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• The number of threads/cores was hardcoded within the AlphaFold internal code, you should request ~8 CPU cores when submitting AlphaFold jobs. Requesting more cores will not improve performance, and it will make your job pend longer before it starts.

• The required database was downloaded into a centralized location (i.e., /n/shared_db/alphafold/) for the benefit of all O2 users. Please don’t download the 2 terabytes yourself, as that would be a waste of space.

• Submit your AlphaFold jobs to a GPU partition. For more about the GPU partitions, please visit our wiki page - Using O2 GPU resources.

• For version 2.2.0, submissions will assume you are running on a GPU by default. If for some reason you desire to run explicitly on CPU, please specify the --use_cpu flag.

• As of version 2.2.0, the base implementation has changed how the amber relaxation step is requested by the user. If you would like to run your analysis with WITHOUT the relaxed models with the 2.2.0 module, please include the --no_run_relax flag (as well as the --enable_gpu_relax flag if you are submitting to a GPU partition).For version 2.2.0, submissions will assume you are running on a GPU by default. If for some reason you desire to run explicitly on CPU, you will have to submit to a partition that does not have GPUs (e.g. short, etc.).

If you have any questions, you can email us at rchelp@hms.harvard.edu.