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fix(vdb-sys): stop a rare crash when threads finish reading a loading reference - #78
Fixes the rare SIGBUS in schema teardown that #77 listed as not fixed (VTableRelease → VSchemaWhack → SProductionWhack). Also proposed upstream as ncbi/ncbi-vdb#291.
0008: heap corruption when several threads finish reading a reference as it loads. When a reference's background loader publishes its final state, every reader that was waiting for it calls cleanUpAsyncThread, which checked self->th and then waited for and released the thread with no synchronisation. With two such readers, the loader's KThread (two references) was released three times, so it was freed while a reader was still in KThreadWait, and that reader then wrote waiting = 0 into the freed block. In both crashes we saw, the block had been reused by another reference table's schema, so the crash came later, when that table was released. The patch has each caller atomically take the thread pointer, and only the one that gets it waits and releases. It also changes what readers get when a background load fails. One reader returned the failure's rc_t as the number of bases read, and every other reader reached readZero, which called abort(). Now every reader gets 0 bases, so fg-sra reports a short-read error instead of aborting.
How it was found
Both crash reports fault in SProductionWhack on index 3 of an SFunction's parameter vector (24 bytes into its array). The bad elements, 0x0000000b_00000000 and 0x00000007_00000000, are heap pointers from the same process with their low 32 bits zeroed. In KThread, offset 24 is waiting, which KThreadWait clears with a 4-byte store after pthread_join returns (add x21, x0, #0x18 … stlr wzr, [x21] in the 0.2.0 binary's KThreadWait).
Verification
ERR14844919 (599 external references, loaded on 8 threads), macOS arm64.
With a test-only hook (not in this PR) that sleeps 50 ms before the loader publishes its final state and 20 ms in cleanUpAsyncThread before the wait:
Before: in all 20 runs, two threads waited for and released the same loader thread, for 4–20 references per run. With ASan, 9 of 10 runs aborted: 5 on heap-use-after-free (a 4-byte write in KThreadWait, 24 bytes into a KThread freed by another reader's KThreadRelease), and 4 on "Joining already joined thread".
After: 0 of 20 and 0 of 10, with 7–25 references per run still reaching the cleanup on several threads at once.
With the hook's logging but no sleeps: before the fix, 1 of 10 runs already released a loader thread twice.
Natural stress with 0001–0008: 600 of 600 runs on ERR14844919 (6 at a time, performance cores) exited cleanly. On the efficiency cores (taskpolicy -b), where the second crash appeared, 30 runs each: fix(vdb-sys): fix two more races reading external references #77 had no crash but 2 runs failed with a short reference read (rcTooShort, as in one earlier unexplained failure); this PR had none. That fits this race but isn't proof; 30 runs are too few to measure a crash rate.
A failed load, forced by a test-only hook that sets the loader's rc: with the PR's first version, 3 of 3 runs aborted (SIGABRT, in readZero); now 3 of 3 exit 1 with failed to read reference … VDB error (rcTooShort).
After the failed-load changes, I repeated the hook comparison (5 runs each: double releases in 5 before, 0 after; plus 5 under ASan for the base-count change: 3 before, 0 after), 300 natural runs (all clean), the output comparison (identical) and the checks below.
Checks:cargo ci-fmt, ci-lint and ci-test pass, with the archive-backed tests enabled. The two stress tests that exceed 120 s in a debug build pass in a release build.
The CHANGELOG is generated by git-cliff, so the commit title is the entry.
Does this introduce a breaking change?
Yes
No
Summary by CodeRabbit
Bug Fixes
Improved reliability when reading from a RefSeq data load that has failed. These reads now report zero available bases instead of causing an error or returning an invalid base count.
Prevented concurrent cleanup from releasing the same background loader thread more than once, reducing the risk of failures during shutdown.
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Walkthrough
The RefSeq patch changes failed-load reads to return zero bases. It also atomically takes and clears the asynchronous loader thread pointer during cleanup, so only the caller that obtains the pointer waits for and releases the thread.
