Help! Seg fault when running any DaphneLib code

[divjakm]

I wanted to try combining Python with DaphneLib but it seems I'm doing something wrong and I can't figure out what.

My OS is Kubuntu 24.04, installed in a QEMU/KVM virtual machine. I cloned the latest version of Daphne source code from GitHub and built it using the build.sh script. Then I followed the instructions for using DaphneLib (https://daphne-eu.github.io/daphne/DaphneLib/Overview/):

• I have the three *.so files in the /lib subfolder
• I installed the latest Anaconda for a complete Python environment
• I set the LD_LIBRARY_PATH, DAPHNELIB_DIR_PATH

At first I didn't install the Daphne Python package, I followed the instructions in the section "Use Without Installation". So I set the PYTHONPATH and I modified the run_python.sh to use the python3 executable from my Anaconda installation. If I try running the simplest provided DaphneLib example with: ./run_python.sh scripts/examples/daphnelib/shift-and-scale.py I get an error message and a segmentation fault:

divjak@DaphneVM:~/Work/daphne$ ./run-python.sh scripts/examples/daphnelib/shift-and-scale.py 
terminate called after throwing an instance of 'std::runtime_error'
  what():  error while parsing kernel catalog file `/home/divjak/Work/daphne/lib/catalog.json`: KernelCatalogParser: error while parsing argument types of kernel `_print__List_DenseMatrix_double__bool__bool` for operation `print` (backend `CPP`): unknown type for argument #0: `List<DenseMatrix<double>>`
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z13handleSignalsi+0x32)[0x717ebb8fad32]
/lib/x86_64-linux-gnu/libc.so.6(+0x45320)[0x717ebfc45320]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x717ebfc9eb1c]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x717ebfc4526e]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x717ebfc288ff]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ffe)[0x717eb94a5ffe]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xbae9c)[0x717eb94bae9c]
/lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x717eb94a5a49]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb128)[0x717eb94bb128]
/home/divjak/Work/daphne/lib/libdaphnelib.so(+0x24175eb)[0x717ebbc175eb]
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z11startDAPHNEiPPKcP15DaphneLibResultPiR16DaphneUserConfig+0xb4a)[0x717ebb92bada]
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z12mainInternaliPPKcP15DaphneLibResult+0x1b7)[0x717ebb9310a7]
/home/divjak/Work/daphne/lib/libdaphnelib.so(daphne+0x54)[0x717ebb8f9944]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(+0xa052)[0x717ebfe68052]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(+0x8925)[0x717ebfe66925]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(ffi_call+0xde)[0x717ebfe6706e]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x97b7)[0x717ebfe787b7]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x8bd5)[0x717ebfe77bd5]
/home/divjak/anaconda3/bin/python3(_PyObject_MakeTpCall+0x2fb)[0x51b30b]
/home/divjak/anaconda3/bin/python3(_PyEval_EvalFrameDefault+0x6d5)[0x525e75]
/home/divjak/anaconda3/bin/python3(PyEval_EvalCode+0xae)[0x5e4dfe]
/home/divjak/anaconda3/bin/python3[0x60a5d7]
/home/divjak/anaconda3/bin/python3[0x605ca7]
/home/divjak/anaconda3/bin/python3[0x61db12]
/home/divjak/anaconda3/bin/python3(_PyRun_SimpleFileObject+0x1b0)[0x61d3b0]
./run-python.sh: line 26: 12537 Segmentation fault      (core dumped) /home/divjak/anaconda3/bin/python3 $@

Then I tried installing the Daphne Python package into a pip virtual environment. The installation was successfull, but when I try to run the example code I get the same error:

