Bug in LinearAlgebra? How to debug a standard library

PetrKryslUCSD · October 12, 2025, 2:29am

Is this known?

[91133] signal 11 (2): Segmentation fault: 11
in expression starting at /Users/pkrysl/ACol.jl/runsim.jl:38
gc_alloc_map_set at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./gc.h:360 [inlined]
gc_sweep_page at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1549 [inlined]
gc_sweep_pool_page at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1574
gc_sweep_prescan at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1640
gc_sweep_wake_all at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1661 [inlined]
gc_sweep_pool at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1806 [inlined]
_jl_gc_collect at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:3645
ijl_gc_collect at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:3893
maybe_collect at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:926 [inlined]
jl_gc_pool_alloc_inner at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1319 [inlined]
jl_gc_pool_alloc_noinline at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/gc.c:1386 [inlined]
jl_gc_alloc_ at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia_internal.h:523
_new_genericmemory_ at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/genericmemory.c:56
GenericMemory at ./boot.jl:516 [inlined]
new_as_memoryref at ./boot.jl:535 [inlined]
Array at ./boot.jl:582 [inlined]
similar at ./array.jl:370 [inlined]
AbstractArray at ./array.jl:627
convert at ./abstractarray.jl:18 [inlined]
QRPivoted at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/LinearAlgebra/src/qr.jl:451
Factorization at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/LinearAlgebra/src/qr.jl:453 [inlined]
ldiv at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/LinearAlgebra/src/LinearAlgebra.jl:643
\ at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/LinearAlgebra/src/LinearAlgebra.jl:631 [inlined]
\ at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/LinearAlgebra/src/generic.jl:1134

Mac M2 Ultra, Julia 1.11.7.

mbauman · October 12, 2025, 2:39am

Segfaults in GC are most frequently due to unrelated corruption (typically an out-of-bounds write). Try running with check bounds=yes … or better yet, use rr and go back in time to see what wrote to the corrupted address (but that’s hard and Linux-only).

giordano · October 12, 2025, 3:55am

Some notes about debugging garbage collector bugs with rr: How I debug issues with Julia GC

PetrKryslUCSD · October 12, 2025, 5:07am

Bounds checking getting turned off was instructive.

ERROR: LoadError: BoundsError: attempt to access 12582-element Vector{ComplexF32} at index [11995693056]
Stacktrace:
  [1] throw_boundserror(A::Vector{ComplexF32}, I::Tuple{Int64})
    @ Base ./essentials.jl:14
  [2] setindex!
    @ ./array.jl:986 [inlined]
  [3] ldiv!(A::LinearAlgebra.QRPivoted{ComplexF32, Matrix{ComplexF32}, Vector{ComplexF32}, Vector{Int64}}, B::Matrix{ComplexF32}, rcond::Float32)
    @ LinearAlgebra ~/julia-1.11.7/share/julia/stdlib/v1.11/LinearAlgebra/src/qr.jl:607
  [4] ldiv!
    @ ~/julia-1.11.7/share/julia/stdlib/v1.11/LinearAlgebra/src/qr.jl:620 [inlined]
  [5] ldiv(F::LinearAlgebra.QRPivoted{ComplexF32, Matrix{ComplexF32}, Vector{ComplexF32}, Vector{Int64}}, B::Matrix{ComplexF32})
    @ LinearAlgebra ~/julia-1.11.7/share/julia/stdlib/v1.11/LinearAlgebra/src/LinearAlgebra.jl:656
  [6] \
    @ ~/julia-1.11.7/share/julia/stdlib/v1.11/LinearAlgebra/src/LinearAlgebra.jl:631 [inlined]
  [7] \(A::Matrix{ComplexF32}, B::Matrix{ComplexF32})
    @ LinearAlgebra ~/julia-1.11.7/share/julia/stdlib/v1.11/LinearAlgebra/src/generic.jl:1134

But I still don’t know what happened. I want to dev LinearAlgebra in order to put some
debugging prints in there, but it doesn’t seem to work. What do I do? I don’t think I had to debug
a standard library before.
This doesn’t seem to have done it:

Sukera · October 12, 2025, 8:13am

Can you maybe share the code you’re executing that results in the error?

