code/compact_v1/build_compact_v1_direct.sbatch

#!/bin/bash
# Build compact_v1 directly from docking PDB poses.
#
# Full build:
#   sbatch --export=ALL,DATA_DIR=/path/to/poses,OUTPUT_DIR=/path/to/compact,METHOD=protenix \
#     build_compact_v1_direct.sbatch
#
# High-CPU adaptive build (one fresh process per source system; no nested pose
# pools):
#   sbatch --cpus-per-task=32 --mem=192G --time=24:00:00 \
#     --export=ALL,DATA_DIR=/path/to/poses,OUTPUT_DIR=/path/to/compact,METHOD=protenix,SYSTEM_WORKERS=28,NUM_WORKERS=1,MEMORY_BUDGET_GIB=150 \
#     build_compact_v1_direct.sbatch
#
# One-system smoke test:
#   sbatch --export=ALL,DATA_DIR=/path/to/poses,OUTPUT_DIR=/path/to/smoke,METHOD=protenix,SYSTEM_ID=tnks2_lig_20,MAX_POSES=2 \
#     build_compact_v1_direct.sbatch

#SBATCH --account=bghp-delta-cpu
#SBATCH --partition=cpu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=96G
#SBATCH --time=24:00:00
#SBATCH --job-name=build_compact
#SBATCH --output=/work/nvme/bghp/hhao/gnncp/system_split_code/build_compact_%j.out
#SBATCH --error=/work/nvme/bghp/hhao/gnncp/system_split_code/build_compact_%j.err
#SBATCH --open-mode=append
#SBATCH --requeue
#SBATCH --mail-type=FAIL

set -Eeuo pipefail
umask 007

: "${DATA_DIR:?Export DATA_DIR=/path/to/docking_results}"
: "${OUTPUT_DIR:?Export OUTPUT_DIR=/path/to/new_compact_dataset}"
: "${METHOD:?Export METHOD=protenix|diffdock|autodock_vina|medusagraph}"

readonly PROJECT_ROOT=/work/nvme/bghp/hhao/gnncp
readonly BUILDER="${PROJECT_ROOT}/system_split_code/build_compact_v1_direct.py"
readonly PYTHON=/u/hhao/anaconda3/envs/gcp/bin/python
readonly SYSTEM_WORKERS="${SYSTEM_WORKERS:-1}"
if (( SYSTEM_WORKERS > 1 )); then
    # Cross-system mode deliberately has one in-process pose builder per child.
    # This avoids multiplying dense N-by-N distance matrices in nested pools.
    readonly NUM_WORKERS="${NUM_WORKERS:-1}"
else
    readonly NUM_WORKERS="${NUM_WORKERS:-4}"
fi
readonly MEMORY_BUDGET_GIB="${MEMORY_BUDGET_GIB:-}"
readonly TARGET_SHARD_MIB="${TARGET_SHARD_MIB:-512}"
readonly ON_ERROR="${ON_ERROR:-abort}"

finish()
{
    local rc=$?
    echo "[$(date --iso-8601=seconds)] job=${SLURM_JOB_ID} exit=${rc}"
}
trap finish EXIT

echo "[$(date --iso-8601=seconds)] host=$(hostname)"
echo "data=${DATA_DIR}"
echo "output=${OUTPUT_DIR}"
echo "method=${METHOD} pose_workers=${NUM_WORKERS} system_workers=${SYSTEM_WORKERS} memory_budget_gib=${MEMORY_BUDGET_GIB:-unset}"

test -x "${PYTHON}"
test -r "${BUILDER}"
test -d "${DATA_DIR}"
mkdir -p "$(dirname "${OUTPUT_DIR}")"

if [[ -s "${OUTPUT_DIR}/manifest.json" ]]; then
    echo "Output already has a manifest; skipping completed build."
    exit 0
fi
if [[ -e "${OUTPUT_DIR}" ]]; then
    echo "Output exists without a manifest; refusing to overwrite: ${OUTPUT_DIR}" >&2
    exit 3
fi

if (( SYSTEM_WORKERS > 1 )); then
    if [[ "${NUM_WORKERS}" != "1" ]]; then
        echo "SYSTEM_WORKERS>1 requires NUM_WORKERS=1; nested process pools are unsafe." >&2
        exit 2
    fi
    : "${MEMORY_BUDGET_GIB:?Set MEMORY_BUDGET_GIB to a usable aggregate worker-memory budget for SYSTEM_WORKERS>1}"
fi
if [[ -n "${SLURM_CPUS_PER_TASK:-}" ]] && (( SYSTEM_WORKERS > SLURM_CPUS_PER_TASK )); then
    echo "SYSTEM_WORKERS=${SYSTEM_WORKERS} exceeds SLURM_CPUS_PER_TASK=${SLURM_CPUS_PER_TASK}" >&2
    exit 2
fi

# Each pose worker performs dense scipy distance calculations. Keep numerical
# libraries single-threaded and parallelise at the pose-process level.
export PYTHONUNBUFFERED=1
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export MALLOC_ARENA_MAX=2

ARGS=(
    --data-dir "${DATA_DIR}"
    --output-dir "${OUTPUT_DIR}"
    --method "${METHOD}"
    --num-workers "${NUM_WORKERS}"
    --system-workers "${SYSTEM_WORKERS}"
    --target-shard-mib "${TARGET_SHARD_MIB}"
    --on-error "${ON_ERROR}"
    --resume
)
if [[ -n "${MEMORY_BUDGET_GIB}" ]]; then
    ARGS+=(--memory-budget-gib "${MEMORY_BUDGET_GIB}")
fi
if [[ -n "${SYSTEM_ID:-}" ]]; then
    ARGS+=(--system-id "${SYSTEM_ID}")
fi
if [[ -n "${MAX_SYSTEMS:-}" ]]; then
    ARGS+=(--max-systems "${MAX_SYSTEMS}")
fi
if [[ -n "${MAX_POSES:-}" ]]; then
    ARGS+=(--max-poses-per-system "${MAX_POSES}")
fi

df -h "$(dirname "${OUTPUT_DIR}")"
/usr/bin/time -v "${PYTHON}" "${BUILDER}" "${ARGS[@]}"

test -s "${OUTPUT_DIR}/manifest.json"
test -s "${OUTPUT_DIR}/system_index.json"
du -sh "${OUTPUT_DIR}"
echo "[$(date --iso-8601=seconds)] compact dataset committed successfully"