perf: ClamAV parallel prefetch, shared pebble pool, PE checksum skip, YARA init guard#3018
perf: ClamAV parallel prefetch, shared pebble pool, PE checksum skip, YARA init guard#3018wmetcalf wants to merge 5 commits into
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… YARA init guard - clamav.py: Add prefetch_clamav() using ThreadPoolExecutor to fan out ALLMATCHSCAN calls in parallel before the sequential per-file loop. Reduces ClamAV wall-clock from sum(scans) to slowest single scan. Adds module-level _CLAMAV_CACHE + _CACHE_LOCK for per-task caching. - CAPE.py: Call prefetch_clamav() with all target + dropped + procdump paths before the per-file processing loop; clear cache on exit. - file_extra_info.py: Share a module-level pebble.ProcessPool singleton (get_extractor_pool()) instead of creating/destroying one per file. Also re-run PortableExecutable() when pe.digital_signers is empty so previously-analysed files get the cert data filled in on reprocess. - parse_pe.py: get_actual_checksum() returns None when the PE reports checksum=0, skipping the expensive O(file_size) recompute. Fix backend.load_der_pkcs7_certificates → pkcs7.load_der_pkcs7_certificates for cryptography ≥ 40.x (old method removed from Backend). - objects.py: Add idempotency guard to File.init_yara() so repeated calls in multi-worker environments don't reload rules unnecessarily. - process.py: Eagerly call File.init_yara() in init_worker() so YARA rules are loaded once at worker startup rather than on first task.
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Code Review
This pull request implements several performance optimizations for CAPE processing, most notably parallelizing ClamAV scans via a new caching mechanism and reusing a process-wide worker pool for file extraction to minimize subprocess overhead. It also reduces processing time by skipping PE checksum recomputations when the reported checksum is zero and ensures YARA rules are eagerly compiled in worker processes. Review feedback identifies a high-severity risk of deadlocks in the worker logging initialization and suggests a more efficient check for digital signers to avoid redundant parsing of unsigned files.
| # Fix for open file handles on rotated logs in workers | ||
| for h in log.handlers[:]: | ||
| if isinstance(h, logging.FileHandler): | ||
| h.close() | ||
| log.removeHandler(h) |
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Re-introducing calls to h.close() and log.removeHandler(h) in the worker initializer risks a deadlock. If the parent process was holding the logging lock (e.g., another thread was logging) during the fork(), the lock will be permanently held in the child process. Attempting to acquire it via these methods will cause the worker to hang.
Furthermore, the subsequent calls to log.addHandler() (lines 207, 225, 234) also attempt to acquire this lock. The previous implementation used direct list operations like log.handlers.clear() and log.handlers.append() specifically to bypass the lock and avoid deadlocks in forked workers. Given that workers are short-lived (maxtasksperchild), the file descriptor leak is a safer trade-off than the risk of deadlocked workers.
| # Fix for open file handles on rotated logs in workers | |
| for h in log.handlers[:]: | |
| if isinstance(h, logging.FileHandler): | |
| h.close() | |
| log.removeHandler(h) | |
| # Avoid fork deadlock: use direct list ops instead of | |
| # handler.close()/removeHandler()/addHandler() which acquire locks. | |
| # Inherited FDs are intentionally leaked: closing them via os.close() | |
| # frees the fd number, but the old Python stream still references it; | |
| # when GC finalizes that stream it may close a new handler's fd. | |
| # Workers are short-lived (max_tasks) so the leak is harmless. | |
| log.handlers.clear() |
| elif not data_dictionary["pe"].get("digital_signers"): | ||
| with PortableExecutable(file_path) as pe: | ||
| data_dictionary["pe"]["digital_signers"] = pe.get_digital_signers(pe.pe) | ||
| data_dictionary["pe"]["guest_signers"] = pe.get_guest_digital_signers(task_id) |
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This check will trigger for every unsigned PE file during reprocessing, as digital_signers will be an empty list. This causes the file to be re-opened and re-parsed, which is a significant performance hit for tasks with many unsigned payloads.
