leonarski_fandClaude Opus 5.5
7eed4a5e0b
shelx_check.py refines the row's published structure (manifest key "cod", cached from the Crystallography Open Database into the site's cod_cache) against rugnux's p.hkl with one fixed recipe: data reindexed into the COD setting (lowest-R1 integer matrix), non-H anisotropic, H fixed, EXTI, MERG 2, three rounds of SHELXL's suggested weights. It records R1/wR2/GooF/EXTI/WGHT/residual density/R(int)/R(sigma)/K of the strongest bin and a fixed-model R1(F) (|Fc| of the COD model as published, gemmi). Reported, never scored. The report gets a small-molecule table; compare lists SHELXL R1/wR2/GooF/EXTI deltas; report/compare fill the check in for older runs. COD entries matched by Niggli-reduced cell and space group: aspirin 7050897, citric acid 5000063, HEPES 2224210, YAG 2003066, L-cystine 1513328 (2005, replaces the 1959 model for refinement), cytidine 2001311, 3,5-dinitrobenzoic acid 4510615, L-alanine 2104782, metformin HCl 2108029, NiCl2(dppe) 2012031. cuhf2 has no reference cell and no match: left without one. SHELXL is called, not shipped (site key "shelxl" or PATH; it comes with CCP4). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
889 lines
42 KiB
Python
889 lines
42 KiB
Python
#!/usr/bin/env python3
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"""Rugnux validation battery: run, score, report, compare.
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Arms and where their truth comes from:
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open public PDB depositions (and a few published small-molecule sets); scored against the
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deposited space group, cell and resolution. Manifest: open.json (committed).
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inhouse standard test crystals measured at PSI (lysozyme, thaumatin, insulin, cytochrome C,
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myoglobin) plus no-crystal controls; scored against XDS (point group only - XDS never
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tests a screw axis). Manifest: inhouse.json (committed).
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private user data, scored like inhouse. Its manifest lives OUTSIDE the repository (path in the
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site config) and a private run gets its own run directory and report.
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Usage (README.md in this directory is the full guide):
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battery.py run --rugnux BIN [--label L] [--arm open,inhouse|private] [--only a,b | --tier smoke]
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[--build-dir DIR] [--gpulock] [--threads N]
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[--model-check] [--baseline RUN|none]
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battery.py list runs under the runs root, with their state
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battery.py compare RUN_A RUN_B [--all] [--rerun-changed]
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battery.py report RUN --out DIR [--baseline RUN] re-render a run's report into DIR/<run>.{md,html}
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battery.py abort RUN [--reason TEXT] mark an unfinished run as aborted
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battery.py recheck RUN [--only a,b] [--jobs N] rerun the model checks of a finished run's open
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arm on its p.mtz files; recorded in the manifest
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battery.py discover [--refresh] open arm: propose inputs for new directories
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battery.py refs --arm inhouse|private [--write] re-read the XDS references from CORRECT.LP
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battery.py remap --arm A MAP.json [--write] follow a rename of the data directories
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The site config (data roots, runs root, lock, gpulock, private manifest, baselines) is --site, else
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$JFJOCH_BATTERY_SITE, else site.json beside this script (not committed; site.example.json is).
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Every set runs once, with one command per arm (COMMAND_DOC): the open arm with the deposited model
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(--model), the XDS arms with XDS's range as a report-only second
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table (--report-resolution). Neither option changes the processing, so the one run is both what a
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user gets and the like-for-like comparison.
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A run writes <runs_root>/<YYYYMMDD-HHMM>_<rugnux git>_<label>/ holding a copy of the binary,
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manifest.json (what was run, on what, with which references), results.json (one row per set),
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report.md + report.html and work/<arm>/<set>/ (log, report, cif). It is made read-only when done.
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A full-arm run (no --only / --tier) takes the site lock and refuses to start if another holds it.
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A run that did not finish is never compared or reported on unless asked (--allow-incomplete).
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"""
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import argparse
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import concurrent.futures
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import datetime
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import fcntl
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import hashlib
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import json
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import os
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import re
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import shutil
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import signal
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import socket
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import stat
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import subprocess
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import sys
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import time
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HERE = os.path.dirname(os.path.abspath(__file__))
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sys.path.insert(0, HERE)
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import inputs # noqa: E402
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import report # noqa: E402
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import score # noqa: E402
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import model_check # noqa: E402 the deposited model (--model); REFMAC check (--model-check)
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import shelx_check # noqa: E402 SHELXL refinement of a small molecule's COD structure
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import depdata_check # noqa: E402 our merge vs the depositor's data, shell by shell
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PDB_ID = re.compile(r"^[0-9][A-Za-z0-9]{3}$")
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# The one command each set runs, by its arm's reference. --model and --report-resolution only add
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# to the report (the merge is the same with and without them), so this one run is what a user
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# gets and carries the like-for-like numbers too.
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COMMAND_DOC = {
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"deposition": "`rugnux --model <deposited coordinates> <input>` (without --model where there is no "
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"deposited model: small molecules, unpublished sets)",
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"xds": "`rugnux --report-resolution <XDS d_min>,<XDS d_max> <input>`: the second statistics "
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"table at XDS's range is report-only; where XDS kept Friedel mates apart the scorer "
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"reads the run's own per-hand table, which needs no flag",
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}
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LOCAL_SITE = os.path.join(HERE, "site.json")
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# ------------------------------------------------------------------ configuration and manifests
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def load_site(path):
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path = path or os.environ.get("JFJOCH_BATTERY_SITE") or LOCAL_SITE
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if not os.path.exists(path):
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sys.exit(f"no site config at {path}: copy {os.path.join(HERE, 'site.example.json')} to "
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f"{LOCAL_SITE} (or anywhere, and point JFJOCH_BATTERY_SITE or --site at it) and "
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"fill in this machine's paths")
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site = json.load(open(path))
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for arm in site["arms"].values():
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arm["manifest"] = os.path.join(HERE, arm["manifest"]) # an absolute path stays as it is
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return site
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def load_sets(site, arm):
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cfg = site["arms"][arm]
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man = json.load(open(cfg["manifest"]))
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for e in man["sets"]:
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e["arm"] = arm
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return man["sets"]
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def select(site, arms, only, tier):
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sets = [e for arm in arms for e in load_sets(site, arm)]
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if only:
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want = [s.strip() for s in only.split(",") if s.strip()]
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unknown = [w for w in want if w not in {e["id"] for e in sets}]
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if unknown:
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sys.exit(f"not in the {'/'.join(arms)} manifest(s): {', '.join(unknown)}")
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sets = [e for e in sets if e["id"] in want]
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if tier:
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sets = [e for e in sets if tier in e.get("tiers", {})]
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return sets
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# ------------------------------------------------------------------ the binary
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def sha256(path):
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h = hashlib.sha256()
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with open(path, "rb") as fh:
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for block in iter(lambda: fh.read(1 << 20), b""):
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h.update(block)
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return h.hexdigest()
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def binary_info(path, build_dir):
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"""Version and git hash as the binary itself prints them, plus the build flags from the
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CMakeCache of its build tree (given, or found above the binary)."""
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out = subprocess.run([path], capture_output=True, text=True, timeout=120).stdout
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m = re.search(r"Version (\S+) \(git (\w+)", out)
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info = {"version": m.group(1) if m else None, "git": m.group(2) if m else "unknown"}
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cache = None
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d = build_dir or os.path.dirname(os.path.realpath(path))
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for _ in range(4):
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if os.path.exists(os.path.join(d, "CMakeCache.txt")):
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cache = os.path.join(d, "CMakeCache.txt")
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break
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d = os.path.dirname(d)
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if cache:
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vals = {}
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for line in open(cache, errors="replace"):
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m = re.match(r"^(CMAKE_BUILD_TYPE|CMAKE_CXX_FLAGS|CMAKE_HOME_DIRECTORY|JFJOCH_USE_CUDA):\w+=(.*)$",
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line.strip())
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if m:
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vals[m.group(1)] = m.group(2)
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info["cmake_cache"] = cache
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info["flags"] = (f"{vals.get('CMAKE_BUILD_TYPE', '?')} CXX_FLAGS='{vals.get('CMAKE_CXX_FLAGS', '')}' "
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f"CUDA={vals.get('JFJOCH_USE_CUDA', '?')}")
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src = vals.get("CMAKE_HOME_DIRECTORY")
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if src:
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info["source"] = src
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info["source_head"] = git(src, "rev-parse", "HEAD")
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info["source_dirty"] = bool(git(src, "status", "--porcelain", "--untracked-files=no"))
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return info
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def git(d, *args):
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r = subprocess.run(["git", "-C", d] + list(args), capture_output=True, text=True)
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return r.stdout.strip() if r.returncode == 0 else None
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def gpu_others():
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"""Number of processes other than ours on the GPU right now (None if nvidia-smi is absent)."""
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try:
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out = subprocess.run(["nvidia-smi", "--query-compute-apps=pid", "--format=csv,noheader"],
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capture_output=True, text=True, timeout=30).stdout
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except (OSError, subprocess.TimeoutExpired):
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return None
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return len([x for x in out.split() if x.strip().isdigit()])
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def gpu_hardware():
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"""[{"name", "memory"}] from nvidia-smi, [] if there are none or it is absent."""
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try:
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out = subprocess.run(["nvidia-smi", "--query-gpu=name,memory.total", "--format=csv,noheader"],
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capture_output=True, text=True, timeout=30).stdout
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except (OSError, subprocess.TimeoutExpired):
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return []
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gpus = []
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for line in out.splitlines():
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parts = [p.strip() for p in line.split(",")]
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if len(parts) == 2:
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gpus.append({"name": parts[0], "memory": parts[1]})
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return gpus
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def linux_hardware():
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blocks = []
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try:
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blocks = [b for b in open("/proc/cpuinfo").read().split("\n\n") if b.strip()]
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except OSError:
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pass
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model = None
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sockets, cores = set(), set()
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for b in blocks:
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m = re.search(r"model name\s*:\s*(.+)", b)
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if m and model is None:
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model = m.group(1).strip()
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p, c = re.search(r"physical id\s*:\s*(\d+)", b), re.search(r"core id\s*:\s*(\d+)", b)
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if p and c:
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sockets.add(p.group(1))
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cores.add((p.group(1), c.group(1)))
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# Nominal (base) clock, never the boost clock: the model-name string, else cpufreq's own
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# base_frequency (intel_pstate, kHz), else ACPI CPPC's nominal_freq (MHz; what AMD's
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# acpi-cpufreq exposes instead - cpuinfo_max_freq on those boxes is the boost clock, not this).
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freq_ghz, freq_source = None, "unknown"
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m = re.search(r"@\s*([\d.]+)\s*GHz", model or "")
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if m:
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freq_ghz, freq_source = float(m.group(1)), "model name"
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else:
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try:
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freq_ghz = int(open("/sys/devices/system/cpu/cpu0/cpufreq/base_frequency").read()) / 1e6
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freq_source = "base_frequency"
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except (OSError, ValueError):
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try:
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freq_ghz = int(open("/sys/devices/system/cpu/cpu0/acpi_cppc/nominal_freq").read()) / 1e3
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freq_source = "acpi_cppc"
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except (OSError, ValueError):
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pass
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# Reported separately, and never as "nominal": cpuinfo_max_freq is the highest boost state.