(test_venv) divjak@DaphneVM:~/Work/daphne$ python3 scripts/examples/daphnelib/shift-and-scale.py
terminate called after throwing an instance of 'std::runtime_error'
  what():  error while parsing kernel catalog file `/home/divjak/Work/daphne/lib/catalog.json`: KernelCatalogParser: error while parsing argument types of kernel `_print__List_DenseMatrix_double__bool__bool` for operation `print` (backend `CPP`): unknown type for argument #0: `List<DenseMatrix<double>>`
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z13handleSignalsi+0x32)[0x783202cfad32]
/lib/x86_64-linux-gnu/libc.so.6(+0x45320)[0x783207045320]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x78320709eb1c]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x78320704526e]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7832070288ff]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ffe)[0x7832008a5ffe]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xbae9c)[0x7832008bae9c]
/lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7832008a5a49]
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb128)[0x7832008bb128]
/home/divjak/Work/daphne/lib/libdaphnelib.so(+0x24175eb)[0x7832030175eb]
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z11startDAPHNEiPPKcP15DaphneLibResultPiR16DaphneUserConfig+0xb4a)[0x783202d2bada]
/home/divjak/Work/daphne/lib/libdaphnelib.so(_Z12mainInternaliPPKcP15DaphneLibResult+0x1b7)[0x783202d310a7]
/home/divjak/Work/daphne/lib/libdaphnelib.so(daphne+0x54)[0x783202cf9944]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(+0xa052)[0x78320725a052]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(+0x8925)[0x783207258925]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/../../libffi.so.8(ffi_call+0xde)[0x78320725906e]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x97b7)[0x78320726a7b7]
/home/divjak/anaconda3/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x8bd5)[0x783207269bd5]
python3(_PyObject_MakeTpCall+0x75)[0x548d15]
python3(_PyEval_EvalFrameDefault+0xa89)[0x5d70f9]
python3(PyEval_EvalCode+0x15b)[0x5d560b]
python3[0x608812]
python3[0x6b50e3]
python3(_PyRun_SimpleFileObject+0x1aa)[0x6b4e4a]
python3(_PyRun_AnyFileObject+0x4f)[0x6b4c7f]
Segmentation fault (core dumped)
(test_venv) divjak@DaphneVM:~/Work/daphne$ 

Does anybody have any idea what I'm doing wrong?

[pdamme]

Hi @divjakm, thanks for reporting this issue. I suspect that your compiled instance of DaphneLib (lib/libdaphnelib.so) is outdated. Please try to rebuild DaphneLib by doing ./build.sh --target daphnelib and then try executing the shift-and-scale.py script again. That might already solve your problem.

---

For some background:

• By default, build.sh builds the daphne executable and all required static/shared libraries (e.g., the DaphneDSL parser, runtime kernels, etc.). However, DaphneLib is not required by the daphne executable, so lib/libdaphnelib.so is not updated unless you specify a target, e.g., ./build.sh --target daphnelib or ./build.sh --target run_tests or ./build.sh --target all.
• The error message

  error while parsing kernel catalog file `/home/divjak/Work/daphne/lib/catalog.json`: KernelCatalogParser: error while parsing argument types of kernel `_print__List_DenseMatrix_double__bool__bool` for operation `print` (backend `CPP`): unknown type for argument #0: `List<DenseMatrix<double>>

  indicates that the list type, which was recently added to DaphneDSL in c4c928af139f4214da13257b49a6cdc327c029ed, is not recognized by the kernel catalog parser.

• Thus, I suspect that you built DaphneLib on your system in the past, but it wasn't rebuilt since lists were introduced to DaphneDSL on Aug 9, 2024.

Further action for the DAPHNE development:

• I can understand that this is an issue a user can easily run into. It would probably be better if build.sh built both the daphne and daphnelib targets by default.
• Furthermore, even if there is such an error when parsing the kernel catalog, it should not result in an uncaught exception and a segmentation fault. We need to better catch this error, such that it does not look like an uncontrolled crash anymore.

[divjakm]

Thank you! Re-compilation solved the problem. I forgot to try that before because I already had the *.so files in the /lib folder after the default building process and I thought it's not necessary to explicitly build DaphneLib. It works now!