Since the cryptography bug is now fixed for new analyses, consider if this 'fallback' for old records is worth the performance cost on all unsigned files. If it must be kept, it would be more efficient to check if the PE has a security directory entry (e.g., via pe.OPTIONAL_HEADER.DATA_DIRECTORY[pefile.DIRECTORY_ENTRY['IMAGE_DIRECTORY_ENTRY_SECURITY']].Size > 0) before performing a full re-extraction.
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Pull request overview
This PR introduces several performance-oriented optimizations across CAPE’s processing pipeline (ClamAV scanning, extractor execution, PE parsing, and YARA initialization) to reduce per-task wall-clock time under heavy file workloads.
Changes:
- Add parallel ClamAV prefetch + a per-process scan result cache to avoid repeated socket scans.
- Reuse a shared
pebble.ProcessPoolfor file extractors instead of creating a new pool per file. - Skip expensive PE checksum recomputation when the reported checksum is zero, and update PKCS7 certificate extraction to a supported cryptography API.
- Make YARA initialization idempotent and eagerly compile rules at worker startup.
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
utils/process.py |
Adjust worker logger handler reset and eagerly initializes YARA rules in each worker. |
modules/processing/CAPE.py |
Adds ClamAV parallel prefetch orchestration before per-file processing. |
lib/cuckoo/common/objects.py |
Adds an idempotency guard (and force) to YARA initialization. |
lib/cuckoo/common/integrations/parse_pe.py |
Skips checksum recompute for zero reported checksum; fixes PKCS7 signer extraction call. |
lib/cuckoo/common/integrations/file_extra_info.py |
Reuses a shared pebble pool for extractors; adds signer re-extraction fallback. |
lib/cuckoo/common/integrations/clamav.py |
Implements threaded batch scanning and a module-level cache for ClamAV results. |
| # Fix for open file handles on rotated logs in workers | ||
| for h in log.handlers[:]: | ||
| if isinstance(h, logging.FileHandler): | ||
| h.close() | ||
| log.removeHandler(h) | ||
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| # Restore Console Handler | ||
| ch = ConsoleHandler() | ||
| ch.setFormatter(FORMATTER) | ||
| log.handlers.append(ch) | ||
| log.addHandler(ch) |
| passed (used after a yara-rule update). Without this guard, repeated | ||
| callers (e.g. some integration paths that didn't go through the | ||
| get_yara() wrapper) re-compiled all six categories on every call.""" | ||
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| if cls.yara_initialized and not force: | ||
| return |
| def get_reported_checksum(self, pe: pefile.PE) -> str: | ||
| """Get checksum from optional header | ||
| @return: checksum or None. | ||
| """ | ||
| return f"0x{pe.OPTIONAL_HEADER.CheckSum:08x}" if pe else None | ||
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| def get_actual_checksum(self, pe: pefile.PE) -> str: | ||
| """Get calculated checksum of PE | ||
| @return: checksum or None. | ||
| @return: checksum string, or None if unavailable / not computed. |
| The recomputed value is only consumed by the | ||
| `static_pe_anomaly` signature, which only compares it against | ||
| the embedded `reported_checksum` when that field is non-zero | ||
| (`if reported and reported != actual` — see | ||
| modules/signatures/all/static_pe_anomaly.py). When the PE has | ||
| no embedded checksum (compilers commonly omit it; almost every | ||
| dropper/packer leaves it 0), the recompute result would never | ||
| be consulted — pure throwaway work. | ||
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| Skip the expensive recompute in that case and return None so | ||
| the field is honestly absent rather than fabricated. The | ||
| signature already gracefully handles missing keys via the | ||
| `if reported and ...` guard, and downstream consumers can | ||
| distinguish "not computed" from "computed and zero". Saves | ||
| ~40s on a 19-payload analysis with reported=0 binaries. |
| # Module-level cache for per-task `prefetch_clamav` results. Keyed by | ||
| # absolute file path. Each value is the same list of match-strings that | ||
| # `get_clamav` would otherwise compute. Populated by `prefetch_clamav` | ||