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max_boost_ghz = None
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try:
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max_boost_ghz = int(open("/sys/devices/system/cpu/cpu0/cpufreq/cpuinfo_max_freq").read()) / 1e6
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except (OSError, ValueError):
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pass
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mem_gib = None
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try:
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for line in open("/proc/meminfo"):
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if line.startswith("MemTotal:"):
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mem_gib = int(line.split()[1]) / 1024 / 1024 # kiB -> GiB
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break
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except OSError:
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pass
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return {"cpu_model": model or "unknown", "cpu_base_ghz": freq_ghz, "cpu_base_source": freq_source,
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"cpu_max_boost_ghz": max_boost_ghz, "sockets": len(sockets) or None,
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"physical_cores": len(cores) or None, "threads": os.cpu_count(), "memory_gib": mem_gib,
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"gpus": gpu_hardware()}
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def macos_hardware():
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def sysctl(key):
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r = subprocess.run(["sysctl", "-n", key], capture_output=True, text=True)
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return r.stdout.strip() if r.returncode == 0 else None
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model = sysctl("machdep.cpu.brand_string")
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freq_ghz, freq_source = None, "unknown"
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m = re.search(r"@\s*([\d.]+)\s*GHz", model or "")
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if m:
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freq_ghz, freq_source = float(m.group(1)), "model name"
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cores = sysctl("hw.physicalcpu")
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p_cores, e_cores = sysctl("hw.perflevel0.physicalcpu"), sysctl("hw.perflevel1.physicalcpu")
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if p_cores and e_cores:
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cores = f"{p_cores}P+{e_cores}E"
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mem = sysctl("hw.memsize")
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return {"cpu_model": model or "unknown", "cpu_base_ghz": freq_ghz, "cpu_base_source": freq_source,
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"cpu_max_boost_ghz": None, "sockets": int(sysctl("hw.packages") or 1), "physical_cores": cores,
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"threads": int(sysctl("hw.logicalcpu") or os.cpu_count()),
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"memory_gib": int(mem) / 1024 ** 3 if mem else None, "gpus": []}
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def hardware_info():
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"""The run host's hardware, for the manifest: CPU model, nominal/base frequency (and where it
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came from) plus max boost frequency separately, physical cores, threads, sockets, memory, GPUs.
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Linux is detailed; macOS is a short best-effort; anywhere else this is just empty, and the
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report says so."""
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try:
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if sys.platform == "darwin":
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return macos_hardware()
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if sys.platform.startswith("linux"):
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return linux_hardware()
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except OSError:
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pass
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return {}
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# ------------------------------------------------------------------ running
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def command(binary, e, opts, model=None):
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cmd = [binary, "-o", "p", "--no-export-unmerged"]
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if opts["threads"]:
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cmd += ["-N", str(opts["threads"])]
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ref = e.get("ref") or {}
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if e["reference"] == "xds":
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# No -A, whatever the reference did. A rotation run decides with Friedel's mates merged
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# either way, and reports the merge counted BOTH ways from that one run; -A only says which
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# of the two tables was asked for. Where XDS merged with FRIEDEL'S_LAW=FALSE the scorer
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# reads rugnux's per-hand block (ANOM_REFRES_*) instead, which is the like-for-like table.
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# a second statistics table over XDS's own range, from the same merge (report only). XDS's
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# own limit, not the derived reference d_min: the manifest's XDS totals are over XDS's range,
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# so only that makes the table like for like. Shells past rugnux's own cut print as not
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# merged.
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dmin = ref.get("dmin_xds") or ref.get("dmin")
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if dmin:
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cmd += ["--report-resolution",
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f"{dmin:.3f}" + (f",{ref['dmax']:.3f}" if ref.get("dmax") else "")]
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if model:
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cmd += ["--model", model]
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cmd += opts["extra_args"]
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cmd.append(e["input_path"])
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if opts["gpulock"]:
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cmd = [opts["gpulock"]] + cmd
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return cmd
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def failure_note(log):
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"""rugnux's own last error message, without the spdlog timestamp and severity prefix."""
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try:
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lines = [l.strip() for l in open(log, errors="replace") if l.strip()]
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except OSError:
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return ""
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for l in reversed(lines):
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if "[error]" in l or "failed" in l.lower():
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return l.split("] ")[-1][:300]
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return lines[-1].split("] ")[-1][:300] if lines else ""
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def deposited_model(e, opts):
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"""(deposition record from model_check's RCSB cache, None) for the entry a set belongs to, or
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(None, why not). A set id may carry a suffix (6h2p_native); the entry is the part before it."""
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pdb = e["id"].split("_")[0].lower()
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if not PDB_ID.match(pdb):
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return None, "no model: not a PDB entry (small molecule or unpublished set)"
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meta = model_check.deposition(pdb, opts["pdb_cache"])
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if meta is None:
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return None, f"no model: coordinates of {pdb} could not be downloaded"
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return meta, None
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def run_one(run_dir, binary, e, opts):
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wd = os.path.join(run_dir, "work", e["arm"], e["id"])
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os.makedirs(wd)
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row = {"set": e["id"], "arm": e["arm"], "tags": e.get("tags", []), "input": e["input_path"],
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"gpu_others": gpu_others(), "model": None, "model_note": None, "rfree_deposited": None,
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"rfree_ratio": None, "cmd": None, "exit_code": None, "elapsed_s": None, "wall_s": None}
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row.update({k: None for k in REFMAC_KEYS + depdata_check.KEYS + shelx_check.KEYS})
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if not os.path.exists(e["input_path"]):
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row.update(score.judge(e, {}, "no input"))
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return row
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meta = None
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if e["reference"] == "deposition":
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# no deposited model (small molecule, unpublished): the same command without --model
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meta, row["model_note"] = deposited_model(e, opts)
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if meta:
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row["model"], row["rfree_deposited"] = meta["xyz"], meta["rfree"]
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cmd = command(binary, e, opts, row["model"])
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row["cmd"] = " ".join(cmd)
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t0 = time.time()
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note = ""
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with open(os.path.join(wd, "run.log"), "w") as log:
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try:
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rc = subprocess.run(cmd, cwd=wd, stdout=log, stderr=subprocess.STDOUT,
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timeout=opts["timeout"]).returncode
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except subprocess.TimeoutExpired:
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rc, note = None, "timeout"
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row["elapsed_s"] = round(time.time() - t0, 1)
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row["exit_code"] = rc
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if rc:
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note = f"exit {rc}: {failure_note(os.path.join(wd, 'run.log'))}"
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row.update(score.judge(e, score.read_report(os.path.join(wd, "p_report.txt")), note))
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# rugnux's own WALL_TIME where it wrote one: the runner's clock also counts the wait for a
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# GPU slot under --gpulock
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row["wall_s"] = row["rugnux_wall_s"] if row["rugnux_wall_s"] is not None else row["elapsed_s"]
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if row["rfree"] and row["rfree_deposited"]:
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row["rfree_ratio"] = round(row["rfree"] / row["rfree_deposited"], 4)
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if row["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
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row.update(depdata_check.check_set(wd, e["id"], opts["pdb_cache"]))
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if opts["model_check"] and e["arm"] == "open":
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row.update(check_model(e, wd))
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if e.get("cod"):
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# small molecule: its published structure refined against our p.hkl (report only)
|
|
row.update(shelx_check.check(wd, e["cod"], opts.get("cod_cache") or shelx_check.DEFAULT_CACHE,
|
|
opts.get("shelxl")))
|
|
return row
|
|
|
|
|
|
# what the REFMAC model check (model_check.py, --model-check) adds to an open-arm row
|
|
REFMAC_REFINED = ("refined_rfree_shared", "refined_rfree_shared_depdata", "refined_rwork",
|
|
"refined_rwork_depdata", "refined_rfree_refmac", "refined_rfree_refmac_depdata",
|
|
"shared_free_n", "refined_reason")
|
|
REFMAC_KEYS = ("refmac_rfree", "refmac_rwork", "refmac_rfree_depflags", "refmac_rfree_depdata",
|
|
"refmac_rfree_ratio", "refmac_twin", "refmac_untwinned", "refmac_status",
|
|
"refmac_reason", "refmac_refined_ratio") + tuple("refmac_" + k for k in REFMAC_REFINED)
|
|
|
|
|
|
def check_model(e, wd):
|
|
"""R-free of the deposited model against this run's merge, by REFMAC (model_check.py)."""
