Comments (6)
canergen
commented on August 16, 2024
Is our installation guide failing? https://docs.scvi-tools.org/en/stable/installation.html
from scvi-tools.
bio-la
commented on August 16, 2024
The instructions are correct, but explicitly installing transitive dependencies (jax) that are already in the environment after installing scvi is the only way to fix the issue. is this behaviour expected?
from scvi-tools.
martinkim0
commented on August 16, 2024
Hi @bio-la, thanks for bringing up this issue. This is expected behavior because, by default, our dependencies don't specify the CUDA build of JAX as a direct dependency since not everyone will be running JAX on GPUs. So if users want CUDA-enabled installations of JAX (and PyTorch!), they should ideally be installing these before scvi-tools.
from scvi-tools.
martinkim0
commented on August 16, 2024
Also I believe pip doesn't auto-detect whether CUDA is available in the system, so calling pip install jax will always resolve to the CPU build. Not 100% sure about this though.
from scvi-tools.
bio-la
commented on August 16, 2024
thanks for the clarification!
from scvi-tools.
martinkim0
commented on August 16, 2024
I'll go ahead and close the issue if there's no additional questions
from scvi-tools.
Related Issues (20)
- 'SCVI' object has no attribute 'eval' HOT 2
- Assistance Required with scvi-tools GPU Setup on Ubuntu HOT 7
- Can we have a scVI with reconstruction distirbution as normal distribution? HOT 4
- Consider non-jitting MRVI tests/long tests pytest flag
- Jax version of VAEMixin
- Scvi in R doesn't update to scvi-tools even after uninstalling and reinstalling (I think :) HOT 3
- flax: Trying to access a property that is accessing a non-existent attribute. - JaxBaseModuleClass HOT 2
- AttributeError: module 'scvi' has no attribute 'autotune' HOT 3
- Support for weighted loss either per-batch or per-cell? HOT 1
- poor integration effect cross species HOT 2
- The scrna_raw_counts_properties method has an error in the calculation method of the raw_normalized_mean2 field, causing the raw_normalized_mean2 indicator to be invalid. HOT 4
- Issues installing recommended packages HOT 4
- Support the latest version of torchmetrics
- different hidden unit in each layer HOT 1
- cannot import name 'MRVI' from 'scvi.external' HOT 2
- bug for custom classifier in adversarial training plan HOT 2
- Error saving MrVI model HOT 2
- ImportError: cannot import name 'packaging' from 'pkg_resources' for Model Tuning using Ray HOT 4
- Issues in Load Dataset with SeuratData and convert to adata HOT 2
- Release 1.1.3
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 scvi-tools.