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I am trying to install the developer version of netcdf4-python version 1.7.1 with parallel hdf5 and parallel netcdf enabled.
I am using the following software versions:
OS: Red Hat Enterprise Linux version 8.4
C Compiler: impi/2019.7.217/intel64/bin/mpicc
HDF5: hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
Netcdf-c: netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
Anaconda: 33.16.6.7
I have built mpi4py and h5py in a conda environment with MPI enabled via the following commands:
When I attempt to install netcdf4-python from source with pip install --no-build-isolation -v ., I receive the following output with an error:
Using pip 24.2 from /home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages/pip (python 3.11)
Processing /home/awikner/netcdf4-python
Running command Preparing metadata (pyproject.toml)
-L/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib -lnetcdf
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
Package 'hdf5', required by 'virtual:world', not found
reading from setup.cfg...
using /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/bin/nc-config...
lib_dirs: ['/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib']
checking /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include...
hdf5 headers not found in /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include
nc-config did provide path to HDF5 headers, search standard locations...
checking /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include...
HDF5 library version: 1.12.0 headers found in /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include
HDF5 library version: 1.12.0 found in /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
lib_dirs: ['/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib', '/software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib']
using netcdf library version 4.7.4
using Cython to compile netCDF4.pyx...
netcdf lib has parallel functions
NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed
running dist_info
creating /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info
writing /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/PKG-INFO
writing dependency_links to /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/dependency_links.txt
writing entry points to /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/entry_points.txt
writing requirements to /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/requires.txt
writing top-level names to /home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/top_level.txt
writing manifest file '/home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/SOURCES.txt'
reading manifest file '/home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'examples/data'
warning: no previously-included files found matching 'src/netCDF4/_netCDF4.c'
adding license file 'LICENSE'
writing manifest file '/home/awikner/pip-modern-metadata-zaxkixg_/netCDF4.egg-info/SOURCES.txt'
creating '/home/awikner/pip-modern-metadata-zaxkixg_/netCDF4-1.7.2.dist-info'
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: cftime in /home/awikner/.local/lib/python3.11/site-packages (from netCDF4==1.7.2) (1.6.4)
Requirement already satisfied: certifi in /home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages (from netCDF4==1.7.2) (2024.8.30)
Requirement already satisfied: numpy in /home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages (from netCDF4==1.7.2) (2.1.1)
Building wheels for collected packages: netCDF4
Running command Building wheel for netCDF4 (pyproject.toml)
-L/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib -lnetcdf
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
Package 'hdf5', required by 'virtual:world', not found
reading from setup.cfg...
using /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/bin/nc-config...
lib_dirs: ['/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib']
checking /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include...
hdf5 headers not found in /software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include
nc-config did provide path to HDF5 headers, search standard locations...
checking /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include...
HDF5 library version: 1.12.0 headers found in /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include
HDF5 library version: 1.12.0 found in /software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
lib_dirs: ['/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib', '/software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/lib']
using netcdf library version 4.7.4
using Cython to compile netCDF4.pyx...