|
|
out = {k: None for k in REFMAC_KEYS}
|
|
pdb = e["id"].split("_")[0]
|
|
mtz = os.path.join(wd, "p.mtz")
|
|
if not PDB_ID.match(pdb):
|
|
return dict(out, refmac_status="skipped", refmac_reason="not a PDB entry")
|
|
if not os.path.exists(mtz):
|
|
return dict(out, refmac_status="skipped", refmac_reason="no merged MTZ")
|
|
try:
|
|
res = model_check.check(mtz, pdb, os.path.join(wd, "model_check"))
|
|
except Exception as ex: # a failing check must not lose the set's processing result
|
|
return dict(out, refmac_status="error", refmac_reason=f"{type(ex).__name__}: {ex}"[:300])
|
|
out.update({"refmac_" + k: res.get(k) for k in ("rfree", "rwork", "rfree_depflags", "rfree_depdata",
|
|
"untwinned") + REFMAC_REFINED},
|
|
refmac_twin=" ".join(res.get("twin_declared") or []) or None,
|
|
refmac_status=res.get("status"),
|
|
refmac_reason=res.get("reason") or res.get("baseline_note"))
|
|
# The fair ratio: our merge and the depositor's structure factors, both scored on the
|
|
# depositor's free set by the same protocol. Our own free set was mostly work reflections
|
|
# for the depositor, so R_free on it reads low.
|
|
if out["refmac_rfree_depflags"] and out["refmac_rfree_depdata"]:
|
|
out["refmac_rfree_ratio"] = round(out["refmac_rfree_depflags"] / out["refmac_rfree_depdata"], 4)
|
|
# the same after refinement of each data set at its own resolution, on the shared free set
|
|
if out["refmac_refined_rfree_shared"] and out["refmac_refined_rfree_shared_depdata"]:
|
|
out["refmac_refined_ratio"] = round(out["refmac_refined_rfree_shared"]
|
|
/ out["refmac_refined_rfree_shared_depdata"], 4)
|
|
return out
|
|
|
|
|
|
def make_read_only(path):
|
|
for dp, dirs, files in os.walk(path):
|
|
for fn in files:
|
|
p = os.path.join(dp, fn)
|
|
if not os.path.islink(p):
|
|
os.chmod(p, os.stat(p).st_mode & ~(stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH))
|
|
for dp, dirs, files in os.walk(path, topdown=False):
|
|
os.chmod(dp, os.stat(dp).st_mode & ~(stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH))
|
|
|
|
|
|
def write_json(path, obj):
|
|
with open(path + ".tmp", "w") as fh:
|
|
json.dump(obj, fh, indent=1)
|
|
os.replace(path + ".tmp", path)
|
|
|
|
|
|
def write_manifest(path, man):
|
|
"""A manifest with one set per line, so a diff of it reads set by set."""
|
|
lines = [json.dumps(e) for e in man["sets"]]
|
|
head = json.dumps({k: v for k, v in man.items() if k != "sets"})[:-1]
|
|
with open(path, "w") as fh:
|
|
fh.write(head + ', "sets": [\n ' + ",\n ".join(lines) + "\n]}\n")
|
|
|
|
|
|
def write_report(run_dir, baseline=None, out_dir=None, allow_incomplete=False):
|
|
"""report.md and report.html (report_PRIVATE.* for a private run) in the run directory, or
|
|
<run name>.md/.html (with _PRIVATE) in out_dir."""
|
|
man = json.load(open(os.path.join(run_dir, "manifest.json")))
|
|
name = os.path.basename(os.path.normpath(run_dir)) if out_dir else "report"
|
|
base = os.path.join(out_dir or run_dir, name + ("_PRIVATE" if man.get("private") else ""))
|
|
doc = report.build(run_dir, baseline, allow_incomplete=allow_incomplete or not out_dir)
|
|
open(base + ".md", "w").write(doc.markdown())
|
|
open(base + ".html", "w").write(doc.html())
|
|
return base + ".html"
|
|
|
|
|
|
def run_sets(site, sets, arms, binary_src, build_dir, label, opts, subset, baseline=None, lock=None):
|
|
"""Run the given manifest rows into a new run directory. Returns the directory."""
