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Fix index-out-of-bounds in gp_matern32_cov by WardBrian · Pull Request #3084 · stan-dev/math · GitHub

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Fix index-out-of-bounds in gp_matern32_cov - #3084

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WardBrian merged 2 commits into
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fix/gp_matern32-indexing-error
Jun 17, 2024
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Fix index-out-of-bounds in gp_matern32_cov#3084
WardBrian merged 2 commits into
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fix/gp_matern32-indexing-error

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WardBrian commented Jun 17, 2024

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Summary

Reported by @tillahoffmann on the forums: https://discourse.mc-stan.org/t/debugging-gp-matern32-cov/35502.

One of the overloads of gp_matern32_cov was using x_size to index over a variable that actually had length l_size. Presumably a copy/paste error.

Tests

I added a minified version of their reproducer. The behavior is undefined in the bug case, so unfortunately the test is not guaranteed to fail on all systems if the bug is re-introduced.

Side Effects

None

Release notes

Fixed an indexing bug inside gp_matern32_cov

Checklist

  • Copyright holder: Simons Foundation

    The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the license the submitted work under the following licenses:
    - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
    - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

  • the basic tests are passing

    • unit tests pass (to run, use: ./runTests.py test/unit)
    • header checks pass, (make test-headers)
    • dependencies checks pass, (make test-math-dependencies)
    • docs build, (make doxygen)
    • code passes the built in C++ standards checks (make cpplint)

  • the code is written in idiomatic C++ and changes are documented in the doxygen

  • the new changes are tested

WardBrian added the bug label Jun 17, 2024
andrjohns approved these changes Jun 17, 2024
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andrjohns left a comment

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

LGTM.

Maybe we should start suggesting/requiring range-based loops where possible instead to avoid this?

WardBrian commented Jun 17, 2024

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That would be nice where it's possible. I wonder if there is a linter rule we could turn on, because enforcing it manually seems impossible to do consistently.

tillahoffmann commented Jun 17, 2024

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Thank you for the fast fix!

stan-buildbot commented Jun 17, 2024

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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.31 0.29 1.06 5.63% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.18 15.17% faster
gp_regr/gen_gp_data.stan 0.02 0.02 1.02 1.94% faster
gp_regr/gp_regr.stan 0.09 0.09 1.05 5.0% faster
sir/sir.stan 68.64 69.81 0.98 -1.69% slower
irt_2pl/irt_2pl.stan 3.87 3.97 0.98 -2.45% slower
eight_schools/eight_schools.stan 0.06 0.06 1.01 1.38% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.25 0.25 1.0 -0.41% slower
pkpd/one_comp_mm_elim_abs.stan 19.18 19.7 0.97 -2.71% slower
garch/garch.stan 0.42 0.45 0.94 -6.6% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.66 2.6 1.02 2.18% faster
arK/arK.stan 1.78 1.75 1.02 1.57% faster
gp_pois_regr/gp_pois_regr.stan 2.9 2.78 1.04 4.27% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.69 8.41 1.03 3.22% faster
performance.compilation 181.06 178.74 1.01 1.28% faster
Mean result: 1.0213906121792329

Jenkins Console Log
Blue Ocean
Commit hash: 5d05984ce6b87a1c09f4a75b73535b72bc57f54b

Machine information No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04 Codename: focal

CPU:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2: Mitigation; IBRS, IBPB conditional, STIBP conditional, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

G++:
g++ (Ubuntu 9.4.0-1ubuntu1~20.04) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Clang:
clang version 10.0.0-4ubuntu1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

WardBrian merged commit 44c91c9 into develop Jun 17, 2024
WardBrian deleted the fix/gp_matern32-indexing-error branch June 17, 2024 22:06
This was referenced Jul 10, 2024
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tillahoffmann commented Sep 3, 2024

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Thank you for the fast fix on this issue, @WardBrian. Do you know when these changes are expected to be released in an upcoming cmdstan version?

cc @skiptoniam

WardBrian commented Sep 3, 2024

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@tillahoffmann the next release is scheduled for October 7th

tillahoffmann commented Sep 3, 2024

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Great, thank you!

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andrjohns andrjohns approved these changes
SteveBronder Awaiting requested review from SteveBronder
rok-cesnovar Awaiting requested review from rok-cesnovar

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