netcdf lib has parallel functions
NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed
running bdist_wheel
running build
running build_py
copying src/netCDF4/__init__.py -> build/lib.linux-x86_64-cpython-311/netCDF4
copying src/netCDF4/utils.py -> build/lib.linux-x86_64-cpython-311/netCDF4
running egg_info
writing src/netCDF4.egg-info/PKG-INFO
writing dependency_links to src/netCDF4.egg-info/dependency_links.txt
writing entry points to src/netCDF4.egg-info/entry_points.txt
writing requirements to src/netCDF4.egg-info/requires.txt
writing top-level names to src/netCDF4.egg-info/top_level.txt
reading manifest file 'src/netCDF4.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'examples/data'
warning: no previously-included files found matching 'src/netCDF4/_netCDF4.c'
adding license file 'LICENSE'
writing manifest file 'src/netCDF4.egg-info/SOURCES.txt'
copying src/netCDF4/__init__.pyi -> build/lib.linux-x86_64-cpython-311/netCDF4
copying src/netCDF4/_netCDF4.pyi -> build/lib.linux-x86_64-cpython-311/netCDF4
copying src/netCDF4/_netCDF4.pyx -> build/lib.linux-x86_64-cpython-311/netCDF4
copying src/netCDF4/py.typed -> build/lib.linux-x86_64-cpython-311/netCDF4
copying src/netCDF4/plugins/empty.txt -> build/lib.linux-x86_64-cpython-311/netCDF4/plugins
running build_ext
building 'netCDF4._netCDF4' extension
gcc -pthread -B /home/awikner/.conda/envs/netcdf4-test/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/awikner/.conda/envs/netcdf4-test/include -fPIC -O2 -isystem /home/awikner/.conda/envs/netcdf4-test/include -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -DNC_COMPLEX_NO_EXPORT=1 -I/software/netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include -I/software/hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1/include -I/home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages/numpy/_core/include -I/home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages/mpi4py/include -Iinclude -Iexternal/nc_complex/include -Iexternal/nc_complex/include/generated_fallbacks -I/home/awikner/.conda/envs/netcdf4-test/include/python3.11 -c external/nc_complex/src/nc_complex.c -o build/temp.linux-x86_64-cpython-311/external/nc_complex/src/nc_complex.o
external/nc_complex/src/nc_complex.c: In function ‘pfnc_def_var’:
external/nc_complex/src/nc_complex.c:637:21: error: ‘NC_FORMATX_NCZARR’ undeclared (first use in this function); did you mean ‘NC_FORMATX_ZARR’?
|| (mode == NC_FORMATX_NCZARR)) {
^~~~~~~~~~~~~~~~~
NC_FORMATX_ZARR
external/nc_complex/src/nc_complex.c:637:21: note: each undeclared identifier is reported only once for each function it appears in
error: command '/usr/bin/gcc' failed with exit code 1
error: subprocess-exited-with-error
× Building wheel for netCDF4 (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
full command: /home/awikner/.conda/envs/netcdf4-test/bin/python /home/awikner/.conda/envs/netcdf4-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /home/awikner/tmpyco_yekk
cwd: /home/awikner/netcdf4-python
Building wheel for netCDF4 (pyproject.toml) ... error
ERROR: Failed building wheel for netCDF4
Failed to build netCDF4
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (netCDF4)
Looking at the netcdf4.h file in the netcdf-c 4.7.4 source code, it indeed does not have a reference to NC_FORMATX_NCZARR. I assume this was added in a more recent version of netcdf-c.
Is there a way to build this version of netcdf4-python to be compatible with this version of netcdf-c? And if not, what was the most recent version that would support this version of netcdf-c?
The text was updated successfully, but these errors were encountered:
I am trying to install the developer version of netcdf4-python version 1.7.1 with parallel hdf5 and parallel netcdf enabled.
I am using the following software versions:
OS: Red Hat Enterprise Linux version 8.4
C Compiler:
impi/2019.7.217/intel64/bin/mpicc
HDF5:
hdf5-1.12.0-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
Netcdf-c:
netcdf-4.7-el8-x86_64+intelmpi-2019.up7+intel-19.1.1
Anaconda: 33.16.6.7
I have built
mpi4py
andh5py
in a conda environment with MPI enabled via the following commands:I additionally had to install a newer version of
openssl
withconda install --channel=conda-forge openssl
.My final environment has the following packages installed:
When I attempt to install netcdf4-python from source with
pip install --no-build-isolation -v .
, I receive the following output with an error:Looking at the
netcdf4.h
file in the netcdf-c 4.7.4 source code, it indeed does not have a reference toNC_FORMATX_NCZARR
. I assume this was added in a more recent version of netcdf-c.Is there a way to build this version of netcdf4-python to be compatible with this version of netcdf-c? And if not, what was the most recent version that would support this version of netcdf-c?
The text was updated successfully, but these errors were encountered: