Comments (4)
@cartal @sruthi-hub Since the repo seems to be inactive, I am pasting here the session info from a working local conda installation of scNym. Maybe this is useful for you to get scNym running locally.
You will also need CUDA toolkit 10.2.89
& cudnn 8.2.4.15
for cuda 10.2. My conda env also has gcc 11.1.0 but I am not sure if this is strictly needed (my HPC system needs a bunch of stuff by default).
absl-py==1.0.0
anndata==0.7.4
anyio==3.5.0
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
asttokens==2.0.5
attrs==21.4.0
Babel==2.10.1
backcall==0.2.0
beautifulsoup4==4.11.1
bleach==5.0.0
cachetools==4.2.4
certifi==2022.9.24
cffi==1.15.0
chardet==3.0.4
charset-normalizer==2.1.1
ConfigArgParse==1.1
cycler==0.11.0
debugpy==1.6.0
decorator==5.1.1
defusedxml==0.7.1
dunamai==1.11.1
entrypoints==0.4
executing==0.8.3
fastjsonschema==2.15.3
fonttools==4.32.0
get_version==3.5.4
google-auth==1.35.0
google-auth-oauthlib==0.4.6
grpcio==1.44.0
h5py==2.10.0
idna==3.4
igraph==0.9.10
importlib-metadata==4.11.3
importlib-resources==5.7.1
ipykernel==6.13.0
ipython==8.2.0
ipython-genutils==0.2.0
jedi==0.18.1
Jinja2==3.1.1
joblib==1.1.0
json5==0.9.6
jsonschema==4.4.0
jupyter-client==7.2.2
jupyter-core==4.10.0
jupyter-server==1.16.0
jupyterlab==3.3.4
jupyterlab-pygments==0.2.2
jupyterlab-server==2.13.0
kiwisolver==1.4.2
legacy-api-wrap==1.2
leidenalg==0.8.0
llvmlite==0.32.1
louvain==0.7.0
Markdown==3.3.6
MarkupSafe==2.1.1
matplotlib==3.5.1
matplotlib-inline==0.1.3
mistune==0.8.4
more-itertools==8.12.0
natsort==8.1.0
nbclassic==0.3.7
nbclient==0.6.0
nbconvert==6.5.0
nbformat==5.3.0
nest-asyncio==1.5.5
networkx==2.8
notebook==6.4.11
notebook-shim==0.1.0
numba==0.49.1
numexpr==2.8.1
numpy==1.23.3
numpy-groupies==0.9.13
oauthlib==3.2.0
packaging==21.3
pandas==1.4.2
pandocfilters==1.5.0
parso==0.8.3
patsy==0.5.2
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.2.0
pluggy==0.13.1
prometheus-client==0.14.1
prompt-toolkit==3.0.29
protobuf==3.20.0
psutil==5.9.0
ptyprocess==0.7.0
pure-eval==0.2.2
py==1.11.0
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycparser==2.21
Pygments==2.11.2
pynndescent==0.5.6
pyparsing==3.0.8
pyrsistent==0.18.1
pytest==5.4.1
python-dateutil==2.8.1
python-igraph==0.9.10
pytz==2022.1
PyYAML==5.3.1
pyzmq==22.3.0
requests==2.28.1
requests-cache==0.5.2
requests-oauthlib==1.3.0
requests-toolbelt==0.9.1
rsa==4.8
scanpy==1.6.0
scikit-learn==0.22.2.post1
scikit-misc==0.1.3
scipy==1.8.0
scnym==0.3.2
seaborn==0.11.2
Send2Trash==1.8.0
setuptools-scm==6.4.2
sinfo==0.3.4
six==1.14.0
sniffio==1.2.0
soupsieve==2.3.2.post1
stack-data==0.2.0
statsmodels==0.13.2
stdlib-list==0.8.0
tables==3.6.1
tensorboard==2.2.1
tensorboard-plugin-wit==1.6.0.post2
tensorboardX==2.1
terminado==0.13.3
texttable==1.6.4
tinycss2==1.1.1
tomli==2.0.1
torch==1.11.0
torchvision==0.12.0
tornado==6.1
tqdm==4.44.1
traitlets==5.1.1
typing_extensions==4.3.0
umap-learn==0.3.10
urllib3==1.26.12
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.3.2
Werkzeug==2.1.1
zipp==3.8.0
from scnym.
I run into the same issue when attempting to run the training on Google Colab (high mem VM with A100 GPU). Installed scNym from github using pip.
Any help is appreciated!
from scnym.
@jacobkimmel any help/advice with this would be much appreciated! Thanks
from scnym.
@cartal @nagendraKU Were you able to fix this? I have the same error.
from scnym.
Related Issues (15)
- segmentation fault after training finished
- Human atlas not available in notebook? HOT 4
- domain_groupby argument missing HOT 3
- Add edge-case testing for "jackpot" cells
- install instructions dont work - scnym won't install with python 3.10 HOT 1
- scnym not working; Reason: image not found HOT 2
- RuntimeError: NaN loss encountered in training HOT 2
- Lack of support for sparse matrices makes scNym unusable for large datasets
- Unable to run the model successfully. HOT 1
- No longer installs HOT 1
- scNym Will Not Install HOT 5
- Problems with scnym installation using conda HOT 2
- Multiple categories HOT 4
- Annotating Seurat clusters HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from scnym.