AlphaFold 3 added to compdemos

_compdemos/alphafold3.md

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+---
+title: AlphaFold-3
+last_modified_at: 2024-12-19
+main_author: John Dey
+primary_reviewers: 
+---
+
+## AlphaFold 3 
+
+How to use AlphaFold3 with the new chorus GPU nodes.
+
+Reference data is available here: `/shared/biodata/alphafold3`
+
+#### Model Parameters
+You will need to download your own personal copy of the parameter data. The request form has been 
+sent to Hutch Legal Console for approval. I will download and share when the paper work is done.
+To request access to the AlphaFold 3 model parameters, please complete 
+[this form](https://forms.gle/svvpY4u2jsHEwWYS6). 
+
+### Sbatch Example 
+
+Example sbatch script to run AlphaFold3. Save a copy of this and modify it to suit your data.
+  - `--cpus==8` is the current max we are working on method to request more. If you ask for
+more your job will stay in pending state.
+  - `--gpus=2` is a serving suggestion. Request 2 or 4 to run AlphaFold3.
+  - Please update the `--job-name` for your work.
+  - This script works from the Rhino's or maestro
+  - You need to define OUTPUT_DIR, JSON_PATHS, and MODEL_PATH 
+
+```
+#!/bin/sh
+#SBATCH --job-name="af3"
+#SBATCH --partition=chorus
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=8
+#SBATCH --mem=1024GB
+#SBATCH --gpus=2
+
+# User defined locations
+export OUTPUT_DIR=$SCRATCH/alphafoldtest/output
+export JSON_PATHS=alphafold_input.json
+
+# Obtaining Model Parameters
+# Contact AlphaFold to get access to model parameters
+#
+export MODEL_PATH=/Path/To/Models
+
+export DOWNLOAD_DIR=/shared/biodata/alphafold3
+SIF=/app/software/AlphaFold/containers/alpafold3.sif
+
+apptainer exec \
+  --nv \
+  --bind $DOWNLOAD_DIR:/root/public_databases \
+  $SIF \
+  python /app/alphafold/run_alphafold.py \
+  --json_path=$JSON_PATHS \
+  --model_dir=$MODEL_PATH \
+  --output_dir=$OUTPUT_DIR
+```
+