diff --git a/README.md b/README.md index c6fabf5..83bda6d 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,24 @@ _4096_ on NVIDIA A100 Graphics card with 80 GB of memory with `--subbatch_size` set to 128 without hitting 70 GB of memory. This version's model is more sensitive to `--subbatch_size`. +### Setting Subbatch + +Subbatch makes a trade-off between time and space. +One can greatly reduce the space requirements by setting `--subbatch_size` +very low. +The default is the number of residues in the sequence and the lowest +possible number is 1. +For now we do not have a rule of thumb for setting the `--subbatch_size`, +but we suggest half the value if you run into GPU memory limitations. + +### MacOS Users + +For macOS users, we support MPS (Apple Silicon) acceleration if the user +installs the latest nightly version of PyTorch. +Also, current code also requires macOS users need to `git clone` the +repository and use `python main. +py` (see below) to run the model. + ## Setup To prepare the environment to run OmegaFold, @@ -55,12 +73,14 @@ omegafold INPUT_FILE.fasta OUTPUT_DIRECTORY And voila! -### Alternatively +### Alternatively (Or MacOS users) Even if this failed, since we use minimal 3rd party libraries, you can always just install the latest [PyTorch](https://pytorch.org) and [biopython](https://biopython.org) (and that's it!) yourself. +For mps accelerator, macOS users may need to install the lastest nightly +version of PyTorch. In this case, you could run ```commandline