9 py310h6a678d5_8
bzip2 1.0.8 h5eee18b_6
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd3eb1b0_0
click 8.1.7 pypi_0 pypi
configparser 7.1.0 pypi_0 pypi
cpuonly 2.0 0 pytorch
cuda-cudart 11.7.99 0 nvidia
cuda-cupti 11.7.101 0 nvidia
cuda-libraries 11.7.1 0 nvidia
cuda-nvrtc 11.7.99 0 nvidia
cuda-nvtx 11.7.91 0 nvidia
cuda-runtime 11.7.1 0 nvidia
cuda-version 12.6 3 nvidia
dgl 2.1.0.cu117 py310_0 dglteam/label/cu117
dllogger 1.0.0 pypi_0 pypi
docker-pycreds 0.4.0 pypi_0 pypi
e3nn 0.3.3 pypi_0 pypi
filelock 3.13.1 py310h06a4308_0
freetype 2.10.4 h0708190_1 conda-forge
frozenlist 1.4.0 py310h5eee18b_0
fsspec 2024.6.1 py310h06a4308_0
giflib 5.2.1 h36c2ea0_2 conda-forge
gitdb 4.0.11 pypi_0 pypi
gitpython 3.1.43 pypi_0 pypi
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py310heeb90bb_0
idna 3.7 py310h06a4308_0
intel-openmp 2023.1.0 hdb19cb5_46306
jinja2 3.1.4 py310h06a4308_0
joblib 1.4.2 py310h06a4308_0
jpeg 9e h166bdaf_1 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.40 h12ee557_0
libcublas 11.10.3.66 0 nvidia
libcufft 10.7.2.124 h4fbf590_0 nvidia
libcufile 1.11.1.6 0 nvidia
libcurand 10.3.7.68 0 nvidia
libcusolver 11.4.0.1 0 nvidia
libcusparse 11.7.4.91 0 nvidia
libffi 3.4.4 h6a678d5_1
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libnpp 11.7.4.75 0 nvidia
libnvjpeg 11.8.0.2 0 nvidia
libpng 1.6.39 h5eee18b_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.2.0 hf544144_3 conda-forge
libuuid 1.41.5 h5eee18b_0
libwebp 1.2.0 h3452ae3_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
llvm-openmp 14.0.6 h9e868ea_0
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markupsafe 2.1.3 py310h5eee18b_0
mkl 2023.1.0 h213fc3f_46344
mkl-service 2.4.0 py310h5eee18b_1
mkl_fft 1.3.10 py310h5eee18b_0
mkl_random 1.2.7 py310h1128e8f_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpmath 1.3.0 py310h06a4308_0
multidict 6.0.4 py310h5eee18b_0
ncurses 6.4 h6a678d5_0
networkx 3.3 py310h06a4308_0
numpy 1.26.4 py310h5f9d8c6_0
numpy-base 1.26.4 py310hb5e798b_0
openssl 3.0.15 h5eee18b_0
opt-einsum 3.4.0 pypi_0 pypi
opt-einsum-fx 0.1.4 pypi_0 pypi
packaging 24.1 pypi_0 pypi
pathtools 0.1.2 pypi_0 pypi
pillow 9.4.0 py310h6a678d5_0
pip 24.2 py310h06a4308_0
promise 2.3 pypi_0 pypi
protobuf 5.28.2 pypi_0 pypi
psutil 5.9.0 py310h5eee18b_0
pybind11-abi 4 hd3eb1b0_1
pyg 2.5.2 py310_torch_2.2.0_cpu pyg
pynvml 11.0.0 pypi_0 pypi
pyparsing 3.1.2 py310h06a4308_0
pysocks 1.7.1 py310h06a4308_0
python 3.10.14 h955ad1f_1
python-dateutil 2.9.0.post0 pypi_0 pypi
pytorch 2.2.2 py3.10_cpu_0 pytorch
pytorch-cuda 11.7 h778d358_5 pytorch
pytorch-mutex 1.0 cpu pytorch
pyyaml 6.0.1 py310h5eee18b_0
readline 8.2 h5eee18b_0
requests 2.32.3 py310h06a4308_0
scikit-learn 1.5.1 py310h1128e8f_0
scipy 1.13.1 py310h5f9d8c6_0
sentry-sdk 2.14.0 pypi_0 pypi
setuptools 75.1.0 py310h06a4308_0
shortuuid 1.0.13 pypi_0 pypi
six 1.16.0 pypi_0 pypi
smmap 5.0.1 pypi_0 pypi
sqlite 3.45.3 h5eee18b_0
subprocess32 3.5.4 pypi_0 pypi
sympy 1.13.2 py310h06a4308_0
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 3.5.0 py310h2f386ee_0
tk 8.6.14 h39e8969_0
torchdata 0.8.0 pypi_0 pypi
torchvision 0.15.2 cpu_py310h83e0c9b_0
tqdm 4.66.5 py310h2f386ee_0
typing_extensions 4.11.0 py310h06a4308_0
tzdata 2024a h04d1e81_0
urllib3 2.2.3 py310h06a4308_0
wandb 0.12.0 pypi_0 pypi
wheel 0.44.0 py310h06a4308_0
xz 5.4.6 h5eee18b_1
yaml 0.2.5 h7b6447c_0
yarl 1.11.0 py310h5eee18b_0
zlib 1.2.13 h5eee18b_1
zstd 1.5.0 ha95c52a_0 conda-forge
I'm running on a linux server, Red Hat Enterprise Linux 8.
Any help would be greatly appreciated!