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The walltime and memory requests are based on the observed job efficiency data when using the T1050.fasta file with `--preset=full_dbs` . These will likely need to be increased for other fasta input files, or when running with a different preset.

Important note.

For later versions of Alphafold you may need to update the flags.  

API changes between v2.0.0 and v2.1.0

We tried to keep the API as much backwards compatible as possible, but we had to change the following:

  • The RunModel.predict() now needs a random_seed argument as MSA sampling happens inside the Multimer model.
  • The preset flag in run_alphafold.py and run_docker.py was split into db_preset and model_preset.
  • The models to use are not specified using model_names but rather using the model_preset flag. If you want to customize which models are used for each preset, you will have to modify the the MODEL_PRESETS dictionary in alphafold/model/config.py.
  • Setting the data_dir flag is now needed when using run_docker.py.

CPU job for AlphaFold/2.0.0-foss-2020b

Code Block
languagebash
titleAlphaFold-CPU-example.job
linenumberstrue
collapsetrue
#!/usr/bin/env bash

#SBATCH --job-name=alphafold-cpu-test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=80G
#SBATCH --time=24:00:00
#SBATCH --output=%x-%j.log


# Load AlphaFold module
module load bio/AlphaFold/2.0.0-foss-2020b

# Path to genetic databases
export ALPHAFOLD_DATA_DIR=/mnt/bb/striped/alphafold_db/20210908/

# Optional: uncomment to change number of CPU cores to use for hhblits/jackhmmer
# export ALPHAFOLD_HHBLITS_N_CPU=8
# export ALPHAFOLD_JACKHMMER_N_CPU=8

# Run AlphaFold
alphafold --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --preset=full_dbs --output_dir=$PWD --model_names=model_1,model_2,model_3,model_4,model_5


GPU example job AlphaFold/2.0.0-foss-2020b

Code Block
languagebash
titleAlphaFold-CPU-example.job
linenumberstrue
collapsetrue
#!/usr/bin/env bash

#SBATCH --job-name=alphafold-gpu-test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=10
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu
#SBATCH --time=4:00:00
#SBATCH --output=%x-%j.log

# Load AlphaFold module
module load bio/AlphaFold/2.0.0-fosscuda-2020b

# Path to genetic databases
export ALPHAFOLD_DATA_DIR=/mnt/bb/striped/alphafold_db/20210908/

# Optional: uncomment to change number of CPU cores to use for hhblits/jackhmmer
# export ALPHAFOLD_HHBLITS_N_CPU=8
# export ALPHAFOLD_JACKHMMER_N_CPU=8

# Run AlphaFold
alphafold --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --preset=full_dbs --output_dir=$PWD --model_names=model_1,model_2,model_3,model_4,model_5

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