| #!/bin/bash |
| set -euo pipefail |
|
|
| SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" |
| PROJECT_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)" |
|
|
| MODEL_ROOT="${ONESCIENCE_MODELS_DIR:-${PROJECT_ROOT}/weight}" |
| MODEL_DIR="${ALPHAFOLD3_MODEL_DIR:-${MODEL_ROOT}}" |
| MMSEQS_HOME="${ALPHAFOLD3_MMSEQS_HOME:-${MODEL_DIR}/mmseqs}" |
| export PATH="${MMSEQS_HOME}/bin:${PATH}" |
| export LD_LIBRARY_PATH="${MMSEQS_HOME}/lib:${LD_LIBRARY_PATH:-}" |
| export TF_CPP_MIN_LOG_LEVEL="${TF_CPP_MIN_LOG_LEVEL:-0}" |
| export JAX_TRACEBACK_FILTERING="${JAX_TRACEBACK_FILTERING:-off}" |
| export XLA_PYTHON_CLIENT_ALLOCATOR="${XLA_PYTHON_CLIENT_ALLOCATOR:-platform}" |
| export TRITON_ENABLE_GLOBAL_TO_LOCAL="${TRITON_ENABLE_GLOBAL_TO_LOCAL:-1}" |
| export TRITON_USE_MAKE_BLOCK_PTR="${TRITON_USE_MAKE_BLOCK_PTR:-1}" |
| export TRITON_DEFAULT_ENABLE_NUM_VGPRS512="${TRITON_DEFAULT_ENABLE_NUM_VGPRS512:-1}" |
| export HIP_VISIBLE_DEVICES="${HIP_VISIBLE_DEVICES:-0}" |
|
|
| DATASET_ROOT="${ALPHAFOLD3_DATASET_ROOT:-${ONESCIENCE_DATASETS_DIR:-${PROJECT_ROOT}/data}/alphafold3}" |
| DB_DIRS="${ALPHAFOLD3_DB_DIR:-${DATASET_ROOT}/public_databases}" |
| MMSEQS_DB_DIRS="${ALPHAFOLD3_MMSEQS_DB_DIR:-${DATASET_ROOT}/mmseqsDB}" |
| JSON_PATH="${ALPHAFOLD3_JSON_PATH:-${PROJECT_ROOT}/inputs/t1119_search.json}" |
| OUTPUT_DIR="${ALPHAFOLD3_OUTPUT_DIR:-${PROJECT_ROOT}/outputs}" |
| RUN_INFERENCE="${ALPHAFOLD3_RUN_INFERENCE:-false}" |
| FLASH_ATTENTION="${ALPHAFOLD3_FLASH_ATTENTION:-triton}" |
| MMSEQS_OPTIONS="${ALPHAFOLD3_MMSEQS_OPTIONS:---num-iterations 1 --db-load-mode 2 -a --max-seqs 10000 --prefilter-mode 3}" |
|
|
| mkdir -p "${OUTPUT_DIR}" |
|
|
| python "${PROJECT_ROOT}/scripts/run_alphafold.py" \ |
| --json_path="${JSON_PATH}" \ |
| --model_dir="${MODEL_DIR}" \ |
| --output_dir="${OUTPUT_DIR}" \ |
| --run_data_pipeline=true \ |
| --run_inference="${RUN_INFERENCE}" \ |
| --flash_attention_implementation="${FLASH_ATTENTION}" \ |
| --db_dir="${DB_DIRS}" \ |
| --mmseqs_db_dir="${MMSEQS_DB_DIRS}" \ |
| --use_mmseqs=true \ |
| --use_mmseqs_gpu=true \ |
| --mmseqs_options="${MMSEQS_OPTIONS}" |
|
|
