Create submit_iter.sh

submit/multiple/submit_iter.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+#SBATCH --job-name="af3_iter"
+#SBATCH --partition=GPU
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=32
+#SBATCH --mem=256GB
+#SBATCH --gres=gpu:L40S:2
+#SBATCH --time=1:00:00
+
+module load singularity
+
+export AF3_RESOURCES_DIR=/users/cford/alphafold3_resources
+
+export AF3_IMAGE=${AF3_RESOURCES_DIR}/image/alphafold3.sif
+export AF3_CODE_DIR=${AF3_RESOURCES_DIR}/code
+export AF3_INPUT_DIR=${AF3_RESOURCES_DIR}/examples/${1}
+export AF3_OUTPUT_DIR=${AF3_RESOURCES_DIR}/examples/${1}/output
+export AF3_MODEL_PARAMETERS_DIR=${AF3_RESOURCES_DIR}/weights
+export AF3_DATABASES_DIR=${AF3_RESOURCES_DIR}/databases
+
+singularity exec \
+     --nv \
+     --bind $AF3_INPUT_DIR:/root/af_input \
+     --bind $AF3_OUTPUT_DIR:/root/af_output \
+     --bind $AF3_MODEL_PARAMETERS_DIR:/root/models \
+     --bind $AF3_DATABASES_DIR:/root/public_databases \
+     $AF3_IMAGE \
+     python ${AF3_CODE_DIR}/alphafold3/run_alphafold.py \
+     --json_path=/root/af_input/alphafold_input.json \
+     --model_dir=/root/models \
+     --db_dir=/root/public_databases \
+     --output_dir=/root/af_output