Wheel built with `pyodide-build` works on the browser but fails in Python from `pyodide venv`

[IvanIsCoding]

Related to pyodide/pyodide-recipes#90 and Qiskit/rustworkx#1447

I built a Pyodide wheel for rustworkx with:

• rustc nightly-2025-02-01
• pyoide-build==0.30.2
• emsdk 4.0.8
• Custom RUST_FLAGS specified in Add rustworkx alpha recipe pyodide-recipes#90

A copy of the built wheel is available at https://github.com/IvanIsCoding/rustworkx/releases/download/v0.17.0a3/rustworkx-0.17.0a3-cp39-abi3-pyodide_2025_0_wasm32.whl.

If I execute it in the browser, the wheels work fine. I tested with Pyodide 0.27.5 from the CDN both with Chrome 136 and Firefox 138.

However, if I execute it in the environment provided by pyodide venv, I get the following error:

(.venv-pyodide) ➜  tests git:(more-uv-features) python
which: no grealpath in (/home/ivan/Projects/.venv-pyodide/bin:/home/ivan/.local/bin:/usr/share/Modules/bin:/home/ivan/.cargo/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/var/lib/snapd/snap/bin:/home/ivan/.dotnet/tools:/home/ivan/.dotnet/tools)
Python 3.13.2 (main, Apr  3 2025, 07:34:46) [Clang 21.0.0git (https:/github.com/llvm/llvm-project 4775e6d9099467df9363e1a3cd on emscripten
Type "help", "copyright", "credits" or "license" for more information.
warning: can't use pyrepl: No module named 'msvcrt'
>>> import rustworkx
Pyodide has suffered a fatal error. Please report this to the Pyodide maintainers.
The cause of the fatal error was:
Error: Dynamic linking error: cannot resolve symbol invoke_ii
    at stubs.<computed> (/home/ivan/.cache/.pyodide-xbuildenv-0.30.2/0.28.0a1/xbuildenv/pyodide-root/dist/pyodide.asm.js:9:19341)
    at wasm://wasm/0122615e:wasm-function[3874]:0x3ca8c6
    at wasm://wasm/020b656e:wasm-function[4078]:0x2a30bc
    at wasm://wasm/020b656e:wasm-function[4054]:0x2a0f12
    at wasm://wasm/020b656e:wasm-function[4070]:0x2a28c5
    at wasm://wasm/020b656e:wasm-function[2181]:0x1ad753
    at wasm://wasm/020b656e:wasm-function[1119]:0x16345c
    at wasm://wasm/020b656e:wasm-function[1121]:0x163668
    at wasm://wasm/020b656e:wasm-function[1122]:0x1636e6
    at wasm://wasm/020b656e:wasm-function[3519]:0x25a95b {
  pyodide_fatal_error: true
}
Stack (most recent call first):
  File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1320 in create_module
  File "<frozen importlib._bootstrap>", line 813 in module_from_spec
  File "<frozen importlib._bootstrap>", line 921 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
  File "/home/ivan/Projects/.venv-pyodide/lib/python3.13/site-packages/rustworkx/__init__.py", line 14 in <module>
  File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1026 in exec_module
  File "<frozen importlib._bootstrap>", line 935 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
  File "<stdin>-0", line 1 in <module>
  File "/lib/python313.zip/_pyrepl/main.py", line 30 in interactive_console
  File "/lib/python313.zip/_pyrepl/__main__.py", line 6 in <module>
  File "<frozen runpy>", line 88 in _run_code
  File "<frozen runpy>", line 198 in _run_module_as_main
Error: Dynamic linking error: cannot resolve symbol invoke_ii
    at stubs.<computed> (/home/ivan/.cache/.pyodide-xbuildenv-0.30.2/0.28.0a1/xbuildenv/pyodide-root/dist/pyodide.asm.js:9:19341)
    at wasm://wasm/0122615e:wasm-function[3874]:0x3ca8c6
    at wasm://wasm/020b656e:wasm-function[4078]:0x2a30bc
    at wasm://wasm/020b656e:wasm-function[4054]:0x2a0f12
    at wasm://wasm/020b656e:wasm-function[4070]:0x2a28c5
    at wasm://wasm/020b656e:wasm-function[2181]:0x1ad753
    at wasm://wasm/020b656e:wasm-function[1119]:0x16345c
    at wasm://wasm/020b656e:wasm-function[1121]:0x163668
    at wasm://wasm/020b656e:wasm-function[1122]:0x1636e6
    at wasm://wasm/020b656e:wasm-function[3519]:0x25a95b {
  pyodide_fatal_error: true
}

Is this expected or am I passing the wrong flags to Rust? I was wondering if there was an easy way to make things work. I am very new to Emscrioten and Pyodide.

[agriyakhetarpal]

Hi @IvanIsCoding, thanks for the bug report! What I see here is that rustworkx was built with the Pyodide "dev" version (Emscripten 4.0.8), but pyodide venv is running with Pyodide 0.27.5 (stable version, Emscripten 3.1.58). Pyodide versions are not ABI-compatible, and Emscripten versions aren't either. Also, we have been using a custom Rust sysroot that's tied to the Emscripten version, so it's not easy/possible to mix and match Pyodide versions when building Rust packages: github.com/pyodide/rust-emscripten-wasm-eh-sysroot/

Could you please build with a stable version of Pyodide (0.27.5) and see if that works for you? I think this arose because the pyodide-recipes repository is slightly ahead of the Pyodide repository, as we will be migrating to the former for all the recipes.

