Skip to content
This repository has been archived by the owner on Sep 19, 2024. It is now read-only.

Commit

Permalink
improving readme
Browse files Browse the repository at this point in the history
  • Loading branch information
jkobject committed Aug 14, 2024
1 parent a6db713 commit 0c7961f
Showing 1 changed file with 6 additions and 8 deletions.
14 changes: 6 additions & 8 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -60,16 +60,12 @@ scPRINT can be used to perform the following analyses:

For the moment scPRINT has been tested on MacOS and Linux (Ubuntu 20.04) with Python 3.10.

If you want to be using flashattention2, know that it only supports triton 2.0 MLIR's version and torch==2.0.0 for now.

```bash
conda create -n "[whatever]" python==3.10
conda create -n "[whatever]" python==3.10 #scprint might work with python >3.10, but it is not tested
#one of
pip install scprint # OR
pip install scprint[dev] # for the dev dependencies (building etc..) OR
pip install scprint[flash] && pip install -e "git+https:/
/github.com/triton-lang/triton.git@legacy-backend
#egg=triton&subdirectory=python" # to use flashattention2, you will need to install triton 2.0.0.dev20221202 specifically, working on removing this dependency # only if you have a compatible gpu (e.g. not available for apple GPUs for now, see https://github.com/triton-lang/triton?tab=readme-ov-file#compatibility)
pip install scprint[flash] # to use flashattention2 with triton: only if you have a compatible gpu (e.g. not available for apple GPUs for now, see https://github.com/triton-lang/triton?tab=readme-ov-file#compatibility)
#OR pip install scPRINT[dev,flash]
```

Expand All @@ -85,10 +81,12 @@ Please refer to their documentation for more information:

scPRINT can run on machines without GPUs, but it will be slow. It is highly recommended to use a GPU for inference.

Once you have a GPU, and installed the required drivers, you might need to install a specific version of pytorch that is compatible with your drivers (e.g. nvidia 550 drivers will lead to a nvidia toolkit 11.7 or 11.8 which will mean you need to install pytorch 2.2.0 using the command:
`pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu118` on linux
Once you have a GPU, and installed the required drivers, you might need to install a specific version of pytorch that is compatible with your drivers (e.g. nvidia 550 drivers will lead to a nvidia toolkit 11.7 or 11.8 which might mean you need to re-install a different flavor of pytorch for things to work. e.g. using the command:
`pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu118` on my case on linux
).

I was able to test it with nvidia 11.7, 11.8, 12.2.

### lamin.ai

⚠️ if you want to use the scDataloader's multi-dataset mode or if you want to preprocess datasets and other functions of the model, you will need to use lamin.ai.
Expand Down

0 comments on commit 0c7961f

Please sign in to comment.