|
|
private = any(site["arms"][a].get("private") for a in arms)
|
|
if private and len(arms) > 1:
|
|
sys.exit("the private arm runs on its own: its results must not share a run or a report")
|
|
if baseline:
|
|
report.check_baseline(baseline, private)
|
|
lock_fh = None
|
|
if lock:
|
|
os.makedirs(os.path.dirname(lock), exist_ok=True)
|
|
lock_fh = open(lock, "w")
|
|
try:
|
|
fcntl.flock(lock_fh, fcntl.LOCK_EX | fcntl.LOCK_NB)
|
|
except BlockingIOError:
|
|
sys.exit(f"another full battery run holds {lock}; refusing to start a second one")
|
|
|
|
info = binary_info(binary_src, build_dir)
|
|
label = label or info.get("version") or "run"
|
|
stamp = datetime.datetime.now().strftime("%Y%m%d-%H%M")
|
|
run_dir = os.path.join(opts["runs_root"],
|
|
f"{stamp}_{info['git']}_{label}" + ("_private" if private else ""))
|
|
os.makedirs(run_dir) # never reuse or overwrite a run directory
|
|
binary = os.path.join(run_dir, "bin", "rugnux")
|
|
os.makedirs(os.path.dirname(binary))
|
|
shutil.copy2(binary_src, binary)
|
|
info.update(copied_from=os.path.realpath(binary_src), sha256=sha256(binary))
|
|
|
|
for e in sets:
|
|
e["reference"] = site["arms"][e["arm"]]["reference"]
|
|
e.setdefault("input_path", os.path.join(site["arms"][e["arm"]]["data_root"], e["input"]))
|
|
man = {"label": label, "arms": arms, "private": private, "subset": subset, "baseline": baseline,
|
|
"command_doc": {arm: COMMAND_DOC[site["arms"][arm]["reference"]] for arm in arms},
|
|
"binary": info,
|
|
"runner_git": git(HERE, "rev-parse", "--short", "HEAD") or "unknown",
|
|
"runner_dirty": bool(git(HERE, "status", "--porcelain", "--", ".")),
|
|
"host": socket.gethostname(), "hardware": hardware_info(), "pid": os.getpid(),
|
|
"start": datetime.datetime.now().isoformat(timespec="seconds"),
|
|
"end": None, "complete": False, "results_schema": report.RESULTS_SCHEMA, "options": {k: v for k, v in opts.items() if k != "runs_root"},
|
|
"gpu_shared": bool(opts["gpulock"]), "sets": sets}
|
|
write_json(os.path.join(run_dir, "manifest.json"), man)
|
|
print(f"run directory {run_dir}", flush=True)
|
|
|
|
results = []
|
|
# a kill by SIGTERM is recorded like Ctrl-C: the run directory then says it was aborted
|
|
signal.signal(signal.SIGTERM, interrupted)
|
|
try:
|
|
for e in sets:
|
|
row = run_one(run_dir, binary, e, opts)
|
|
results.append(row)
|
|
if row.get("gpu_others"):
|
|
man["gpu_shared"] = True
|
|
write_json(os.path.join(run_dir, "results.json"), results)
|
|
print(f"[{len(results)}/{len(sets)}] {e['arm']:8s} {e['id']:24s} {row['verdict']:8s} "
|
|
f"{row.get('sg') or '-':12s} d={report.f(row.get('d_min'))} "
|
|
f"t={report.f(row.get('wall_s'), '{:.0f}')}s {row.get('reason') or ''}", flush=True)
|
|
except KeyboardInterrupt:
|
|
mark_aborted(run_dir, f"interrupted after {len(results)} of {len(sets)} sets")
|
|
sys.exit(f"aborted; {run_dir} is marked as such")
|
|
|
|
man.update(end=datetime.datetime.now().isoformat(timespec="seconds"), complete=True)
|
|
write_json(os.path.join(run_dir, "manifest.json"), man)
|
|
print(f"report {write_report(run_dir, baseline)}", flush=True)
|
|
make_read_only(run_dir)
|
|
if lock_fh:
|
|
lock_fh.close()
|
|
return run_dir
|
|
|
|
|
|
def interrupted(*_):
|
|
raise KeyboardInterrupt
|
|
|
|
|
|
def mark_aborted(run_dir, reason):
|
|
man = json.load(open(os.path.join(run_dir, "manifest.json")))
|
|
man["aborted"] = {"at": datetime.datetime.now().isoformat(timespec="seconds"), "reason": reason}
|
|
write_json(os.path.join(run_dir, "manifest.json"), man)
|
|
make_read_only(run_dir)
|
|
|
|
|
|
def default_baseline(site, arms, given):
|
|
"""--baseline, else the site's persisted baseline for this kind of run ('none' = no delta)."""
|
|
if given:
|
|
return None if given == "none" else given
|
|
private = any(site["arms"][a].get("private") for a in arms)
|
|
return site.get("baseline_private" if private else "baseline") or None
|
|
|
|
|
|
# ------------------------------------------------------------------ subcommands
|
|
|
|
def cmd_run(a, site):
|
|
arms = [x.strip() for x in a.arm.split(",")]
|
|
for arm in arms:
|
|
if arm not in site["arms"]:
|
|
sys.exit(f"unknown arm {arm}; the site config has {', '.join(site['arms'])}")
|
|
sets = select(site, arms, a.only, a.tier)
|
|
if not sets:
|
|
sys.exit("nothing selected")
|
|
subset = a.only or (f"tier {a.tier}" if a.tier else None)
|
|
opts = {"threads": a.threads, "timeout": a.timeout, "model_check": a.model_check and "open" in arms,
|
|
"pdb_cache": site.get("pdb_cache") or model_check.DEFAULT_CACHE,
|
|
"cod_cache": site.get("cod_cache") or shelx_check.DEFAULT_CACHE,
|
|
"shelxl": shelx_check.find_shelxl(site.get("shelxl")),
|
|
"gpulock": site["gpulock"] if a.gpulock else None, "extra_args": a.extra.split(),
|
|
"runs_root": a.runs_root or site["runs_root"]}
|
|
if a.gpulock and not site.get("gpulock"):
|
|
sys.exit("--gpulock: the site config names no gpulock")
|
|
run_sets(site, sets, arms, a.rugnux, a.build_dir, a.label, opts, subset,
|
|
default_baseline(site, arms, a.baseline), lock=None if subset else site["lock_file"])
|
|
|
|
|
|
def cmd_list(a, site):
|
|
root = a.runs_root or site["runs_root"]
|
|
for d in sorted(os.listdir(root)):
|
|
run = os.path.join(root, d)
|
|
if not os.path.exists(os.path.join(run, "manifest.json")):
|
|
continue
|
|
man = json.load(open(os.path.join(run, "manifest.json")))
|
|
state = report.run_state(man)
|
|
n = len(json.load(open(os.path.join(run, "results.json")))) \
|
|
if os.path.exists(os.path.join(run, "results.json")) else 0
|
|
mark = " <- baseline" if run in (site.get("baseline"), site.get("baseline_private")) else ""
|
|
print(f"{d:48s} {state:10s} {n:3d}/{report.expected_rows(man):3d} rows "
|
|
f"{man.get('subset') or 'full arm':20.20s} {','.join(man['arms'])}{mark}")
|
|
|
|
|
|
def cmd_abort(a, site):
|
|
man = json.load(open(os.path.join(a.run, "manifest.json")))
|
|
state = report.run_state(man)
|
|
if state not in ("unfinished", "running") or (state == "running" and not a.force):
|
|
sys.exit(f"{a.run} is {state}; only an unfinished run can be marked aborted "
|
|
"(a live one needs --force)")
|
|
mark_aborted(a.run, a.reason)
|
|
print(f"{a.run}: marked aborted ({a.reason})")
|
|
|
|
|
|
def cmd_compare(a, site):
|
|
man_a, res_a = report.load_run(a.run_a, a.allow_incomplete)
|
|
man_b, res_b = report.load_run(a.run_b, a.allow_incomplete)
|
|
report.fill_shelx(a.run_a, man_a, res_a)
|
|
report.fill_shelx(a.run_b, man_b, res_b)
|
|
rows = report.compare_rows(res_a, res_b)
|
|
doc = report.Doc(f"{os.path.basename(os.path.normpath(a.run_a))} vs "
|
|
f"{os.path.basename(os.path.normpath(a.run_b))}")
|
|
doc.p(f"A: rugnux {man_a['binary'].get('version')} ({man_a['binary']['sha256'][:12]}); "
|
|
f"B: rugnux {man_b['binary'].get('version')} ({man_b['binary']['sha256'][:12]}). "
|
|
f"{len(rows)} sets, {sum(1 for r in rows if r[3])} changed beyond noise.")
