CFD Online Discussion Forums - Python/Foam error with import

Hi everyone,

I'm experimenting with passing arrays between openfoam9 and python 3.8 using the numpy C api (inside a custom solver called myPisoFoam). The application compiles fine with wmake, but when run, FOAM exits due to a floating point exception and almost 70 lines of errors which I do not understand. I have narrowed down the issue to the use of "import_array()" to initialise the numpy array API.

**EDIT**

I can now see that upon compilation (only if import_array(), or its component function PyImport_ImportModule("numpy.core._multiarray_umat h") is called, wmake will compile successfully but with the warnings :

Code:

could not open file ndarrayobject.h for source file myPisoFoam.C due to No such file or directory

could not open file npy_interrupt.h for source file myPisoFoam.C due to No such file or directory

could not open file noprefix.h for source file myPisoFoam.C due to No such file or directory

Clearly it is struggling to find the required numpy libraries, so perhaps I am not linking to them properly inside Make/options?

-----------------------------------------------------------------------------------------------------------------------

The C code (on top of the normal solver code) looks like this:

Code:

/* Initialize Python and add current directory to path*/

Py_Initialize ();

PyRun_SimpleString("import sys");

PyRun_SimpleString("sys.path.append (".")");



/* initialize numpy array library */

import_array1(-1);





/* -----More code after this but foam has already exited-----*/

-----------------------------------------------------------------------------------------------------------------------

The following is additionally included at the top of the main solver:

Code:

#include "Python.h"

#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION

#include "/home/daep/a.del-ser/.local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h"

-----------------------------------------------------------------------------------------------------------------------

The following python related things are included in Make/options:

Code:

EXE_INC = \

    -I/usr/include/python3.8/ \

    -I/home/daep/a.del-ser/.local/lib/python3.8/site-packages/numpy/core/include





EXE_LIBS = \

     -lpython3.8

-----------------------------------------------------------------------------------------------------------------------

The error stream looks like this (I have no idea what the question marks are indicating all over the place):

Code:

#0  Foam::error::printStack(Foam::Ostream&) at ??:?

#1  Foam::sigFpe::sigHandler(int) at ??:?

#2  ? in "/lib/x86_64-linux-gnu/libc.so.6"

#3  ? at scalarmath.c:?

#4  PyNumber_Multiply in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#5  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#6  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#7  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#8  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#9  _PyEval_EvalCodeWithName in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#10  PyEval_EvalCodeEx in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#11  PyEval_EvalCode in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#12  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#13  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#14  PyVectorcall_Call in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#15  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#16  _PyEval_EvalCodeWithName in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#17  _PyFunction_Vectorcall in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#18  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#19  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#20  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#21  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#22  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#23  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#24  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#25  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#26  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#27  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#28  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#29  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#30  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#31  _PyObject_CallMethodIdObjArgs in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#32  PyImport_ImportModuleLevelObject in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#33  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#34  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#35  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#36  _PyEval_EvalCodeWithName in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#37  _PyFunction_Vectorcall in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#38  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#39  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#40  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#41  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#42  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#43  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#44  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#45  _PyObject_CallMethodIdObjArgs in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#46  PyImport_ImportModuleLevelObject in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#47  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#48  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#49  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#50  _PyEval_EvalCodeWithName in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#51  _PyFunction_Vectorcall in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#52  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#53  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#54  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#55  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#56  _PyEval_EvalFrameDefault in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#57  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#58  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#59  _PyObject_CallMethodIdObjArgs in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#60  PyImport_ImportModuleLevelObject in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#61  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#62  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#63  _PyObject_MakeTpCall in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#64  ? in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#65  PyObject_CallFunction in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#66  PyImport_Import in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#67  PyImport_ImportModule in "/lib/x86_64-linux-gnu/libpython3.8.so.1.0"

#68  ? in "/home/daep/a.del-ser/OpenFOAM/a.del-ser-9/platforms/linux64GccDPInt32Opt/bin/myPisoFoam"

#69  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"

#70  ? in "/home/daep/a.del-ser/OpenFOAM/a.del-ser-9/platforms/linux64GccDPInt32Opt/bin/myPisoFoam"

Floating point exception (core dumped)

-----------------------------------------------------------------------------------------------------------------------

Additionally, I'd rather run this in a python virtual environment but haven't been able to get the local path working within Make/options. If anyone has any insight there too it would be great.

Thanks!