Can't install h5py==3.1.0 with hdf5-1.13.1

 * Operating System: Red Hat Enterprise Linux Server

 * Python version 3.6.8

 * <s> Where Python was acquired: Compiled from source </s>

 * h5py version: 3.1.0

 * HDF5 version 1.13.1



I am trying to install (or even build) h5py from source on a redhat server. 

I compiled from source the hdf5 library, and I try to build the h5py module with the command: 



```

HDF5_DIR=/home/hdf5-1.13.1/hdf5/ python3 setup.py build

```

I get the following stack, saying at the end the error: ‘H5E_BADATOM’ undeclared 





```

running build

running build_py

running build_ext

********************************************************************************

                       Summary of the h5py configuration



HDF5 include dirs: [

  '/home/hdf5-1.13.1/hdf5/include'

]

HDF5 library dirs: [

  '/home/hdf5-1.13.1/hdf5/lib'

]

     HDF5 Version: (1, 13, 1)

      MPI Enabled: False

 Rebuild Required: True



********************************************************************************

Executing cythonize()

[ 1/24] Cythonizing /home/h5py-3.1.0/h5py/_conv.pyx

[ 2/24] Cythonizing /home/h5py-3.1.0/h5py/_errors.pyx

[ 3/24] Cythonizing /home/h5py-3.1.0/h5py/_objects.pyx

[ 4/24] Cythonizing /home/h5py-3.1.0/h5py/_proxy.pyx

[ 5/24] Cythonizing /home/h5py-3.1.0/h5py/_selector.pyx

[ 6/24] Cythonizing /home/h5py-3.1.0/h5py/defs.pyx

[ 7/24] Cythonizing /home/h5py-3.1.0/h5py/h5.pyx

[ 8/24] Cythonizing /home/h5py-3.1.0/h5py/h5a.pyx

[ 9/24] Cythonizing /home/h5py-3.1.0/h5py/h5ac.pyx

[10/24] Cythonizing /home/h5py-3.1.0/h5py/h5d.pyx

[11/24] Cythonizing /home/h5py-3.1.0/h5py/h5ds.pyx

[12/24] Cythonizing /home/h5py-3.1.0/h5py/h5f.pyx

[13/24] Cythonizing /home/h5py-3.1.0/h5py/h5fd.pyx

[14/24] Cythonizing /home/h5py-3.1.0/h5py/h5g.pyx

[15/24] Cythonizing /home/h5py-3.1.0/h5py/h5i.pyx

[16/24] Cythonizing /home/h5py-3.1.0/h5py/h5l.pyx

[17/24] Cythonizing /home/h5py-3.1.0/h5py/h5o.pyx

[18/24] Cythonizing /home/h5py-3.1.0/h5py/h5p.pyx

[19/24] Cythonizing /home/h5py-3.1.0/h5py/h5pl.pyx

[20/24] Cythonizing /home/h5py-3.1.0/h5py/h5r.pyx

[21/24] Cythonizing /home/h5py-3.1.0/h5py/h5s.pyx

[22/24] Cythonizing /home/h5py-3.1.0/h5py/h5t.pyx

[23/24] Cythonizing /home/h5py-3.1.0/h5py/h5z.pyx

[24/24] Cythonizing /home/h5py-3.1.0/h5py/utils.pyx

building 'h5py.defs' extension

gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DH5_USE_18_API -DNPY_NO_DEPRECATED_API=0 -I./h5py -I/home/hdf5-1.13.1/hdf5/include -I/home/h5py-3.1.0/lzf -I/home/h5py-3.1.0/lzf/lzf -I/home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include -I/usr/include/python3.6m -c /home/h5py-3.1.0/h5py/defs.c -o build/temp.linux-x86_64-3.6/home/h5py-3.1.0/h5py/defs.o

In file included from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1788,

                 from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18,

                 from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4,

                 from /home/h5py-3.1.0/h5py/defs.c:661:

/home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \

  ^~~~~~~

/home/h5py-3.1.0/h5py/defs.c: In function ‘__pyx_f_4h5py_4defs_H5Pget_driver_info’:

/home/h5py-3.1.0/h5py/defs.c:26849:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]

   __pyx_v_r = H5Pget_driver_info(__pyx_v_plist_id);

             ^

gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/home/h5py-3.1.0/h5py/defs.o -L/home/hdf5-1.13.1/hdf5/lib -L/usr/lib64 -Wl,--enable-new-dtags,-R/home/hdf5-1.13.1/hdf5/lib -lhdf5 -lhdf5_hl -lpython3.6m -o build/lib.linux-x86_64-3.6/h5py/defs.cpython-36m-x86_64-linux-gnu.so

building 'h5py._errors' extension

gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DH5_USE_18_API -DNPY_NO_DEPRECATED_API=0 -I./h5py -I/home/hdf5-1.13.1/hdf5/include -I/home/h5py-3.1.0/lzf -I/home/h5py-3.1.0/lzf/lzf -I/home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include -I/usr/include/python3.6m -c /home/h5py-3.1.0/h5py/_errors.c -o build/temp.linux-x86_64-3.6/home/h5py-3.1.0/h5py/_errors.o