|
|
report.compare_table(doc, rows, only_changed=not a.all)
|
|
print(doc.markdown())
|
|
if not a.rerun_changed:
|
|
return
|
|
# Rerun the changed sets with A's own binary and options: a set that moves again under the
|
|
# same binary was noise; one that reproduces A was changed by B for real.
|
|
changed = {k for k, ra, rb, ch in rows if ra and rb and [c for c in ch if c != "time"]}
|
|
if not changed:
|
|
print("nothing changed beyond noise; no rerun")
|
|
return
|
|
if man_a.get("results_schema", 1) < report.RESULTS_SCHEMA:
|
|
sys.exit("--rerun-changed: A ran the older variant commands; rerun it with this runner instead")
|
|
sets = [e for e in man_a["sets"] if (e["arm"], e["id"]) in changed]
|
|
opts = dict(man_a["options"], runs_root=a.runs_root or site["runs_root"])
|
|
opts["gpulock"] = opts["gpulock"] and site.get("gpulock")
|
|
opts.setdefault("pdb_cache", site.get("pdb_cache") or model_check.DEFAULT_CACHE)
|
|
opts.setdefault("cod_cache", site.get("cod_cache") or shelx_check.DEFAULT_CACHE)
|
|
opts.setdefault("shelxl", shelx_check.find_shelxl(site.get("shelxl")))
|
|
label = "rerunA-" + man_a["label"]
|
|
rerun = run_sets(site, sets, man_a["arms"], os.path.join(a.run_a, "bin", "rugnux"), None, label,
|
|
opts, ",".join(e["id"] for e in sets))
|
|
_, res_a2 = report.load_run(rerun)
|
|
again = {k: ch for k, ra, ra2, ch in report.compare_rows(res_a, res_a2) if ra and ra2}
|
|
doc = report.Doc("Changed sets, rerun with A's binary")
|
|
rows_out = []
|
|
for k, ra, rb, ch in rows:
|
|
if k not in changed:
|
|
continue
|
|
noise = [c for c in again.get(k, []) if c != "time"]
|
|
rows_out.append([k[1], k[0], ", ".join(c for c in ch if c != "time"),
|
|
", ".join(noise) or "-",
|
|
"NOISE - A itself moved" if noise else "REAL - A reproduces"])
|
|
doc.table(["set", "arm", "A -> B", "A -> A again", "reading"], rows_out)
|
|
doc.p(f"rerun directory: {rerun}")
|
|
print(doc.markdown())
|
|
|
|
|
|
def cmd_report(a, site):
|
|
# a finished run directory is read-only, so a re-render goes elsewhere, named after the run
|
|
man, _ = report.load_run(a.run, a.allow_incomplete)
|
|
repo = git(HERE, "rev-parse", "--show-toplevel")
|
|
out = os.path.realpath(a.out)
|
|
if man.get("private") and repo and (out + os.sep).startswith(os.path.realpath(repo) + os.sep):
|
|
sys.exit("a private run's report must not be written into the repository")
|
|
os.makedirs(a.out, exist_ok=True)
|
|
print(write_report(a.run, a.baseline, a.out, a.allow_incomplete))
|
|
|
|
|
|
def recheck_one(e, wd, pdb_cache):
|
|
"""The post-processing checks of one open-arm row, on the run's own p.mtz (a worker process)."""
|
|
out = {}
|
|
if e["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
|
|
out.update(depdata_check.check_set(wd, e["id"], pdb_cache))
|
|
out.update(check_model(e, wd))
|
|
return out
|
|
|
|
|
|
def set_writable(paths):
|
|
for p in paths:
|
|
os.chmod(p, os.stat(p).st_mode | stat.S_IWUSR)
|
|
|
|
|
|
def cmd_recheck(a, site):
|
|
"""Rerun model_check / depdata_check on a finished run's open-arm merges and update its
|
|
results.json in place. The previous results.json is kept beside it and the recheck is recorded
|
|
in manifest.json ("rechecks": which runner version produced the refmac_* / dep_* numbers)."""