| # and consumed transparently by `get_clamav`. Cleared at task boundary | ||
| # via `clear_clamav_cache` to avoid leaking results across analyses on | ||
| # a long-lived worker process. | ||
| _CACHE_LOCK = threading.Lock() | ||
| _CLAMAV_CACHE = {} | ||
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| if "pe" not in data_dictionary: | ||
| with PortableExecutable(file_path) as pe: | ||
| data_dictionary["pe"] = pe.run(task_id) | ||
| elif not data_dictionary["pe"].get("digital_signers"): | ||
| with PortableExecutable(file_path) as pe: | ||
| data_dictionary["pe"]["digital_signers"] = pe.get_digital_signers(pe.pe) | ||
| data_dictionary["pe"]["guest_signers"] = pe.get_guest_digital_signers(task_id) |
…traction - process.py: Replace h.close()/removeHandler()/addHandler() calls with direct log.handlers[:] = [] and log.handlers.append() to avoid acquiring logging locks in child processes after fork() (deadlock risk if parent held the lock at fork time). - file_extra_info.py: Only re-run PortableExecutable cert extraction when DigiSig.json confirms the file is signed (aux_signers non-empty). Without this guard, every unsigned PE would trigger a redundant re-parse on reprocess.
Setting it inside the HAVE_YARA try block marked init complete after the first successful category (binaries), so any concurrent or subsequent init_yara() call would short-circuit before CAPE was reached — KeyError: CAPE in get_yara. Also fixes YARA_X path which never set yara_initialized at all.
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Fixed test_get_yaras failure (3b7ca00) Root cause: Kevin's fix commit added the flag to the YARA_X path but also inside the per-category loop, same bug. Fix: single |
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Hi @kevoreilly — the Should be ready to merge now if you're happy with the rest of the changes. |
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@kevoreilly to clarify what this PR does and why the diff looks the way it does: The original bug (still in your current master): Your commit 68ccb06 added This PR's fix: moves the single Net result vs your master:
If tests are still failing on your side let me know what the output is and I'll take a look. |
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The tests are still failing, link from above to failed tests is https://github.com/kevoreilly/CAPEv2/actions/runs/25920160083/job/76186792607?pr=3018 |
Summary
Four independent processing-pipeline performance improvements observed under profiling on heavy tasks:
ClamAV parallel prefetch (
clamav.py,CAPE.py): Fan outALLMATCHSCANcalls viaThreadPoolExecutorbefore the sequential per-file loop. ClamAV was measured at ~58% of CAPE module wall-clock on tasks with 10–20 dropped/extracted files; parallel prefetch cuts that fromsum(per-file scan times)toslowest single scan. Adds a per-task LRU cache to avoid rescanning the same binary twice within one analysis.Shared pebble pool (
file_extra_info.py): Replace thewith pebble.ProcessPool(...) as pool:pattern that was creating and tearing down a worker pool for every file with a module-level singleton (get_extractor_pool()). Pool startup was ~85 s on a 70-file task.PE checksum skip (
parse_pe.py):get_actual_checksum()returnsNonewhen the PE's reported checksum is 0, skipping the O(file-size) Python loop recompute. No loss of signal — a zero reported checksum means no comparison can be made anyway.pkcs7 extraction fix (
parse_pe.py):backend.load_der_pkcs7_certificates()was removed from theBackendclass incryptography≥ 40.x. The call silently failed insidesuppress(Exception), leavingdigital_signersempty for every signed PE. Switched topkcs7.load_der_pkcs7_certificates(). Also adds a fallback infile_extra_info.pyto re-run cert extraction on reprocess ifdigital_signerswas previously populated as empty.YARA init guard (
objects.py,process.py):File.init_yara()now short-circuits on repeated calls;init_worker()loads YARA rules eagerly at worker startup so the first task in each worker doesn't pay the load cost.Test plan
digital_signersis non-empty for signed PEs after the pkcs7 fixprocess.py -r <id>reprocess populatesdigital_signersfor previously-empty entriesactual_checksumis absent (not0x00000000) for PEs with checksum field = 0🤖 Generated with Claude Code