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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 < 2.3.1, and /n/shared_db/alphafold-2.3 for 2.3.1) 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 WITHOUT the relaxed models with the 2.2.0 module, please include the --no_run_relax flag.

• There is a known issue with Alphafold (all versions) not being able to successfully perform the relaxation step if requested via GPU (the default option); we can only recommend that users refrain from utilizing the relaxation option until the developers address this. We have received user reports that using CPU relaxation is successful, however (--enable_cpu_relax), so users can attempt to use this flag if relaxation is required.

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