In file included from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1788,

                 from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18,

                 from /home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4,

                 from /home/h5py-3.1.0/h5py/_errors.c:661:

/home/h5py-3.1.0/.eggs/numpy-1.12.0-py3.6-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \

  ^~~~~~~

/home/h5py-3.1.0/h5py/_errors.c: In function ‘__pyx_f_4h5py_7_errors_walk_cb’:

/home/h5py-3.1.0/h5py/_errors.c:1856:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]

   __pyx_t_3 = (__pyx_v_desc[0]).desc;

             ^

/home/h5py-3.1.0/h5py/_errors.c: In function ‘__pyx_f_4h5py_7_errors_set_exception’:

/home/h5py-3.1.0/h5py/_errors.c:1973:64: warning: passing argument 3 of ‘H5Ewalk2’ from incompatible pointer type [-Wincompatible-pointer-types]

   __pyx_t_1 = ((H5Ewalk(((hid_t)H5E_DEFAULT), H5E_WALK_UPWARD, __pyx_f_4h5py_7_errors_walk_cb, (&__pyx_v_err)) < 0) != 0);

                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/hdf5-1.13.1/hdf5/include/hdf5.h:26,

                 from /home/h5py-3.1.0/h5py/api_compat.h:27,

                 from /home/h5py-3.1.0/h5py/_errors.c:667:

/home/hdf5-1.13.1/hdf5/include/H5Epublic.h:491:80: note: expected ‘H5E_walk2_t’ {aka ‘int (*)(unsigned int,  const struct H5E_error2_t *, void *)’} but argument is of type ‘herr_t (*)(int,  H5E_error2_t *, void *)’ {aka ‘int (*)(int,  struct H5E_error2_t *, void *)’}

 H5_DLL herr_t H5Ewalk2(hid_t err_stack, H5E_direction_t direction, H5E_walk2_t func, void *client_data);

                                                                    ~~~~~~~~~~~~^~~~

/home/h5py-3.1.0/h5py/_errors.c:2172:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]

   __pyx_t_8 = __pyx_v_err.err.desc;

             ^

/home/h5py-3.1.0/h5py/_errors.c:2223:66: warning: passing argument 3 of ‘H5Ewalk2’ from incompatible pointer type [-Wincompatible-pointer-types]

   __pyx_t_1 = ((H5Ewalk(((hid_t)H5E_DEFAULT), H5E_WALK_DOWNWARD, __pyx_f_4h5py_7_errors_walk_cb, (&__pyx_v_err)) < 0) != 0);

                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/hdf5-1.13.1/hdf5/include/hdf5.h:26,

                 from /home/h5py-3.1.0/h5py/api_compat.h:27,

                 from /home/h5py-3.1.0/h5py/_errors.c:667:

/home/hdf5-1.13.1/hdf5/include/H5Epublic.h:491:80: note: expected ‘H5E_walk2_t’ {aka ‘int (*)(unsigned int,  const struct H5E_error2_t *, void *)’} but argument is of type ‘herr_t (*)(int,  H5E_error2_t *, void *)’ {aka ‘int (*)(int,  struct H5E_error2_t *, void *)’}

 H5_DLL herr_t H5Ewalk2(hid_t err_stack, H5E_direction_t direction, H5E_walk2_t func, void *client_data);

                                                                    ~~~~~~~~~~~~^~~~

/home/h5py-3.1.0/h5py/_errors.c:2255:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]

   __pyx_t_8 = __pyx_v_err.err.desc;

             ^

/home/h5py-3.1.0/h5py/_errors.c: In function ‘__pyx_pymod_exec__errors’:

/home/h5py-3.1.0/h5py/_errors.c:4274:44: error: ‘H5E_BADATOM’ undeclared (first use in this function); did you mean ‘H5E_BADITER’?

   __pyx_t_2 = __Pyx_PyInt_From_H5E_minor_t(H5E_BADATOM); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 39, __pyx_L1_error)

                                            ^~~~~~~~~~~

                                            H5E_BADITER

/home/h5py-3.1.0/h5py/_errors.c:4274:44: note: each undeclared identifier is reported only once for each function it appears in

error: command 'gcc' failed with exit status 1



```



My guess is that the commit from @[ajelenak](https://github.com/h5py/h5py/commits?author=ajelenak) committed on Apr 11, 2021  9909d4818043dc0be4c52c0676578d0e95c119c1 could fix my problem if it were backported into the h5py==3.1.0 version.



Do you have any thought ? 



Thanks

[]