# Strange bug in compiled binaries about SuiteSparse

**URL:** <https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027>\
**Category:** General Usage\
**Created:** [December 25, 2023, 7:04am UTC](https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027 "2023-12-25T07:04:44Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![jsjie](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jsjie/32/22477_2.png) [@jsjie](https://discourse.julialang.org/u/jsjie)\
**Post date:** [December 25, 2023, 7:04am UTC](https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027/1 "2023-12-25T07:04:44Z")

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I’m still trying to find a MWE. But let me describe some facts that I’ve figured out.  
Our code, compiled on Dec 14th, works well. However, when compiled on Dec 23rd, the binary will output the following when running:

```julia
┌ Error: Error during initialization of module CHOLMOD
│ exception =
│ could not load library "libcholmod"
│ libcholmod.so: cannot open shared object file: No such file or directory
│ Stacktrace:
│ [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
│ @ Base.Libc.Libdl ./libdl.jl:117
│ [2] dlopen (repeats 2 times)
│ @ ./libdl.jl:117 [inlined]
│ [3] __init__ ()
│ @ SuiteSparse.CHOLMOD ~/opt/hylanemos_1.3.0.0.17/share/julia/stdlib/v1.7/SuiteSparse/src/cholmod.jl:161
└ @ SuiteSparse.CHOLMOD /root/julia-1.7.1/share/julia/stdlib/v1.7/SuiteSparse/src/cholmod.jl:245

```

Yes, we compiled it with Julia 1.7.1, not current stable version 1.9.4 There are a few reasons:

1. The most recent LTS of Julia is in fact 1.6.7, and we want to stick to LTS, because it sounds to be more stable. However, `MKL.jl` requires at least 1.7, so we use 1.7.1. We don’t want to change it unless a new LTS is released or some other dependencies require so.
2. We heard that the memory usage of 1.9 is a bit larger than before.

Back to the main point. Comparing the two binaries we’ve gotten, we found the main difference occurs when `PackageCompiler.jl` boudles stdlibs. The outputs are the following, respectively:

```julia
├── Stdlibs:
  │ ├── LibCURL_jll
  │ │ ├── libcurl.so.4.7.0 - 638.750 KiB
  │ ├── LibGit2_jll
  │ │ ├── libgit2.so.1.1.0 - 1.467 MiB
  │ ├── LibSSH2_jll
  │ │ ├── libssh2.so.1.0.1 - 278.742 KiB
  │ ├── MbedTLS_jll
  │ │ ├── libmbedcrypto.so.2.24.0 - 586.603 KiB
  │ │ ├── libmbedtls.so.2.24.0 - 308.078 KiB
  │ │ ├── libmbedx509.so.2.24.0 - 179.938 KiB
  │ ├── OpenBLAS_jll
  │ │ ├── libopenblas64_.0.3.13.so - 30.227 MiB
  │ ├── SuiteSparse_jll
  │ │ ├── libamd.so.2.4.6 - 38.144 KiB
  │ │ ├── libbtf.so.1.2.6 - 12.801 KiB
  │ │ ├── libcamd.so.2.4.6 - 42.451 KiB
  │ │ ├── libccolamd.so.2.9.6 - 46.535 KiB
  │ │ ├── libcholmod.so.3.0.14 - 982.336 KiB
  │ │ ├── libcolamd.so.2.9.6 - 30.518 KiB
  │ │ ├── libklu.so.1.3.8 - 208.845 KiB
  │ │ ├── libldl.so.2.2.6 - 12.979 KiB
  │ │ ├── librbio.so.2.2.6 - 64.918 KiB
  │ │ ├── libspqr.so.2.0.9 - 202.683 KiB
  │ │ ├── libsuitesparseconfig.so.5.10.1 - 10.641 KiB
  │ │ ├── libumfpack.so.5.7.9 - 744.107 KiB
  │ ├── libblastrampoline_jll
  │ │ ├── libblastrampoline.so - 2.849 MiB
  │ ├── nghttp2_jll
  │ │ ├── libnghttp2.so.14.20.0 - 661.260 KiB

