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Folding@Home Utility Scripts and Notebooks

This repository contains my scripts and notebooks to manage folding@home data. Use them as you wish but beware of bugs! Please let me know if you find some bug or problem and please share your improvements to the code!

Current Files

  • fah-progress.ipynb: this notebook will download the leveldb of the workserver and help-you study the state of your data.
  • environment.yml: this will install with conda the necessary libraries to run the code of this repository.
  • environment-mac.yml: this will install with conda necessary libraries for MacOS X systems except for the plyvel library

Install Environment

Linux

You must also install leveldb to use the fah-progress.ipynb.

conda env create -f environment.yml
conda activate fah-leveldb
ipython kernel install --user --name=fah-leveldb

MacOS X - by Sukrit Singh (sukrit.singh@choderalab.org)

To actually install the environment, first do:

conda env create -f environment-mac.yml
conda activate fah-leveldb
ipython kernel install --user --name=fah-leveldb

However, you must do a manual installation of the plyvel library due to differences in the Darwin OS.

Next, download the plyvel library manually from the github page.

Unzip and navigate into the plyvel package:

unzip plyvel-master.zip
cd plyvel-master

Next, in plyvel-master/setup.py, replace Line 17 with an updated version:

extra_compile_args = ['-Wall', '-g', '-x', 'c++', '-std=c++11', '-fno-rtti']

Save the updated setup.py.

Next we will install leveldb: It turns out that the plyvel repo already has the scripts you need to setup leveldb. Simply go to plyvel-master/scripts and run the following scripts - Run them in the following order (note that you need cmake):

  1. ./cibuildwheel-before-build.sh
  2. ./install-leveldb.sh
  3. ./install-snappy.sh

One alternative approach : To install leveldb on MacOS, you can use Homebrew

brew install leveldb

Note that homebrew installation can be a bit tricky on MacOS Big Sur

Once you leveldb installed:

Run the following commands in the same directory where setup.py is:

make
python setup.py install

Test whether plyvel works using python -c 'import plyvel' - this should return no output if everything worked!

Now feel free to use fah-progress.ipynb for anything you want!