Undefined symbol : pfnc_inq_vardimid during import netCDF4 #1417

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1. jswhit commented on Aug 5, 2025

   

   jswhit

   on Aug 5, 2025

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   @ZedThree ?
2. jswhit commented on Aug 5, 2025

   

   jswhit

   on Aug 5, 2025

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   When you say 'netcdf-c: 4.9.3 (custom build, with nc_complex enabled)' do you mean that it's a modified version of the C-lib with nc_complex included? If so, I suspect that there is a conflict between the two versions of nc_complex (the one in the C lib and the one included in the python module).
3. ZedThree commented on Aug 6, 2025

   

   ZedThree

   on Aug 6, 2025

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   I thought that we build nc_complex as part of the Cython build?

   netcdf4-python/setup.py

   Lines 428 to 437 in 57b9a80

   	nc_complex_dir = pathlib.Path("./external/nc_complex")
   	source_files = [
   	netcdf4_src_pyx,
   	str(nc_complex_dir / "src/nc_complex.c"),
   	]
   	include_dirs = inc_dirs + [
   	"include",
   	str(nc_complex_dir / "include"),
   	str(nc_complex_dir / "include/generated_fallbacks"),
   	]

   So I don't think you need to have built it separately.
4. ocefpaf commented on Aug 6, 2025

   

   ocefpaf

   on Aug 6, 2025

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   Also, I cannot reproduce that with the built wheel. Your pip install is probably from source, right? If so, something is amiss with your build.
5. Cor0n4V1rus commented on Sep 15, 2026

   

   Cor0n4V1rus

   on Sep 15, 2026

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   I had the same issue, with at least 1.7.2 and 1.7.4 and fixed it with two 'dirty' patches.
   Since I am no expert with python, cython, numpy, hdf5 or netcdf, someone with
   deeper knowledge might want to fix it properly.

   First one removes 'inline' from the two functions AND makes them invisible, if a
   compile unit defines 'NO_INLINE_FUNCTIONS', otherwise the linker would complain about
   multiple symbol definitions.

   Second patch defines 'NO_INLINE_FUNCTIONS' before including the header.

   --- external/nc_complex/include/nc_complex/nc_complex.h.original
   +++ external/nc_complex/include/nc_complex/nc_complex.h
   @@ -242,14 +242,16 @@
        int* nattsp
    );
    
   +#ifndef NO_INLINE_FUNCTIONS
    // NOLINTBEGIN(modernize-use-nullptr)
   -NC_COMPLEX_EXPORT inline int pfnc_inq_varndims(int ncid, int varid, int* ndimsp) {
   +NC_COMPLEX_EXPORT int pfnc_inq_varndims(int ncid, int varid, int* ndimsp) {
        return pfnc_inq_var(ncid, varid, NULL, NULL, ndimsp, NULL, NULL);
    }
   -NC_COMPLEX_EXPORT inline int pfnc_inq_vardimid(int ncid, int varid, int* dimidsp) {
   +NC_COMPLEX_EXPORT int pfnc_inq_vardimid(int ncid, int varid, int* dimidsp) {
        return pfnc_inq_var(ncid, varid, NULL, NULL, NULL, dimidsp, NULL);
    }
    // NOLINTEND(modernize-use-nullptr)
   +#endif
    
    NC_COMPLEX_EXPORT int pfnc_def_var_chunking(
        int ncid, int varid, int storage, const size_t* chunksizesp
   

   --- external/nc_complex/src/nc_complex.c.original
   +++ external/nc_complex/src/nc_complex.c
   @@ -1,3 +1,4 @@
   +#define NO_INLINE_FUNCTIONS
    #include "nc_complex/nc_complex.h"
    
    #include <ctype.h>
   

   For the record (with gcc 16.2.0) :

   Without my patches, building it with

   (
   export CFLAGS+=" -Wno-incompatible-pointer-types"
   export USE_NCCONFIG=1
   export NETCDF_PLUGIN_DIR=/usr/lib/netcdf/plugin
   
   python -m build -v --wheel --no-isolation
   )
   

   and testing it with

   (
   export NO_NET=1
   export PYTHONPATH="${PWD}"/build/lib.linux-x86_64-cpython-314
   
   pushd test
   python -B ./run_all.py
   popd
   )
   

   yields

   Traceback (most recent call last):
     File "/tmp/build-bot/netcdf-1.7.4/test/./run_all.py", line 2, in <module>
       from netCDF4 import __hdf5libversion__,__netcdf4libversion__,__version__, Dataset
     File "/tmp/build-bot/netcdf-1.7.4/build/lib.linux-x86_64-cpython-314/netCDF4/__init__.py", line 11, in <module>
       from ._netCDF4 import *
   ImportError: /tmp/build-bot/netcdf-1.7.4/build/lib.linux-x86_64-cpython-314/netCDF4/_netCDF4.cpython-314-x86_64-linux-gnu.so: undefined symbol: pfnc_inq_vardimid
   

   while with the patches its

   netcdf4-python version: 1.7.4
   HDF5 lib version:       2.2.0
   netcdf lib version:     4.10.1
   numpy version           2.5.3
   cython version          3.3.0
   s...................................................................s...........................s..........compressed lossy with shuffle and standard quantization =  187676  max err =  0.00024412745124813284
   compressed lossy with shuffle and alternate quantization =  155270  max err =  0.00048827517723559755
   compressed lossy with shuffle and alternate quantization =  162934  max err =  0.0002441371616678234
   ......s.
   ----------------------------------------------------------------------
   Ran 115 tests in 113.330s
   
   OK (skipped=4)