Installing OpenFold Locally on O2

Set Up for Install

First, start an interactive session that uses GPU resources (https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1629290761) :

Load modules needed for later steps:

Navigate to the directory you would like to install OpenFold in and clone the repository:

Install Main OpenFold Conda Package

While inside the OpenFold directory, create a Conda (https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1594263516) environment. In this example the name of the environment we will create is openfold_test. This can be changed here, but it will carry over to other options in some later steps.

Activate this new environment using the command

The prompt inside the terminal should change to contain the Conda environment name in parenthesis, in this case (openfold_test). We will add additional python modules and set up CUDA kernels using the commands below

Download Parameters and Other Components

Here, we will open another terminal and ssh into transfer.rc.hms.harvard.edu. This node is configured to efficiently download data to O2. For more information, please visit https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1588662157 .

Download dependent files. These files are put into the correct directory automatically as long as we are in the OpenFold directory cloned earlier.

Export Paths

Afterwards, we will export the path to this directory. If you would like to have this program featured every time you log in , add the export line to your .bashrc file.