examples/alphafold3.md
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## AlphaFold3 Example
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In order to run AlphaFold3 with SBGrid you must:
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1. Obtain the AF3 models
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2. Download the AF3 databases
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-### Obtain the AF3 models.
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+### Obtain the AF3 models
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-SBGrid cannot distribute these. You must apply through this form:
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+SBGrid cannot distribute the AF3 models. Currently, you must apply to obtain them yourself through this form:
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https://forms.gle/svvpY4u2jsHEwWYS6
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### Download databases
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-The databases for AlphaFold3 (AF3) must be downloaded.
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+The databases for AlphaFold3 (AF3) must be downloaded. The uncompressed files require ~1TB of space.
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AlphaFold provides a script for downloading these in the github repo:
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The resulting layout should look like this:
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```
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-/programs//local/alphafold-3.0.0/databases/
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+/programs/local/alphafold-3.0.0/databases/
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├── bfd-first_non_consensus_sequences.fasta
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├── compressed
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│   ├── bfd-first_non_consensus_sequences.fasta.zst
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```
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#!/usr/bin/env bash
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-#SBATCH --partition=bch-gpu
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+#SBATCH --partition=my-gpu-partition
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#SBATCH --gres=gpu:large:1
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#SBATCH --mem-per-cpu=24G
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#SBATCH --time=04:00:00
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-#SBATCH --job-name=JV-AF3
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+#SBATCH --job-name=AF3-Example
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nvidia-smi --query-gpu=name,memory.total --format=csv
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## Nov 11, 2024
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## Start SBGrid environment
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-source /programs/biogrids.shrc
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+source /programs/sbgrid.shrc
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export ALPHAFOLD_X=3.0.0
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export XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
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export XLA_PYTHON_CLIENT_PREALLOCATE=true
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export XLA_CLIENT_MEM_FRACTION=0.95
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-PROJECT_DIR=/temp_work/ch199734/121503_alphafold3_3.0.0
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-MODEL_DIR=/home/ch199734/models
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-DATABASE_DIR=/programs/local/biogrids/alphafold-3.0.0/databases
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+PROJECT_DIR=/tmp_space/user123/alphafold3_3.0.0
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+MODEL_DIR=/home/user123/models
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+DATABASE_DIR=/programs/local/alphafold-3.0.0/databases
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cd ${PROJECT_DIR}
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