NOTICE: FULL O2 Cluster Outage, January 3 - January 10th

O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10

  • on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
  • on Jan 3 (6:00 PM): O2 systems will start being powered off.

This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.

Specifically:

  • The O2 Cluster will be completely offline, including O2 Portal.
  • All data on O2 will be inaccessible.
  • Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
  • Websites on O2 will be completely offline, including all web content.

More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation

Installing OpenFold Locally on O2

Owned by Calvin Cox
Last updated: Jun 01, 2023
2 min read

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 bash

Load modules needed for later steps:

$ module load gcc/9.2.0 miniconda3/4.10.3 cuda/11.7 git/2.35.3 cmake/3.22.2

Navigate 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=$PWD

Install 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.

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