Eric Coissac
52f26809af
ci.yml / build (pull_request) Successful in 3m49s
Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
105 lines
3.2 KiB
Bash
Executable File
105 lines
3.2 KiB
Bash
Executable File
#!/usr/bin/env bash
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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RUN_DIR="${SCRIPT_DIR}/run"
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BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
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IDX_DIR="${RUN_DIR}/specimen_index_count"
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OUTPUT="${RUN_DIR}/global_index_count"
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STATS_DIR="${RUN_DIR}/stats/merge_count"
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mkdir -p "${STATS_DIR}"
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run_n=$(printf '%03d' "$(find "${STATS_DIR}" -maxdepth 1 -name 'run_*.csv' | wc -l | tr -d ' ')")
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CSV="${STATS_DIR}/run_${run_n}.csv"
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printf 'run,n_sources,bootstrap_wall_s,bootstrap_rss_b,spectrums_wall_s,spectrums_rss_b,merge_partitions_wall_s,merge_partitions_rss_b,pack_wall_s,pack_rss_b,total_wall_s,total_rss_b\n' >"${CSV}"
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parse_reporter() {
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local run="$1" n_sources="$2" logfile="$3"
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python3 - "$run" "$n_sources" "$logfile" <<'PYEOF'
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import sys, re
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run, n_sources, logfile = sys.argv[1], sys.argv[2], sys.argv[3]
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def strip_ansi(s):
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return re.sub(r'\x1b\[[\x30-\x3f]*[\x20-\x2f]*[\x40-\x7e]', '', s)
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def parse_wall(s):
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s = s.strip()
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if s.endswith('ms'): return float(s[:-2]) / 1000.0
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if s.endswith('s'): return float(s[:-1])
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return 0.0
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def parse_rss(s):
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m = re.match(r'([\d.]+)\s*(GB|MB|KB|B)', s.strip())
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if not m: return 0
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return int(float(m.group(1)) * {'GB': 1<<30, 'MB': 1<<20, 'KB': 1024, 'B': 1}[m.group(2)])
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def is_sep(s):
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return bool(s) and not re.search(r'[A-Za-z0-9]', s)
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stats = {}
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state = 'scan'
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with open(logfile, errors='replace') as fh:
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for raw in fh:
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line = strip_ansi(raw.rstrip('\n'))
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s = line.strip()
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if state == 'scan':
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if re.search(r'\bstage\b.*\bwall\b', line):
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state = 'in_header'
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elif state == 'in_header':
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if is_sep(s):
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state = 'rows'
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elif state == 'rows':
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if is_sep(s):
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state = 'total'
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elif s:
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parts = re.split(r' +', s)
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if len(parts) >= 4:
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stats[parts[0]] = (parse_wall(parts[1]), parse_rss(parts[3]))
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elif state == 'total':
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if s:
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parts = re.split(r' +', s)
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if len(parts) >= 3:
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stats[parts[0]] = (parse_wall(parts[1]),
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parse_rss(parts[3]) if len(parts) > 3 else 0)
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break
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STAGE_ORDER = ['bootstrap', 'spectrums', 'merge_partitions', 'pack']
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row = [run, n_sources]
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for stage in STAGE_ORDER:
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w, r = stats.get(stage, ('', ''))
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row += [f'{w:.3f}' if isinstance(w, float) else '', str(r)]
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tw, tr = stats.get('TOTAL', ('', ''))
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row += [f'{tw:.3f}' if isinstance(tw, float) else '', str(tr)]
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print(','.join(row))
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PYEOF
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}
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mapfile -t sources < <(find "${IDX_DIR}" -mindepth 1 -maxdepth 1 -type d | sort)
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if [[ ${#sources[@]} -eq 0 ]]; then
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echo "ERROR: no indexes found in ${IDX_DIR}" >&2
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exit 1
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fi
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echo "Merging ${#sources[@]} count indexes → ${OUTPUT}"
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printf ' %s\n' "${sources[@]}"
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STDERR_LOG=$(mktemp)
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trap 'rm -f "${STDERR_LOG}"' EXIT
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"${BINARY}" merge \
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--output "${OUTPUT}" \
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--force \
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"${sources[@]}" \
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2>"${STDERR_LOG}"
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cat "${STDERR_LOG}" >&2
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parse_reporter "${run_n}" "${#sources[@]}" "${STDERR_LOG}" >>"${CSV}"
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echo "Done. Run ${run_n} → ${CSV}"
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