|
|
run = os.path.abspath(a.run)
|
|
report.load_run(run, False) # refuses a run that did not finish
|
|
# the raw files: load_run rescores rows, and results.json keeps the verdicts as they were scored
|
|
man = json.load(open(os.path.join(run, "manifest.json")))
|
|
results = json.load(open(os.path.join(run, "results.json")))
|
|
only = set(a.only.split(",")) if a.only else None
|
|
rows = [r for r in results if r["arm"] == "open" and (only is None or r["set"] in only)]
|
|
if only and len(rows) != len(only):
|
|
sys.exit("not open-arm rows of this run: " + ", ".join(sorted(only - {r["set"] for r in rows})))
|
|
if not rows:
|
|
sys.exit("nothing to recheck")
|
|
stamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
|
|
entry = {"date": datetime.datetime.now().isoformat(timespec="seconds"),
|
|
"runner_git": git(HERE, "rev-parse", "--short", "HEAD") or "unknown",
|
|
"runner_dirty": bool(git(HERE, "status", "--porcelain", "--", ".")),
|
|
"sets": [r["set"] for r in rows],
|
|
"fields": list(REFMAC_KEYS + depdata_check.KEYS),
|
|
"previous_results": "results.json.pre-recheck-" + stamp,
|
|
"command": " ".join(sys.argv)}
|
|
pdb_cache = site.get("pdb_cache") or model_check.DEFAULT_CACHE
|
|
# a finished run directory is read-only: open up only what the recheck writes
|
|
wds = [os.path.join(run, "work", "open", r["set"]) for r in rows]
|
|
set_writable([run, os.path.join(run, "results.json"), os.path.join(run, "manifest.json")] + wds)
|
|
for wd in wds: # the previous check's files stay, renamed
|
|
if os.path.isdir(os.path.join(wd, "model_check")):
|
|
set_writable([os.path.join(wd, "model_check")])
|
|
os.rename(os.path.join(wd, "model_check"), os.path.join(wd, "model_check.pre-recheck-" + stamp))
|
|
shutil.copy2(os.path.join(run, "results.json"), os.path.join(run, "results.json.pre-recheck-" + stamp))
|
|
with concurrent.futures.ProcessPoolExecutor(a.jobs) as pool:
|
|
futures = {pool.submit(recheck_one, {"id": r["set"], "model": r.get("model")}, wd, pdb_cache): r
|
|
for r, wd in zip(rows, wds)}
|
|
for n, fut in enumerate(concurrent.futures.as_completed(futures), 1):
|
|
r = futures[fut]
|
|
r.update(fut.result())
|
|
print(f"[{n}/{len(rows)}] {r['set']:24s} {r['refmac_status'] or '-':8s} "
|
|
f"R_free depflags {report.f(r.get('refmac_rfree_depflags'), '{:.4f}')} "
|
|
f"depdata {report.f(r.get('refmac_rfree_depdata'), '{:.4f}')} "
|
|
f"{r.get('refmac_reason') or ''}",
|
|
flush=True)
|
|
write_json(os.path.join(run, "results.json"), results)
|
|
man.setdefault("rechecks", []).append(dict(entry, end=datetime.datetime.now().isoformat(timespec="seconds")))
|
|
write_json(os.path.join(run, "manifest.json"), man)
|
|
for name in ("report", "report_PRIVATE"):
|
|
for ext in (".md", ".html"):
|
|
if os.path.exists(os.path.join(run, name + ext)):
|
|
set_writable([os.path.join(run, name + ext)])
|
|
os.rename(os.path.join(run, name + ext),
|
|
os.path.join(run, f"{name}{ext}.pre-recheck-{stamp}"))
|
|
print(f"report {write_report(run, man.get('baseline'))}", flush=True)
|
|
make_read_only(run)
|
|
|
|
|
|
def cmd_discover(a, site):
|
|
"""Propose an input for every open-arm directory the manifest does not have yet; with
|
|
--refresh, also show where today's discovery disagrees with the manifest's (unpinned) input."""
|
|
cfg = site["arms"]["open"]
|
|
root = cfg["data_root"]
|
|
by_dir = {} # a directory can hold several sets (6h2p_native, 6h2p_1p89A)
|
|
for e in load_sets(site, "open"):
|
|
by_dir.setdefault(e["input"].split("/")[0], []).append(e)
|
|
for d in sorted(os.listdir(root)):
|
|
if d.startswith(".") or not os.path.isdir(os.path.join(root, d)):
|
|
continue
|
|
sets = by_dir.get(d, [])
|
|
if (sets and not a.refresh) or len(sets) > 1 or (sets and sets[0].get("pinned")):
|
|
continue
|
|
path, fmt, note = inputs.find_input(os.path.join(root, d))
|
|
rel = os.path.relpath(path, root) if path else None
|
|
if not sets:
|
|
print(f"NEW {d:10s} {rel} [{note}]")
|
|
elif rel != sets[0]["input"]:
|
|
print(f"DIFF {d:10s} manifest {sets[0]['input']}\n {'':10s} discover {rel} [{note}]")
|
|
for d in sorted(set(by_dir) - set(os.listdir(root))):
|
|
print(f"GONE {d:10s} in the manifest, not on disk")
|
|
|
|
|
|
def cmd_refs(a, site):
|
|
"""Re-read every set's XDS reference from the CORRECT.LP beside its input."""
|
|
cfg = site["arms"][a.arm]
|
|
if cfg["reference"] != "xds":
|
|
sys.exit(f"the {a.arm} arm is not referenced to XDS")
|
|
man = json.load(open(cfg["manifest"]))
|
|
for e in man["sets"]:
|
|
lp = os.path.join(cfg["data_root"], os.path.dirname(e["input"]), "CORRECT.LP")
|
|
if not os.path.exists(lp):
|
|
print(f"{e['id']:24s} no CORRECT.LP")
|
|
continue
|
|
new = inputs.parse_correct_lp(lp)
|
|
old = e.get("ref") or {}
|
|
diff = [f"{k} {old.get(k)} -> {new.get(k)}" for k in sorted(set(old) | set(new))
|
|
if old.get(k) != new.get(k)]
|
|
if diff:
|
|
print(f"{e['id']:24s} " + "; ".join(diff))
|
|
e["ref"] = new
|
|
if a.write:
|
|
write_manifest(cfg["manifest"], man)
|
|
|
|
|
|
def cmd_remap(a, site):
|
|
"""Follow a rename of data directories. MAP is a JSON object {old: new}: a string renames the
|
|
set of that id and, wherever it is the first directory of an input, that directory; an object
|
|
{"id": ..., "input": ...} gives one set's new id and input outright. A renamed set's old id is
|
|
kept under "aliases", so runs made before the rename still compare set by set."""
