# Memory Errors at Julia-C interface and Safe Pointer Usage
**URL:** https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484
**Category:** General Usage
**Created:** [January 6, 2025, 10:18pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484 "2025-01-06T22:18:09Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 6, 2025, 10:18pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/1 "2025-01-06T22:18:09Z")
I have a snippet of code that runs just fine in C, but when I try to make the same code work in Julia, I get memory errors: either `Illegal instruction` or `Segmentation fault`. It’s a part of a larger project, creating a Julia wrapper for an Apple Accelerate sparse matrix binary. I’ve created a minimum working example, but you’ll be unable to run it unless you’re on an Apple Silicon Mac.
[mwe.jl](https://discourse.julialang.org/uploads/short-url/yLFiezCxPendqk3f3fsPHaXJP4O.jl) (5.0 KB)
Here’s the equivalent C, which runs just fine. The site won’t let me upload it with a `.c` extension, so here it is with a `.jl` extension. Compile with `clang -Wall -framework Accelerate -x c mwe-c.jl`.
[mwe-c.jl](https://discourse.julialang.org/uploads/short-url/1jpaflLUYfpkDe3u5z401A2FBk7.jl) (1.0 KB)
However, my question isn’t so much “what’s wrong here” as “how does one go about troubleshooting such things in a comprehensive manner?” I’ve tried several things (`GC.@preserve` pointed-to objects, read and re-read [the docs](https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/), compare to the C the header, inner structs are `isbits`) but to no avail. Is there some way to compare the arguments received by the library from the pure C versus from the Julia `@ccall`? Part of it is also my lack of familiarity with Julia’s garbage collector and memory model. I don’t understand the relationship between the scope of an object vs the validity of its (possibly heap-allocated) data in Julia, which makes dealing with pointers feel mildly hazardous. And because I’m interfacing with a C library, I have no choice but to deal with pointers (at least a little bit).
---
### Author:  [@stevengj](https://discourse.julialang.org/u/stevengj)
#### Post date: [January 6, 2025, 10:36pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/2 "2025-01-06T22:36:13Z")
> [@luke-kiernan](#):
>
> but when I try to make the same code work in Julia, I get memory errors: either `Illegal instruction` or `Segmentation fault`.
Usually this just means that you’re misunderstanding how to translate types from one language to another. If it happens every time you do the `ccall`, it’s not about GC safety.
I would focus on a _single_ call that is crashing. Delete all extraneous code except for this call, to get a _minimal_ reproducible example. What is the type signature in C, and how are you calling it in Julia?
PS. You don’t generally need `GC.@preserve` unless you are manually constructing your own pointers to Julia objects. If you use `ccall` to do your conversions (correctly), all the GC safety is handled for you.
---
### Author:  [@giordano](https://discourse.julialang.org/u/giordano)
#### Post date: [January 6, 2025, 11:24pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/3 "2025-01-06T23:24:26Z")
Make `LIBSPARSE` constant, as [requested in the documentation](https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/index.html).
---
### Author:  [@sgaure](https://discourse.julialang.org/u/sgaure)
#### Post date: [January 7, 2025, 10:57am UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/4 "2025-01-07T10:57:00Z")
> [@luke-kiernan](#):
>
> However, my question isn’t so much “what’s wrong here” as “how does one go about troubleshooting such things in a comprehensive manner?”
First of all, figure out which call fails. I suppose it’s one of the `@ccall`s. This can be figured out by a `println` before and after, or you may run julia under a low level debugger. I’d guess that one of the structs are bad, or should or should not be passed as pointer, or something like that. I’m not familiar with mac, so I don’t have anything to afford in terms of debuggers. There is perhaps a `gdb` there? Or something more visual. With a decent debugger you can examine the content of the arguments passed to whatever routine which fails, and compare the julia and the C-version.
---
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 7, 2025, 4:50pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/5 "2025-01-07T16:50:36Z")
> I’d guess that one of the structs are bad, or should or should not be passed as pointer, or something like that.
~~Aha! Change `mutable struct` to `struct` and it’s fine.~~ My educated guess: **all objects passed by value to C need to be `isbits`**. Otherwise, the C gets a Julia reference (basically a pointer) when it expects a value. EDIT: nope, not my only issue. Ran it a dozen times and I still got memory errors a couple times. See bottom for updated minimum working example.
> You don’t generally need `GC.@preserve` unless you are manually constructing your own pointers to Julia objects.
Good to know. I guess I went a bit overboard with the `GC.@preserve`s.
