# C struct garbage collection not run frequently enough

**URL:** <https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919>\
**Category:** General Usage\
**Tags:** garbage-collection, mutable-structure, c, gc\
**Created:** [July 11, 2024, 3:38pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919 "2024-07-11T15:38:28Z")\
**Posts on this page:** 9\
**Page:** 2

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**Author:** ![mattsignorelli](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mattsignorelli/32/221502_2.png) [@mattsignorelli](https://discourse.julialang.org/u/mattsignorelli)\
**Post date:** [July 12, 2024, 3:18pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/21 "2024-07-12T15:18:47Z")

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Also I tried just including and linking with `libjulia`, but it doesn’t have a symbol for `jl_free`?

```julia
nm $HOME/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/lib/libjulia.dylib | grep 'jl_malloc\|jl_calloc\|jl_realloc\|jl_free'
00000000000029b8 T _jl_calloc
000000000000c718 s _jl_calloc_addr
0000000000003480 T _jl_malloc
000000000000ce48 s _jl_malloc_addr
000000000000348c T _jl_malloc_stack
000000000000ce50 s _jl_malloc_stack_addr
0000000000003888 T _jl_realloc
000000000000d0f8 s _jl_realloc_addr

```

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**Author:** ![Sukera](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@Sukera](https://discourse.julialang.org/u/Sukera)\
**Post date:** [July 12, 2024, 3:25pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/22 "2024-07-12T15:25:57Z")

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> [@mattsignorelli](#):
>
> If I understand correctly, with this pointer I then `unsafe_load` into my `RTPSA` struct.

“into” is not really correct - `unsafe_load(p, i)` just “dereferences” the pointer. It’s the same as if you’d do `p[i-1]` in C, which is the same as doing `*(p + sizeof(<type-p-points-to>)*(i-1))` . For `i == 1`, this is the same as `*p`. You get the object at that exact memory location, just in regular julia semantics.

> [@mattsignorelli](#):
>
> Now when the finalizer is eventually called, I pass it `pointer_from_objref` for that `RTPSA`. This pointer is _different_ from the pointer originally returned by the C code during construction.

Different in what sense? They should be egal, i.e. have the same address. The one thing that might be different is provenance, but since this is FFI, that’s gone anyway.

> [@mattsignorelli](#):
>
> I cannot compile the C to a shared library with these undefined symbols `jl_free` and `jl_malloc`. So I’m not exactly sure what you mean by it will “just work”?

> [@mattsignorelli](#):
>
> Also I tried just including and linking with `libjulia`, but it doesn’t have a symbol for `jl_free`?

It’s in `libjulia-internal`, since it’s part of the runtime and not codegen. I don’t think it’s in the h-file, but you should be able to define it on your end with `extern`. At that point, the dynamic linker should find everything when you load the .so in julia, no need for manual linking.

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<div class="post-metadata">

**Author:** ![mattsignorelli](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mattsignorelli/32/221502_2.png) [@mattsignorelli](https://discourse.julialang.org/u/mattsignorelli)\
**Post date:** [July 12, 2024, 4:25pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/23 "2024-07-12T16:25:32Z")

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> [@Sukera](#):
>
> “into” is not really correct - `unsafe_load(p, i)` just “dereferences” the pointer. It’s the same as if you’d do `p[i-1]` in C, which is the same as doing `*(p + sizeof(<type-p-points-to>)*(i-1))` . For `i == 1`, this is the same as `*p`. You get the object at that exact memory location, just in regular julia semantics.

> [@Sukera](#):
>
> Different in what sense? They should be egal, i.e. have the same address. The one thing that might be different is provenance, but since this is FFI, that’s gone anyway.

The C code constructor spits out a pointer to the struct that the C allocated (not Julia). So given some `Ptr{RTPSA}`, how exactly do I construct a new Julia `RTPSA` object?

e.g. I modified the code to make `RTPSA` mutable. I can’t just return `unsafe_load` because now that allocates a new object:

```julia
julia> tpsa = GTPSA.mad_tpsa_newd(d.desc, GTPSA.MAD_TPSA_SAME) # this is C ctor
Ptr{GTPSA.RTPSA} @0x00006000004f4b08

julia> pointer_from_objref(unsafe_load(tpsa)) 
Ptr{Nothing} @0x000000010bdc67d0

julia> @allocations unsafe_load(tpsa)
1

julia> unsafe_pointer_to_objref(tpsa)

[70941] signal (11.2): Segmentation fault: 11

```

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<div class="post-metadata">

**Author:** ![Sukera](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@Sukera](https://discourse.julialang.org/u/Sukera)\
**Post date:** [July 12, 2024, 4:29pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/24 "2024-07-12T16:29:52Z")

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> [@mattsignorelli](#):
>
> The C code constructor spits out a pointer to the struct that the C allocated (not Julia)

It doesn’t matter to `unsafe_load` who allocated the memory behind the pointer. It simply loads the value behind the pointer, i.e. it dereferences the pointer.