|
|
cfg = site["arms"][a.arm]
|
|
man = json.load(open(cfg["manifest"]))
|
|
mp = json.load(open(a.map))
|
|
aliases = man.setdefault("aliases", {})
|
|
for e in man["sets"]:
|
|
new = mp.get(e["id"])
|
|
head, _, rest = e["input"].partition("/")
|
|
if isinstance(new, dict):
|
|
new_id, new_input = new.get("id", e["id"]), new.get("input", e["input"])
|
|
else:
|
|
new_id = new or e["id"]
|
|
new_input = (mp[head] if isinstance(mp.get(head), str) else head) + "/" + rest
|
|
if (new_id, new_input) == (e["id"], e["input"]):
|
|
continue
|
|
there = os.path.exists(os.path.join(cfg["data_root"], new_input))
|
|
print(f"{e['id']:24s} -> {new_id:24s} {new_input}" + ("" if there else " NOT FOUND"))
|
|
if new_id != e["id"]:
|
|
for old in [k for k, v in aliases.items() if v == e["id"]]:
|
|
aliases[old] = new_id
|
|
aliases[e["id"]] = new_id
|
|
e["id"], e["input"] = new_id, new_input
|
|
if a.write:
|
|
write_manifest(cfg["manifest"], man)
|
|
|
|
|
|
def load_aliases(site):
|
|
"""{arm: {old set id: current id}} from the manifests, applied when runs are compared."""
|
|
out = {}
|
|
for arm, cfg in site["arms"].items():
|
|
if os.path.exists(cfg["manifest"]):
|
|
out[arm] = json.load(open(cfg["manifest"])).get("aliases", {})
|
|
return out
|
|
|
|
|
|
def main():
|
|
ap = argparse.ArgumentParser(description=__doc__.split("\n")[0])
|
|
ap.add_argument("--site", help="site config (default: $JFJOCH_BATTERY_SITE, else site.json "
|
|
"beside this script)")
|
|
sub = ap.add_subparsers(dest="cmd", required=True)
|
|
|
|
r = sub.add_parser("run")
|
|
r.add_argument("--rugnux", required=True)
|
|
r.add_argument("--label", help="short name, part of the run directory's name "
|
|
"(default: the rugnux version)")
|
|
r.add_argument("--arm", default="open,inhouse", help="comma-separated (default: open,inhouse)")
|
|
r.add_argument("--only", help="comma-separated set ids")
|
|
r.add_argument("--tier", help="named subset from the manifests, e.g. smoke")
|
|
r.add_argument("--build-dir", help="build tree whose CMakeCache.txt records the flags")
|
|
r.add_argument("--gpulock", action="store_true",
|
|
help="queue each rugnux behind the site's GPU lock (timing is then not a reference)")
|
|
r.add_argument("--threads", type=int, default=0, help="-N for rugnux (default: its own choice)")
|
|
r.add_argument("--timeout", type=int, default=10800, help="per rugnux run, in s")
|
|
r.add_argument("--model-check", action="store_true",
|
|
help="open arm: also score each merge against the deposited model with "
|
|
"REFMAC (model_check.py; needs CCP4)")
|
|
r.add_argument("--extra", default="", help="extra rugnux arguments, applied to every set")
|
|
r.add_argument("--baseline", help="earlier run directory to report the delta against (default: "
|
|
"the site's persisted baseline; 'none' for no delta)")
|
|
r.add_argument("--runs-root")
|
|
|
|
c = sub.add_parser("compare")
|
|
c.add_argument("run_a")
|
|
c.add_argument("run_b")
|
|
c.add_argument("--all", action="store_true", help="list unchanged sets too")
|
|
c.add_argument("--rerun-changed", action="store_true",
|
|
help="rerun the changed sets with A's saved binary to separate real change from noise")
|
|
c.add_argument("--runs-root")
|
|
c.add_argument("--allow-incomplete", action="store_true",
|
|
help="compare a run that did not finish (aborted, killed or still running)")
|
|
|
|
p = sub.add_parser("report")
|
|
p.add_argument("run")
|
|
p.add_argument("--baseline")
|
|
p.add_argument("--out", required=True, help="directory for the re-rendered report")
|
|
p.add_argument("--allow-incomplete", action="store_true",
|
|
help="render a run that did not finish; the report says so")
|
|
|
|
ls = sub.add_parser("list")
|
|
ls.add_argument("--runs-root")
|
|
|
|
ab = sub.add_parser("abort")
|
|
ab.add_argument("run")
|
|
ab.add_argument("--reason", default="aborted by hand")
|
|
ab.add_argument("--force", action="store_true", help="even if its runner still seems alive")
|
|
|
|
rc = sub.add_parser("recheck")
|
|
rc.add_argument("run")
|
|
rc.add_argument("--only", help="comma-separated set ids (default: every open-arm row)")
|
|
rc.add_argument("--jobs", type=int, default=8, help="sets checked in parallel (CPU; REFMAC)")
|
|
|
|
d = sub.add_parser("discover")
|
|
d.add_argument("--refresh", action="store_true")
|
|
|
|
m = sub.add_parser("remap")
|
|
m.add_argument("--arm", required=True)
|
|
m.add_argument("map", help="JSON file {old: new}")
|
|
m.add_argument("--write", action="store_true")
|
|
|
|
f = sub.add_parser("refs")
|
|
f.add_argument("--arm", required=True)
|
|
f.add_argument("--write", action="store_true")
|
|
|
|
a = ap.parse_args()
|
|
site = load_site(a.site)
|
|
report.ALIASES = load_aliases(site)
|
|
report.PDB_CACHE = site.get("pdb_cache") or model_check.DEFAULT_CACHE
|
|
report.COD_CACHE = site.get("cod_cache") or shelx_check.DEFAULT_CACHE
|
|
report.SHELXL = shelx_check.find_shelxl(site.get("shelxl"))
|
|
report.MANIFESTS = {arm: {e["id"]: e for e in load_sets(site, arm)}
|
|
for arm, cfg in site["arms"].items() if os.path.exists(cfg["manifest"])}
|
|
{"run": cmd_run, "list": cmd_list, "compare": cmd_compare, "report": cmd_report,
|
|
"abort": cmd_abort, "recheck": cmd_recheck, "discover": cmd_discover, "refs": cmd_refs, "remap": cmd_remap}[a.cmd](a, site)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|