Pared-down minimum working example
[mwe.jl](https://discourse.julialang.org/uploads/short-url/akBOSK5E66MI8XXbaF1wfFUaIp8.jl) (3.7 KB)
---
### Author:  [@fatteneder](https://discourse.julialang.org/u/fatteneder)
#### Post date: [January 7, 2025, 5:48pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/6 "2025-01-07T17:48:38Z")
Your C version works with `float` data, but you use `Float64` on the Julia side, but you should be using `Float32`.
---
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 9, 2025, 3:59pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/7 "2025-01-09T15:59:24Z")
I’ve discovered and fixed one issue: my strategy of using a `Cshort` to emulate a C struct of packed bitfields was messing with field alignment. Changing that to a `Cuint` makes it _usually_ run successfully, but it still gives memory errors every now and then. Checking the offsets of the struct fields (as in the help entry for `fieldoffset`), they now all match between the C and the Julia, so that’s not the problem.
Useful things learned while debugging: `ccall(:jl_, Cvoid, (Any,), x)` is a nice way to get low-level info about `x`. Julia’s `-g` debug flag made the memory error more consistent. `lldb` is a neat tool, but not very useful in this case (no debug symbols in the compiled C library).
I’ve updated my minimum working example to incorporate the above comments and a few other things: eg to compare apples to apples, I ought to heap allocate the arrays in the C. You may need to run the Julia file a couple times in order to get the memory error (`-g` flag recommended).
[mwe.jl](https://discourse.julialang.org/uploads/short-url/A511DjNJ6RQSRybH767EZPxQw8V.jl) (3.7 KB)
[mwe.c.jl](https://discourse.julialang.org/uploads/short-url/dxHBtYKUYLzHMITHdf7MkuLIBs2.jl) (1.8 KB)
---
### Author:  [@Sukera](https://discourse.julialang.org/u/Sukera)
#### Post date: [January 9, 2025, 4:23pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/8 "2025-01-09T16:23:24Z")
> [@luke-kiernan](#):
>
> my strategy of using a `Cshort` to emulate a C struct of packed bitfields was messing with field alignment.
If I may, what C struct definition are you trying to emulate? I’ve built FieldFlags.jl for that exact purpose (with some caveats due to the semantics of julia), which I’ve been using for data from registers on embedded devices. Maybe it’s useful for you here.
If you’re talking about [`SparseKind_t`](https://developer.apple.com/documentation/accelerate/sparsekind_t), that is indeed best matched by an `Cuint`, since the underlying data seems to be `UInt32`.
> [@luke-kiernan](#):
>
> it still gives memory errors every now and then.
Have you checked that the factorizations are good? There seem to be some error indicators: [SparseOpaqueFactorization\_Double | Apple Developer Documentation](https://developer.apple.com/documentation/accelerate/sparseopaquefactorization_double#overview)
(I hope these links are correct, I’m not on a Mac)
---
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 9, 2025, 6:34pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/9 "2025-01-09T18:34:06Z")
> If I may, what C struct definition are you trying to emulate?
It’s `SparseAttributes_t`. From the header, here’s the layout:
```julia
typedef struct {
bool transpose: 1;
SparseTriangle_t triangle: 1;
SparseKind_t kind: 2;
unsigned int _reserved: 11;
bool _allocatedBySparse: 1;
} SparseAttributes_t;
```
Here `SparseKind_t` and `SparseTriangle_t` are enums, declared to be of type `unsigned int` and `unsigned char`, with values 0-3 and 0-1, respectively. i.e. `kind` does actually fit in 2 bits, and `triangle` in 1. Can your FieldFlags.jl library handle this sort of nesting? I briefly tried to figure this out myself: writing `x:1` in the body of an `@bitfield struct` is okay, but writing `x::MyEnum:1` (trying to specify the type) I get errors.
I added a call that tries to symbolically factor the matrix, with an `@assert` afterward to make sure the symbolic factorization is valid (status \>= 0). No change. I believe the memory error happens during the call to `SparseFactor`, so it doesn’t even reach the `@assert`.
---
### Author:  [@fatteneder](https://discourse.julialang.org/u/fatteneder)
#### Post date: [January 9, 2025, 7:23pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/11 "2025-01-09T19:23:36Z")
Just another guess (although you say the issue occurs already for the `SparseFactor` call):
Your C program passes `DenseVector_Double` to `SparseSolve`, whereas your Julia version passes a `DenseMatrix_Double`. They aren’t the same, or?
---
### Author:  [@fatteneder](https://discourse.julialang.org/u/fatteneder)
#### Post date: [January 9, 2025, 7:25pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/12 "2025-01-09T19:25:38Z")
Do you know if `SparseFactor` touches on the memory of one of its arguments?
The `SparseMatrix_Double` structs contain various pointers to memory managed by Julia’s GC, and if the C side re-allocs some then you will have troubles.
