Skip to content

Jax cuda pip fix #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ChristinaLK wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Jax cuda pip fix #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0ef36e9
Update README.md
ChristinaLK Apr 14, 2023
ebacf43
Update page to pull jax+CUDA
ChristinaLK Apr 14, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 24 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,22 +6,41 @@ environment.

Build instructions from [non-docker setting](https://github.com/kalininalab/alphafold_non_docker) by kalininalab were used.

## Setup

Clone repository into your home directory and `cd` into the cloned folder.

## Build container
```
# build base container
sudo /usr/software/singularity/bin/singularity build base.sif base.def
apptainer build base.sif base.def
# build alphafold container
sudo /usr/software/singularity/bin/singularity build alphafold.sif alphafold.def
apptainer build alphafold.sif alphafold.def
```

## Run AlphaFold
## Run AlphaFold Job

Customize or add the following options to a typical CHTC HTCondor submit file:

```
./alphafold.py /path/to/fasta/file
universe = container
container_image = alphafold.sif
requirements = (HasGpulabData == true)

transfer_executable = false
# replace with multimer.sh if applicable
executable = /opt/alphafold/monomer.sh
arguments = /gpulab_data/alphafold FASTA_file

transfer_input_files = alphafold.sif, FASTA_file

# request CPUs, GPUS, etc.
```


### Notes

* The alphafold.py run script has no requirements and should run in vanilla python 3.8.
* The run script allows customizing the database location and max_template_date. Call with `-h` to see usage information.
* By default, this uses the `monomer` model for monomers and the `multimer` model for multimers,
and uses the `full_dbs` option for better quality results. For more details, see https://github.com/deepmind/alphafold#running-alphafold
and uses the `full_dbs` option for better quality results. For more details, see https://github.com/deepmind/alphafold#running-alphafold
2 changes: 1 addition & 1 deletion alphafold.def
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ From: base.sif
wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0
pip install --upgrade jax jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_releases.html
pip install --upgrade jax jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
pip install -r alphafold/requirements.txt

cd /opt/miniconda3/envs/alphafold/lib/python3.8/site-packages/ && patch -p0 < $alphafold_path/docker/openmm.patch
Expand Down