Testing framework hits errors in building/finding 'capabilities'

[ajdubas]

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Issue or question about MOOSE

On building a MOOSE app (doesn't seem to matter which one) and executing the ./run_tests function, the testing framework seems to hit an error with building/importing 'capabilities'. This occurs on a fresh build attempt in CI on ubuntu-latest as well as on a fresh install on Debian 12.

(Optional) code in question / simulation log / errors

./run_tests
Building and linking /home/runner/moose/framework/contrib/capabilities/capabilities.so...
INFO: Building capabilities with "make capabilities" in /home/runner/moose/test
ERROR: Failed to import capabilities after building
Traceback (most recent call last):
  File "/home/runner/moose/python/pycapabilities/__init__.py", line 13, in <module>
    import capabilities
ModuleNotFoundError: No module named 'capabilities'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/moose/python/pycapabilities/__init__.py", line 18, in <module>
    import capabilities
ImportError: /home/runner/moose/framework/contrib/capabilities/capabilities.so: undefined symbol: _ZN7libMesh8demangleB5cxx11EPKc

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/proteus/proteus/./run_tests", line 12, in <module>
    TestHarness.buildAndRun(sys.argv, 'proteus', MOOSE_DIR)
  File "/home/runner/moose/python/TestHarness/TestHarness.py", line 251, in buildAndRun
    harness = TestHarness.build(argv, app_name, moose_dir, *args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/moose/python/TestHarness/TestHarness.py", line 247, in build
    return TestHarness(argv, moose_dir, moose_python_dir, test_root)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/moose/python/TestHarness/TestHarness.py", line 337, in __init__
    import pycapabilities
  File "/home/runner/moose/python/pycapabilities/__init__.py", line 28, in <module>
    import capabilities
ImportError: /home/runner/moose/framework/contrib/capabilities/capabilities.so: undefined symbol: _ZN7libMesh8demangleB5cxx11EPKc
Error: Process completed with exit code 1.

Encountering Errors? Please include diagnostic output

No response

[GiudGiud]

Hello

you have to install that Python package.
if you used the conda installation route, ‘conda update moose-dev’ would do it

[lindsayad]

I'm experiencing a similar issue

(moose-python) lindad@rod:/data/lindad/projects/moose/test(fv_array)$ ./run_tests -j32 --re "array_kernels.*test$"
INFO: Building capabilities with "make capabilities" in /data/lindad/projects/moose/test
Building and linking /data/lindad/projects/moose/framework/contrib/capabilities/capabilities.so...
ERROR: Failed to import capabilities after building
Traceback (most recent call last):
  File "/data/lindad/projects/moose/python/pycapabilities/__init__.py", line 13, in <module>
    import capabilities
ModuleNotFoundError: No module named 'capabilities'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/lindad/projects/moose/python/pycapabilities/__init__.py", line 18, in <module>
    import capabilities
ImportError: /usr/local/cuda-12.9/lib64/libcublas.so.12: undefined symbol: cublasLtGetEnvironmentMode, version libcublasLt.so.12

[lindsayad]

Hmm this is unrelated to your issue. I tracked my problem to multiple libcublasLt.so installations

[lindsayad]

Wait now that I've fixed the cublas issue, I actually see the same undefined symbol you see

undefined symbol: PyBool_Type   (./capabilities.so)
undefined symbol: PyExc_ValueError      (./capabilities.so)
undefined symbol: PyUnicode_FromString  (./capabilities.so)
undefined symbol: PyUnicode_AsUTF8      (./capabilities.so)
undefined symbol: PyErr_SetString       (./capabilities.so)
undefined symbol: PyLong_AsLong (./capabilities.so)
undefined symbol: PyLong_FromLong       (./capabilities.so)
undefined symbol: PyModule_Create2      (./capabilities.so)
undefined symbol: PyObject_IsTrue       (./capabilities.so)
undefined symbol: _ZN7libMesh8demangleB5cxx11EPKc       (./capabilities.so)
undefined symbol: PyTuple_GetItem       (./capabilities.so)
undefined symbol: PyList_Size   (./capabilities.so)
undefined symbol: PyList_GetItem        (./capabilities.so)
undefined symbol: _PyArg_ParseTuple_SizeT       (./capabilities.so)
undefined symbol: PyDict_Items  (./capabilities.so)
undefined symbol: PyModule_AddIntConstant       (./capabilities.so)
undefined symbol: _Py_BuildValue_SizeT  (./capabilities.so)
undefined symbol: PyTuple_Size  (./capabilities.so)

[lindsayad]

Ok the issue is that somebody put the libmesh libraries and link flags before the capability src files in the compilation/link line and on systems where the compiler/linker defaults to --as-needed, libmesh_foo.so will get dropped from the library link. I'll put up a fix shortly

[lindsayad]

#31546 fixed my issue

[ajdubas]

Also fixes my issue, thank you!

[wangzhaohao]

I met the similar error.

[/home/wang/projects/moose/framework/moose.mk:243: /home/wang/projects/moose/framework/c

ontrib/capabilities/capabilities.so] Error 1

make: *** Waiting for unfinished jobs....

make[1]: Entering directory '/home/wang/projects/moose/framework/contrib/hit'

Building hit for python with python3-config

mpicxx -std=c++17 -I/home/wang/miniforge/envs/moose/wasp/include -Iinclude -g -fvisibility-inlines

-hidden -fmessage-length=0    -fPIC -fstack-protector-strong -fno-plt  -ffunction-sections -pipe -

isystem /home/wang/miniforge/envs/moose/include  -std=c++17 src/hit/main.cc src/hit/parse.cc src/h

it/lex.cc src/hit/braceexpr.cc -o hit -Wl,-rpath,/home/wang/miniforge/envs/moose/wasp/lib -L/home/

wang/miniforge/envs/moose/wasp/lib -lwaspcore -lwaspddi -lwaspexpr -lwasphalite -lwasphit -lwasphi

ve -lwaspjson -lwasplsp -lwaspplot -lwaspsiren -lwaspson

Finally, I found the reason is the zsh config file. In the .zshrc file, If you are using oh-my-zsh, please set the DISABLE_MAGIC_FUNCTIONS="true" .