---
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 9, 2025, 8:47pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/13 "2025-01-09T20:47:36Z")
> Your C program passes `DenseVector_Double` to `SparseSolve` , whereas your Julia version passes a `DenseMatrix_Double` . They aren’t the same, or?
Correct, they aren’t quite the same. (`mwe.c` started out as a copy-paste of an example from the documentation.) But I can easily fix that.
[mwe.c.jl](https://discourse.julialang.org/uploads/short-url/ro6sjptoSOUQZq5miWDSxiEQqQr.jl) (1.9 KB)
> Do you know if `SparseFactor` touches on the memory of one of its arguments? The `SparseMatrix_Double` structs contain various pointers to memory managed by Julia’s GC, and if the C side re-allocs some then you will have troubles.
I’m not sure how `SparseFactor` operates on the memory. From the headers, I can see that the call eventually becomes `_SparseFactorQR_Double(type, &Matrix, &options, &nfoptions)` where the last 2 args are some default algorithm parameters, but that’s about it. If the `SparseFactor` call re-allocates some memory, wouldn’t that cause issues in the C as well? Or is it that there’s some incompatibility between Julia’s GC and C reallocations? The error thrown by the library typically mentions `SparseWriteMatrix` or `_SparseSymbolicFactorQR`, if that helps.
Aside: I purposefully made `A` in `AX = B` square, so that [`SparseSolve`](https://developer.apple.com/documentation/accelerate/2868160-sparsesolve?language=objc) can overwrite `B` with `X` safely (no buffer overflow).
Edit: to test the hypothesis that Julia’s GC is messing with things, I switched to manipulating all the buffers in `@ccall`s: ie `@ccall malloc(...)`, `unsafe_copyto!`, use, then finally `@ccall free(...)`. Same result: works 80% of the time, gives memory errors 20% of the time.
---
### Author:  [@Sukera](https://discourse.julialang.org/u/Sukera)
#### Post date: [January 9, 2025, 9:22pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/14 "2025-01-09T21:22:16Z")
> [@luke-kiernan](#):
>
> t’s `SparseAttributes_t`. From the header, here’s the layout:
>
> ```julia
> typedef struct {
> bool transpose: 1;
> SparseTriangle_t triangle: 1;
> SparseKind_t kind: 2;
> unsigned int _reserved: 11;
> bool _allocatedBySparse: 1;
> } SparseAttributes_t;
>
> ```
It’s curious that you need `Cuint` for this, since this struct is nominally 16 bits long, and not 32 🤔 There’s also lots of potential issues regarding the order of the fields in that bitfield, since IIRC that is not specified by the standard and is rather implementation defined…
> [@luke-kiernan](#):
>
> Can your [FieldFlags.jl](https://juliaregistries.github.io/General/packages/redirect_to_repo/FieldFlags) library handle this sort of nesting? I briefly tried to figure this out myself: writing `x:1` in the body of an `@bitfield struct` is okay, but writing `x::MyEnum:1` (trying to specify the type) I get errors.
Ah, it’s nested… That complicates things a bit, since I’ve put off implementing that sort of assertion since I haven’t needed it yet 😅 The issue to track for that is [Custom field type annotations · Issue #9 · Seelengrab/FieldFlags.jl · GitHub](https://github.com/Seelengrab/FieldFlags.jl/issues/9), which itself isn’t difficult to implement apart from the mutability caveat (I might be able to do this on the weekend, if I find a few hours 😉 ). Other than that though, the bitsizes should work out just fine, this is what it’s made for after all.
---
### Author:  [@luke-kiernan](https://discourse.julialang.org/u/luke-kiernan)
#### Post date: [January 10, 2025, 11:27pm UTC](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/15 "2025-01-10T23:27:09Z")
Problem resolved! The library was behaving as intended (after [this fix](https://discourse.julialang.org/t/memory-errors-at-julia-c-interface-and-safe-pointer-usage/124484/7)): rather, my error catching was the problem. [Apparently](https://forums.developer.apple.com/forums/thread/758435?answerId=793665022#793665022) Apple’s implementation of the sparse QR factorization throws an error if the matrix is singular. (Why don’t they mention that in the documentation…) In the Julia, I use `sprand` to create a random 3x3 sparse matrix: **the error occurs precisely when that matrix is singular**. The [default error handling](https://developer.apple.com/documentation/accelerate/sparsesymbolicfactoroptions/2868183-reporterror?language=objc) depends on Objective C functionality (`nil`, `os_error_log`), so Julia reports illegal instruction/bad access/etc instead of the intended “Your matrix is singular” message.
In hindsight, I should’ve put _the exact numerical example_ that caused the error into the C, instead of hard-coding a fixed arbitrary matrix structure.