> [@mattsignorelli](#):
>
> So given some `Ptr{RTPSA}`, how exactly do I construct a new Julia `RTPSA` object?

You don’t construct anything; `unsafe_load` gives you the object at the address of that pointer. The object already exists right there. Does the object not exist at that address?

> [@mattsignorelli](#):
>
> e.g. I modified the code to make `RTPSA` mutable. I can’t just return `unsafe_load` because now that allocates a new object:

> [@mattsignorelli](#):
>
> ```julia-auto
> julia> @allocations unsafe_load(tpsa)
> 1
> 
> ```

I am pretty sure that this is an artifact of accessing the non-const global `tpsa`. The allocation should be from the resulting dynamic dispatch.

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<div class="post-metadata">

**Author:** ![Sukera](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@Sukera](https://discourse.julialang.org/u/Sukera)\
**Post date:** [July 12, 2024, 4:35pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/25 "2024-07-12T16:35:11Z")

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> [@mattsignorelli](#):
>
> ```julia-auto
> julia> tpsa = GTPSA.mad_tpsa_newd(d.desc, GTPSA.MAD_TPSA_SAME) # this is C ctor
> Ptr{GTPSA.RTPSA} @0x00006000004f4b08
> 
> julia> pointer_from_objref(unsafe_load(tpsa)) 
> Ptr{Nothing} @0x000000010bdc67d0
> 
> ```

Do you have this version of your package available at some branch? I can’t access the documentation of the GTPSA C library, seems like the link at CERN is dead?

[https://mad.web.cern.ch/mad/releases/madng/html/mad\_mod\_diffalg.html](https://mad.web.cern.ch/mad/releases/madng/html/mad_mod_diffalg.html)

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<div class="post-metadata">

**Author:** ![mattsignorelli](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mattsignorelli/32/221502_2.png) [@mattsignorelli](https://discourse.julialang.org/u/mattsignorelli)\
**Post date:** [July 12, 2024, 4:45pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/26 "2024-07-12T16:45:24Z")

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> [@Sukera](#):
>
> I am pretty sure that this is an artifact of accessing the non-const global `tpsa`. The allocation should be from the resulting dynamic dispatch.

```julia
julia> using BenchmarkTools

julia> @ballocated unsafe_load($tpsa)
48

```

I guess I could have an alias for `Ptr{RTPSA}` and then dispatch on those (does the GC know that `RTPSA` is still in use if there are instances of `Ptr{RTPSA}`?)

> [@Sukera](#):
>
> Do you have this version of your package available at some branch? I can’t access the documentation of the GTPSA C library, seems like the link at CERN is dead?

I’ve created a branch and PR with mutable structs here where we can continue the discussion since it’s getting a bit off topic from the original point now: [mutable rtpsa by mattsignorelli · Pull Request #121 · bmad-sim/GTPSA.jl · GitHub](https://github.com/bmad-sim/GTPSA.jl/pull/121)

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<div class="post-metadata">

**Author:** ![Sukera](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@Sukera](https://discourse.julialang.org/u/Sukera)\
**Post date:** [July 12, 2024, 7:03pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/27 "2024-07-12T19:03:18Z")

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For those keeping track: `unsafe_load` indeed ends up creating a copy of that mutable struct, which is very unfortunate 😕 The approach I outlined above doesn’t work.

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<div class="post-metadata">

**Author:** ![mattsignorelli](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mattsignorelli/32/221502_2.png) [@mattsignorelli](https://discourse.julialang.org/u/mattsignorelli)\
**Post date:** [July 12, 2024, 10:14pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/28 "2024-07-12T22:14:58Z")

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I’ve got the `jl_malloc` et al in the C code, but I’ve found that `memset` of that memory in C to 0 causes a segfault in Julia, any ideas?

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<div class="post-metadata">

**Author:** ![mattsignorelli](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mattsignorelli/32/221502_2.png) [@mattsignorelli](https://discourse.julialang.org/u/mattsignorelli)\
**Post date:** [July 14, 2024, 11:42pm UTC](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919/29 "2024-07-14T23:42:04Z")

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For anyone following, the solution I went with was to instead define the constructor for these special C structs straight in Julia, instead of using those in C, and allocate in Julia via `@ccall jl_malloc`. This now doesn’t have Julia’s memory usage blow up.

[Previous page](https://discourse.julialang.org/t/c-struct-garbage-collection-not-run-frequently-enough/116919.md?page=1)