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rosettaparsl

Code for scaling up Rosetta on Argonne Leadership Computing Facility's HPC systems using Parsl.

https://github.com/ogkdmr/rosettaparsl

Science Score: 44.0%

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Last synced: 6 months ago · JSON representation ·

Repository

Code for scaling up Rosetta on Argonne Leadership Computing Facility's HPC systems using Parsl.

Basic Info
  • Host: GitHub
  • Owner: ogkdmr
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 53.7 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 12 months ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

rosettaparsl

Code for scaling up Rosetta on the ALCF's Aurora supercomputer using Parsl.

Installation

Instructions below assumes the following:

  • Linux Ubuntu 64-bit OS
  • Python 3.12 (in a virtual env)

If your config is different, download a different version of pyRosetta.

```shell

Create the virtual environment.

mamba create -n rosettaparsl-env python=3.12 -y mamba activate rosettaparsl-env

Download and install pyRosetta

mkdir pyRosetta cd pyRosetta

wget https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python312.ubuntu/PyRosetta4.Release.python312.ubuntu.release-395.tar.bz2

tar -vjxf PyRosetta4.Release.python312.ubuntu.release-395.tar.bz2

cd setup python setup.py install

Install the rest of the dependencies for rosettaparsl

pip install -e .

```

Usage

From the root directory of the repository.

shell nohup python -m rosettaparsl.main --config examples/<your_config.yaml> &

Contributing

For development, it is recommended to use a virtual environment. The following commands will create a virtual environment, install the package in editable mode, and install the pre-commit hooks. Perform these after installing pyRosetta.

bash pip install -U pip setuptools wheel pip install -e '.[dev,docs]' pre-commit install

Owner

  • Name: Ozan Gokdemir
  • Login: ogkdmr
  • Kind: user
  • Location: Chicago, IL
  • Company: The University of Chicago

Computer Science PhD Student at the University of Chicago

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it as below.
authors:
  - family-names: Gokdemir
    given-names: Ozan
    orcid: https://orcid.org/0000-0001-5299-1983
license: MIT
repository-code: https://github.com/ogkdmr/rosettaparsl
title: rosettaparsl
url: https://github.com/ogkdmr/rosettaparsl

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Dependencies

pyproject.toml pypi
  • PyYAML *
  • biopython *
  • chai_lab *
  • parsl >=2024.10.14
  • parsl-object-registry @ git+https://github.com/braceal/parsl_object_registry.git
  • pydantic *
  • torch *
  • transformers *