PetrKryslUCSD · October 12, 2025, 1:22pm

I’m afraid I can’t do that. Proprietary data and code. I don’t have an MWE (yet).

PetrKryslUCSD · October 12, 2025, 2:13pm

Does anyone know how to force Julia to pick up a modified version of the LinearAlgebra?
I see

yet the prints are not coming. I think the code still uses the precompiled library.
How do I change that? precompile does not work.

That is the line:

The pivot is garbage.

giordano · October 12, 2025, 2:31pm

github.com/JuliaLang/LinearAlgebra.jl

README.md

28ee87ef5

# LinearAlgebra

This package is part of the Julia standard library (stdlib).

`LinearAlgebra.jl` provides functionality for performing linear algebra operations in Julia.

| **Build Status**                    | **Coverage**                    |
|:-------------------------------:|:-------------------------------:|
[![Build status](https://badge.buildkite.com/4032f509b3a7354c8ce7b34b98c7496d66adc4504b0101cbcf.svg?branch=master)](https://buildkite.com/julialang/linearalgebra-dot-jl) | [![][codecov-img]][codecov-url] |

[codecov-img]: https://codecov.io/gh/JuliaLang/LinearAlgebra.jl/branch/master/graph/badge.svg
[codecov-url]: https://codecov.io/gh/JuliaLang/LinearAlgebra.jl

## Using development versions of this package

This package performs some type piracy and is also included in the sysimage, which makes using a development version slightly more complex than usual.

To use a development version of this package, you can choose one of the following methods:

1. **Prune the sysimg version and load the package:**

This file has been truncated. show original

danielwe · October 12, 2025, 5:03pm

The easiest approach for simple debugging is often to just monkey patch the method you’re working on. No custom sysimage or Julia build needed.

julia> @eval LinearAlgebra function foo(bar, baz)
           # code copied from the real LinearAlgebra.foo
           println("what on earth happens here? x=$x, y=$y")
           # the rest of the real LinearAlgebra.foo
       end

Benny · October 13, 2025, 12:03am

Could Revise.track(#=standard library name=#) work as a way to do those @evals? I wouldn’t want to alter the original source files and don’t actually know the proper way to use that, I’m just curious if LinearAlgebra being part of the sysimage would affect Revise as it affects dev.

bert · October 15, 2025, 5:40pm

Is there a way to view the LinearAlgebra code as it is in Julia 1.11? If you just go to the GitHub repo, the line numbers don’t match up with the error messages, so it’s changed relative to what OP was using.

StevenWhitaker · October 15, 2025, 8:00pm

In GitHub, you can just find the correct 1.11 release tag and browse the code that way:

Or you can launch the version of Julia you want and then use @less or @edit and it will open the correct code. (And you can look at the file path to further browse locally.)

bert · October 15, 2025, 8:34pm

Oh, is this not the right place? GitHub - JuliaLang/LinearAlgebra.jl: Julia Linear Algebra standard library

nsajko · October 15, 2025, 9:52pm

In recent versions of Julia (v1.12 and up, maybe?), LinearAlgebra.jl was separated into a standalone repo. This line in the julia repo points to the relevant Git object in the LinearAlgebra.jl repo.

github.com/JuliaLang/julia

stdlib/LinearAlgebra.version

3a50d6fb4


      
          LINEARALGEBRA_SHA1 = d5681068f1703644d7e5b5a6b7a9b9528d834bce

So append the hash string to, for example, https://github.com/JuliaLang/LinearAlgebra.jl/commit/ to get a Github URL. Like this:

Bump actions/checkout from 4 to 5 (#1434) · JuliaLang/LinearAlgebra.jl@d568106 · GitHub

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Bug in LinearAlgebra? How to debug a standard library

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