Changes: RefSeq loader behavior
Layer / File(s)
Summary
Thread cleanup and failure return crates/fg-sra-vdb-sys/vendor/patches/ncbi-vdb/0008-refseq-loader-thread-cleanup-race.patch
readZero returns zero bases instead of asserting and aborting after a failed load. cleanUpAsyncThread atomically takes and clears the thread pointer; only the caller that receives it waits for and releases the thread. If cleanup reports a loader failure, RefSeq_getBases returns zero bases.
Failed reference loads now report short reads instead of aborting. No merge-blocking risk was identified.
Pre-merge checks: 5
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The title clearly and concisely describes the main change: fixing a rare crash caused by a thread-cleanup race during reference loading.
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No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
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A rabbit reads the RefSeq flow, Zero bases come when loads say no. One thread is taken, cleared from view, One caller waits, then frees it too. The loader’s counts now stay true.
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Actionable comments posted: 1
Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at
@crates/fg-sra-vdb-sys/vendor/patches/ncbi-vdb/0008-refseq-loader-thread-cleanup-race.patch:
- Line 37: Update cleanUpAsyncThread and the failed-load handling around
TAKE_LOADER_THREAD so readers that do not obtain the loader thread preserve the
failure result and return a short read instead of recursing into RefSeq_getBases
with self->reader set to readZero. Ensure the failure state is shared across all
readers, not only the thread that takes th.
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… reference
When an external reference finished loading in the background, every
thread that had waited for it to publish its final state could wait for
and release the loader thread. Its KThread was then released once too
often and freed while one of them still waited on it, and that thread
wrote into the freed memory. In both crashes we saw, the block had been
reused by another reference table's schema, and the program crashed
later (SIGBUS in SProductionWhack) when that table was released.
Vendored patch 0008 lets only the thread that atomically takes the
loader thread wait for and release it.
When a background load failed, the patch also makes every reader of that
reference get no bases, so fg-sra reports a short read as an error.
Before, one reader returned the failure code as a base count and the
others aborted.
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Summary
Fixes the rare SIGBUS in schema teardown that #77 listed as not fixed (
VTableRelease→VSchemaWhack→SProductionWhack). Also proposed upstream as ncbi/ncbi-vdb#291.cleanUpAsyncThread, which checkedself->thand then waited for and released the thread with no synchronisation. With two such readers, the loader'sKThread(two references) was released three times, so it was freed while a reader was still inKThreadWait, and that reader then wrotewaiting = 0into the freed block. In both crashes we saw, the block had been reused by another reference table's schema, so the crash came later, when that table was released. The patch has each caller atomically take the thread pointer, and only the one that gets it waits and releases. It also changes what readers get when a background load fails. One reader returned the failure'src_tas the number of bases read, and every other reader reachedreadZero, which calledabort(). Now every reader gets 0 bases, so fg-sra reports a short-read error instead of aborting.How it was found
Both crash reports fault in
SProductionWhackon index 3 of anSFunction's parameter vector (24 bytes into its array). The bad elements,0x0000000b_00000000and0x00000007_00000000, are heap pointers from the same process with their low 32 bits zeroed. InKThread, offset 24 iswaiting, whichKThreadWaitclears with a 4-byte store afterpthread_joinreturns (add x21, x0, #0x18…stlr wzr, [x21]in the 0.2.0 binary'sKThreadWait).Verification
ERR14844919 (599 external references, loaded on 8 threads), macOS arm64.
cleanUpAsyncThreadbefore the wait:heap-use-after-free(a 4-byte write inKThreadWait, 24 bytes into aKThreadfreed by another reader'sKThreadRelease), and 4 on "Joining already joined thread".taskpolicy -b), where the second crash appeared, 30 runs each: fix(vdb-sys): fix two more races reading external references #77 had no crash but 2 runs failed with a short reference read (rcTooShort, as in one earlier unexplained failure); this PR had none. That fits this race but isn't proof; 30 runs are too few to measure a crash rate.rc: with the PR's first version, 3 of 3 runs aborted (SIGABRT, inreadZero); now 3 of 3 exit 1 withfailed to read reference … VDB error (rcTooShort).Checks:
cargo ci-fmt,ci-lintandci-testpass, with the archive-backed tests enabled. The two stress tests that exceed 120 s in a debug build pass in a release build.The CHANGELOG is generated by git-cliff, so the commit title is the entry.
Does this introduce a breaking change?
Summary by CodeRabbit