```

and

```julia
  ├── Stdlibs:
  │ ├── libblastrampoline_jll
  │ │ ├── libblastrampoline.so - 2.849 MiB
  │ ├── OpenBLAS_jll
  │ │ ├── libopenblas64_.0.3.13.so - 30.227 MiB
  │ ├── LibSSH2_jll
  │ │ ├── libssh2.so.1.0.1 - 278.742 KiB
  │ ├── LibCURL_jll
  │ │ ├── libcurl.so.4.7.0 - 638.750 KiB
  │ ├── MbedTLS_jll
  │ │ ├── libmbedcrypto.so.2.24.0 - 586.603 KiB
  │ │ ├── libmbedtls.so.2.24.0 - 308.078 KiB
  │ │ ├── libmbedx509.so.2.24.0 - 179.938 KiB
  │ ├── nghttp2_jll
  │ │ ├── libnghttp2.so.14.20.0 - 661.260 KiB

```

A week later, `SuiteSparse_jll` vanishes from the list, which results in the lack of `libcholmod`.  
The problem is:

1. we don’t use `SuiteSparse` in our code. There are no related things in our `Manifest.toml`. Why the compiled binary will ever need it and throw exceptions?
2. Even if there is some magic resulting in `SuiteSparse` being used under the hood. What happens during the week, resulting in the difference?

For the second problem, we examined the output of `PackageCompiler`, and find that three packages have changed their version:

1. ChainRulesCore 1.18.0 → 1.19.0
2. Parsers 2.8.0 → 2.8.1
3. StatisticArrays 1.7.0 → 1.8.1

But, after examining the change log of these three packages, we still cannot find the reason why `SuiteSparse_jll` is lost. Any ideas?

PS: We currently use the work around to directly declare `SuiteSparse_jll` as one of our dependencies.  
PS2: `SparseArrays` will use `SuiteSparse_jll` in Julia 1.9, so it might not be a problem. But we have not tested it yet.

---

<div class="post-metadata">

**Author:** ![HanD](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/hand/32/213908_2.png) [@HanD](https://discourse.julialang.org/u/HanD)\
**Post date:** [January 19, 2024, 3:59pm UTC](https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027/2 "2024-01-19T15:59:01Z")

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Hah, I just ran into the same issue with Julia 1.8.5, `libcholmod.so` is not bundled with the binary output of `PackageCompiler.jl`. Perhaps it’s not a Julia thing, maybe it’s a PackageCompiler thing…

Maybe its related to this issue? [Dropping more libraries · Issue #865 · JuliaLang/PackageCompiler.jl · GitHub](https://github.com/JuliaLang/PackageCompiler.jl/issues/865)

Or this change? [only bundle libraries that are needed (#823) · JuliaLang/PackageCompiler.jl@b4045fa · GitHub](https://github.com/JuliaLang/PackageCompiler.jl/commit/b4045fa8b986ac6d2dfb89281f5098d9cabf78b0)

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<div class="post-metadata">

**Author:** ![HanD](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/hand/32/213908_2.png) [@HanD](https://discourse.julialang.org/u/HanD)\
**Post date:** [January 19, 2024, 4:20pm UTC](https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027/3 "2024-01-19T16:20:08Z")

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After some further inspection, I start to think it _is_ a change between Julia 1.7 and Julia 1.8 afterall. The .so files are part of the `SuiteSparse_jll` library dependencies. In Julia 1.7, this library, in turn, is a direct dependency of `SuiteSparse`, it appears in `julia/stdlib/v1.7/SuiteSparse/gen/Project.toml`. From there, it is picked up by `PackageCompiler`, I guess, in [`gather_stdlibs_project`](https://github.com/JuliaLang/PackageCompiler.jl/blob/d5a8618d3bfa7d78e61e206a78e9319eb258bab0/src/PackageCompiler.jl#L104) (?).

From Julia 1.8 up, however, something strange is going on, because `SuiteSparse_jll` disappeared from the `Project.toml` and `Manifest.toml` files. Since it’s no longer there, PackageCompiler doesn’t pick it up, and doesn’t bundle it with the binary.

_Update:_ In Julia 1.9, it changed again.

---

<div class="post-metadata">

**Author:** ![HanD](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/hand/32/213908_2.png) [@HanD](https://discourse.julialang.org/u/HanD)\
**Post date:** [January 19, 2024, 4:27pm UTC](https://discourse.julialang.org/t/strange-bug-in-compiled-binaries-about-suitesparse/108027/4 "2024-01-19T16:27:19Z")

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@kristoffer.carlsson , care to comment?