Alternatively, you may try the nightly build environments (experimental; we're planning to use them more soon enough). As I write this, I see that the one built on 10th May seems to be broken, and I've opened an issue about it: pyodide/pyodide-build-environment-nightly#17.

However, the 20250503 release (3rd May) the 20250510 release on 10th May can be tried out (it should work with Python 3.13).

Once you build a wheel with the nightly build environment via https://github.com/pyodide/pyodide-build-environment-nightly#usage, i.e.,

pyodide xbuildenv install --url "https://github.com/pyodide/pyodide-build-environment-nightly/releases/download/20250510/xbuildenv.tar.bz2"
pyodide build

will build a wheel against Emscripten 4.0.8, and then if you create a virtual environment using pyodide venv .venv-pyodide, it will match what you built it with.

Also, from your comment on your PR in Qiskit/rustworkx#1447 (comment), I would say yes, it would be great to test things out as a part of your CI, it helps us a lot! :) You may perform an out-of-tree build in CI (which is what the command above is doing), so that you won't need to clone the pyodide-recipes repository for this: https://pyodide.org/en/0.24.0/development/building-and-testing-packages.html#building-binary-packages-for-pyodide

[IvanIsCoding]

Thanks for the heads up. I tried building it with emsdk 4.0.8 instead of 4.0.6, I ran the xbuildenv command you suggested. My output suggests it got picked:

Successfully built /home/ivan/Projects/rustworkx-dev/dist/rustworkx-0.17.0a3-cp39-abi3-emscripten_4_0_8_wasm32.whl
Unpacking to: /tmp/tmpyl_1cov6/rustworkx-0.17.0a3...OK
Repacking wheel as /home/ivan/Projects/rustworkx-dev/dist/rustworkx-0.17.0a3-cp39-abi3-pyodide_2025_0_wasm32.whl...OK

I still got Error: Dynamic linking error: cannot resolve symbol invoke_ii, so the error message is still the same.

I will try the alternative route of downgrading the Python from my environment to Python 3.12.

[hoodmane]

That seems to be because you built with -fexceptions and not -fwasm-exceptions somehow.

[IvanIsCoding]

That seems to be because you built with -fexceptions and not -fwasm-exceptions somehow.

I need to study where to pass that flag (I have no clue how emcc works), but given https://emscripten.org/docs/porting/exceptions.html#webassembly-exception-handling-based-support and rayon-rs/rayon#1155 your answer makes a lot of sense.

[IvanIsCoding]

So, it has to do with exceptions. Originally, I was excluding -Z emscripten-wasm-eh in my Rust flags. But now I have a weird problem.

If I build with:

RUSTFLAGS="-C target-feature=+atomics,+bulk-memory,+mutable-globals -C link-arg=-sSIDE_MODULE=2 -C link-arg=-sWASM_BIGINT -Z emscripten-wasm-eh" pyodide build

My code works in the Pyodide env:

(.venv-pyodide) ➜  dist git:(pyodide-alpha-release) python
which: no grealpath in (/home/ivan/Projects/.venv-pyodide/bin:/home/ivan/.local/bin:/usr/share/Modules/bin:/home/ivan/.cargo/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/var/lib/snapd/snap/bin:/home/ivan/.dotnet/tools:/home/ivan/.dotnet/tools)
Python 3.13.2 (main, Apr  3 2025, 07:34:46) [Clang 21.0.0git (https:/github.com/llvm/llvm-project 4775e6d9099467df9363e1a3cd on emscripten
Type "help", "copyright", "credits" or "license" for more information.
warning: can't use pyrepl: No module named 'msvcrt'
>>> import rustworkx
>>> rx = rustworkx
>>> graph = rx.generators.cycle_graph(10)

Hower, now the code in the browser starts failing with this error message:

pyodide.asm.js:10 Loading rustworkx
pyodide.asm.js:10 Failed to load rustworkx
pyodide.asm.js:10 The following error occurred while loading rustworkx:
logStderr @ pyodide.asm.js:10
loadPackage @ pyodide.asm.js:10
await in loadPackage
main @ (index):12
await in main
(anonymous) @ (index):47
pyodide.asm.js:10 WebAssembly.instantiate(): Import #182 "env" "__cpp_exception": tag import requires a WebAssembly.Tag
logStderr @ pyodide.asm.js:10
loadPackage @ pyodide.asm.js:10
await in loadPackage
main @ (index):12
await in main
(anonymous) @ (index):47
pyodide.asm.js:10 Uncaught (in promise) PythonError: Traceback (most recent call last):
  File "/lib/python312.zip/_pyodide/_base.py", line 597, in eval_code_async
    await CodeRunner(
  File "/lib/python312.zip/_pyodide/_base.py", line 411, in run_async
    coroutine = eval(self.code, globals, locals)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<exec>", line 26, in <module>
  File "<exec>", line 13, in test_isomorphism
  File "/lib/python3.12/site-packages/rustworkx/__init__.py", line 14, in <module>
    from .rustworkx import *
ImportError: dynamic module does not define module export function (PyInit_rustworkx)

Ideally I'd like to find a solution that works in both environments.

[IvanIsCoding]

Alright, the error in the browser is indeed from Pyodide versions as @agriyakhetarpal mentioned. I switched to using the dev version instead of 0.27.5 in the browswer and now both environments pass.

Thanks @hoodmane for the suggestion of exception handling. If it wasn't for that I'd never have found https://doc.rust-lang.org/nightly/unstable-book/compiler-flags/emscripten-wasm-eh.html.