Ok, I could cobble together a surprisingly simple reproducer here:

https://github.com/floooh/emsc-calloc-emmalloc-repro

-flto is indeed needed. So the 4 ingredients are:

1. malloc+memset being 'optimized' to a call to calloc via -O1 or better
2. ...where malloc is called through a function pointer
3. ...and emmalloc is used instead of the vanilla allocator
4. ...and -flto must be enabled

...if any of this is missing, it works :D

Should I write an Emscripten ticket too?
On Tuesday, 6 September 2022 at 18:43:52 UTC+2 Floh wrote:

> Part of the mystery can be solved because clang replaces malloc+memset 
> pairs with a single calloc call (only when optimization is enabled):
>
> https://www.godbolt.org/z/8r3Ydjs6a
>
> ...which explains why the problem shows up in release mode, but not debug 
> mode.
>
> There still must be something else going on though, because I'm using the 
> malloc+memset combo all the time together with emmalloc (and I guess the 
> missing piece is that the malloc call is going through the function 
> pointer).
>
> I'll tinker around a bit more with compiler options (but since this is a 
> library, I cannot dictate what compiler options the code is built with).
>
> Cheers!
>
> On Monday, 5 September 2022 at 19:31:17 UTC+2 [email protected] wrote:
>
>> The other thing this could be related to is LTO.  IIUC LTO itself can 
>> generate calls to buildin functions (such as malloc and calloc) that are 
>> not present in the original program.   Does disabling LTO fix the problem?
>>
>> On Mon, Sep 5, 2022 at 10:28 AM Sam Clegg <[email protected]> wrote:
>>
>>> Can you trying building with `-Wl,--trace-symbol=calloc` rather than 
>>> `LLD_REPORT_UNDEFINED=1` (I guess there are still some issues with that 
>>> setting).
>>>
>>> Does the link time error tell you why calloc is being pulled in?  (The 
>>> JS compiler linker errors should do this but they often just say "top level 
>>> C/C++").
>>>
>>> On Sat, Sep 3, 2022 at 6:03 AM Floh <[email protected]> wrote:
>>>
>>>> I just stumbled over a very weird problem in a new sample for my sokol 
>>>> headers which includes a non-trivial 3rd party C library - the spine-c 
>>>> runtime (
>>>> https://github.com/EsotericSoftware/spine-runtimes/tree/4.1/spine-c/spine-c
>>>> )
>>>>
>>>> When building in release mode (but not in debug mode) the linker 
>>>> complains about an unresolved 'calloc' call. Adding detailed output 
>>>> via LLD_REPORT_UNDEFINED=1 I get tons of:
>>>>
>>>> wasm-ld: error: 
>>>> /Users/floh/projects/fips-sdks/emsdk/upstream/emscripten/cache/sysroot/lib/wasm32-emscripten/lto/libemmalloc.a(emmalloc.o):
>>>>  
>>>> undefined symbol: calloc
>>>>
>>>> ... how does that even make sense when emmalloc is supposed to provide 
>>>> an implementation of calloc... anyway...
>>>>
>>>> The error goes away when compiling in debug mode (some differences that 
>>>> come to mind to the release mode is that debug mode doesn't use -flto, and 
>>>> also doesn't run the closure compiler).
>>>>
>>>> The problem also goes away when not building with emmalloc.
>>>>
>>>> Now the weird thing is that the entire code this sample is built from 
>>>> doesn't appear to call calloc anywhere... and that other samples which 
>>>> actually use calloc build just fines.
>>>>
>>>> Has anybody seen a similar problem yet, before I jump myself into the 
>>>> rabbit hole? :)
>>>>
>>>> The problematic command line is:
>>>>
>>>> em++ -s DISABLE_EXCEPTION_CATCHING=1  -fno-exceptions -fno-rtti 
>>>> -fstrict-aliasing -Wall -Wno-multichar -Wextra -Wno-unknown-pragmas 
>>>> -Wno-ignored-qualifiers -Wno-long-long -Wno-overloaded-virtual 
>>>> -Wno-deprecated-writable-strings -Wno-unused-volatile-lvalue 
>>>> -Wno-inconsistent-missing-override -Wno-warn-absolute-paths 
>>>> -Wno-expansion-to-defined  -flto -O3 -DNDEBUG -s 
>>>> DISABLE_EXCEPTION_CATCHING=1  --memory-init-file 0 -s 
>>>> INITIAL_MEMORY=33554432 -s ERROR_ON_UNDEFINED_SYMBOLS=1 -s 
>>>> NO_EXIT_RUNTIME=1 -s LLD_REPORT_UNDEFINED=1 -s ALLOW_MEMORY_GROWTH=1 -s 
>>>> USE_WEBGL2=1 -s "MALLOC='emmalloc'" -s NO_FILESYSTEM=1 -s WASM=1 
>>>>  --shell-file /Users/floh/projects/sokol-samples/webpage/shell.html -O3 
>>>>  -flto  --closure 1 -s ASSERTIONS=0 
>>>> sapp/CMakeFiles/spine-sapp.dir/spine-sapp.c.obj 
>>>> sapp/CMakeFiles/spine-sapp.dir/spine-assets.c.obj -o 
>>>> /Users/floh/projects/fips-deploy/sokol-samples/sapp-webgl2-wasm-vscode-release/spine-sapp.html
>>>>  
>>>>  libs/sokol/libsokol.a  libs/spine-c/libspine-c.a  libs/stb/libstb.a 
>>>>  libs/util/libfileutil.a  fips-cimgui_cimgui/libcimgui.a
>>>>
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>>>>  
>>>> <https://groups.google.com/d/msgid/emscripten-discuss/c47cee25-6e4b-4fbe-9f6f-0d7da7e02562n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>

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