...
- Create a suitable directory for your calculations on scratch, e.g.
/scratch/tmp/$USER/AlphaFold/ - Create sub-directories for any locations you additionally want to use inside the container (here we create a
resultsfolder as well as a folder for storing the initialfastafile)- Those directories have to be bind-mounted into the container! (The -B flag in the singularity
runcommand)
- Those directories have to be bind-mounted into the container! (The -B flag in the singularity
- Create a Job-Script or use an interactive SLURM session to request resources on the cluster. You should request a minimum of 8 cores and 64GB of memory. GPUs are supported as well.
...
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#!/bin/bash #SBATCH --partition=gpu2080 #SBATCH --nodes=1 #SBATCH --gres=gpu:4 #SBATCH --cpus-per-task=24 #SBATCH --mem=170G #SBATCH --time=12:00:00 #SBATCH --job-name=alphafold module load AlphaFold/2.0.0-singularity singularity run \ --env TF_FORCE_UNIFIED_MEMORY=1,XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 \ -B /Applic.HPC/data/alphafold:/data \ -B .:/etc \ -B ./results:/results \ -B ./fasta:/fasta \ --pwd /app/alphafold \ --nv $ALPHAFOLD_SIFIMAGE \ --fasta_paths /fasta/Chitin-synthase-deacetylase.fasta \ --output_dir /results/ \ --max_template_date 2021-07-31 \ --data_dir /data/ \ --uniref90_database_path /data/uniref90/uniref90.fasta \ --mgnify_database_path /data/mgnify/mgy_clusters.fa \ --uniclust30_database_path /data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ --small_bfd_database_path /data/small_bfd/bfd-first_metaclustnon_clu_complete_id30_c90_final_seq.sorted_optconsensus_sequences.fasta \ --pdb70_database_path /data/pdb70/pdb70 \ --template_mmcif_dir /data/pdb_mmcif/mmcif_files \ --obsolete_pdbs_path /data/pdb_mmcif/obsolete.dat \ --model_names model_1,model_2,model_3,model_4,model_5 \ --preset reduced_dbs |