File size: 4,491 Bytes
0cb481f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 | #!/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"
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