Installing OpenFold Locally on O2
- Calvin Cox
Set Up for Install
First, start an interactive session that uses GPU resources (Using O2 GPU resources) :
$ srun --pty -p gpu --gres=gpu:1 -t 0-05:00 --mem 24G -c 4 bashLoad modules needed for later steps:
$ module load gcc/9.2.0 miniconda3/4.10.3 cuda/11.7 git/2.35.3 cmake/3.22.2Navigate to the directory you would like to install OpenFold in and clone the repository:
$ git clone https://github.com/aqlaboratory/openfold.git
$ cd openfold
$ openfold_dir=$PWDInstall Main OpenFold Conda Package
While inside the OpenFold directory, create a Conda (Conda on O2) 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 File Transfer .
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.
Note: When OpenFold is running it will require HH-Suite, which is now installed as a module on O2. Run module load hh-suite/3.3.0 to enable to enable the module during runs.