New fatal errors in scipy tests on main branch #4249
Description
🐛 Bug
There are new tests with fatal errors in the scipy tests from https://github.com/lesteve/scipy-tests-pyodide.
Last working commit (2 days ago): 408bffb
First broken commit (yesterday): 429dcd4
❯ git l 408bffb7..429dcd4b
* 429dcd4b - Use externrefs for some ffi code (2) (#4226) (2 days ago) <Hood Chatham>
* 2d55a3e7 - xfail syncify_not_supported in node (2 days ago) <Hood Chatham>
* 7a7691c2 - Make jspi work correctly with nodylink builds (2 days ago) <Hood Chatham>
* 4bafdafc - Update JSPI patch for Emscripten 3.1.45 (2 days ago) <Hood Chatham>
* 6117d7c9 - Stack switching (#3210) (2 days ago) <Hood Chatham>
* d97eaa58 - Use branch in macro to choose trampoline (#3990) (2 days ago) <Hood Chatham>
* 31c1345a - Move stack switching logic into a new stack switching folder. (#3987) (2 days ago) <Hood Chatham>
* c931b06a - Patch CPython to use a type reflection trampoline if possible (#3964) (2 days ago) <Hood Chatham>
* 3085cb9d - Use Wasm Exceptions for invoke stubs if they exist (#3957) (2 days ago) <Hood Chatham>
Full log is here. Error seem similar to the ones in #4140 when the JSPI changes were reverted.
Here are the submodules with issue (below are the stacktraces from the log):
--------------------------------------------------------------------------------
Unexpected test results
--------------------------------------------------------------------------------
scipy.fft.tests result expected in ['passed'], got 'fatal error or timeout' instead
scipy.optimize.tests result expected in ['failed'], got 'fatal error or timeout' instead
scipy.sparse.linalg._dsolve.tests result expected in ['passed'], got 'fatal error or timeout' instead
scipy.special.tests result expected in ['failed'], got 'fatal error or timeout' instead
scipy.stats.tests result expected in ['failed'], got 'fatal error or timeout' instead
scipy.fft.tests
The cause of the fatal error was:
RuntimeError: Aborted(). Build with -sASSERTIONS for more info.
at abort (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:651:15)
at _abort (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:16651:7)
at pyodide.asm.wasm.fatal_error_exit (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[3803]:0x2bc266)
at pyodide.asm.wasm.fatal_error (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[3788]:0x2b143a)
at pyodide.asm.wasm._Py_FatalErrorFunc (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[3801]:0x2bc004)
at pyodide.asm.wasm._Py_FatalError_TstateNULL (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[3201]:0x260659)
at pyodide.asm.wasm.PyThreadState_Get (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[3848]:0x2c0bf0)
at pyodide.asm.wasm.tupledealloc (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[2383]:0x1f4781)
at pyodide.asm.wasm._Py_Dealloc (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[2186]:0x1e9ed9)
at pyodide.asm.wasm._PyObject_MakeTpCall (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[1085]:0x1a3722) {
pyodide_fatal_error: true
}
scipy.optimize.tests
RuntimeError: memory access out of bounds
at pyodide.asm.wasm.__get_exception_message (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[12687]:0x4d0c6f)
at Module.___get_exception_message (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:94457:48)
at /home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8214:9
at withStackSave (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:7880:17)
at getExceptionMessageCommon (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8211:7)
at Object.getExceptionMessage (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8227:40)
at convertCppException (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5633:31)
at API.fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5647:48)
at API.maybe_fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5685:17)
at Module.callPyObjectKwargs (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:4349:17)
scipy.sparse.linalg._dsolve.tests
RuntimeError: memory access out of bounds
at pyodide.asm.wasm.__get_exception_message (wasm://wasm/pyodide.asm.wasm-025c25ae:wasm-function[12687]:0x4d0c6f)
at Module.___get_exception_message (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:94457:48)
at /home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8214:9
at withStackSave (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:7880:17)
at getExceptionMessageCommon (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8211:7)
at Object.getExceptionMessage (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:8227:40)
at convertCppException (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5633:31)
at API.fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5647:48)
at API.maybe_fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5685:17)
at Module.callPyObjectKwargs (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:4349:17)
scipy.special
CppException boost::wrapexcept<std::domain_error>: Error in function boost::math::erf_inv<double>(double, double): Argument outside range [-1, 1] in inverse erf function (got p=-10).
at convertCppException (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5634:18)
at API.fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5647:48)
at API.maybe_fatal_error (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5685:17)
at Module.callPyObjectKwargs (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:4349:17)
at Module.callPyObject (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:4398:25)
at Qe.apply (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5395:22)
at Object.apply (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/node_modules/pyodide/pyodide.asm.js:5277:22)
at main (/home/runner/work/scipy-tests-pyodide/scipy-tests-pyodide/scipy-pytest.js:56:24) {
ty: 'boost::wrapexcept<std::domain_error>',
pyodide_fatal_error: true
}
scipy.stats
no traceback in the log for some reason
To Reproduce
I can post more details if needed but using https://github.com/lesteve/scipy-tests-pyodide will reproduce.
An example Python code that shows the issue (fatal error on main and return nan in stable):
import numpy as np
from scipy.special import powm1
powm1(np.nan, 1)Expected behavior
No error