From [email protected] on December 10, 2009 08:45:25

Can you please capture all the output of "python setup.py build" and post it here?

This is unrelated to your problem, but you should probably be using a more recent
netcdf (netcdf-4.1 rc is available).

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From [email protected] on December 10, 2009 08:59:04

Sure, here's the output:

$ python setup.py build
/Library/Frameworks/Python.framework/Versions/5.0.0/lib/python2.5/distutils/dist.py:263:
UserWarning: Unknown distribution option: 'summary'
warnings.warn(msg)
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
building py_modules sources
building extension "netCDF4" sources
running build_py
creating build
creating build/lib.macosx-10.3-i386-2.5
copying netCDF4_utils.py -> build/lib.macosx-10.3-i386-2.5
creating build/lib.macosx-10.3-i386-2.5/netcdftime
copying netcdftime/init.py -> build/lib.macosx-10.3-i386-2.5/netcdftime
copying netcdftime/netcdftime.py -> build/lib.macosx-10.3-i386-2.5/netcdftime
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'netCDF4' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fno-common -dynamic -no-cpp-precomp
-mno-fused-madd -DNDEBUG -arch i386 -g -O3 -I/usr/local/include -I/opt/local/include

creating build/temp.macosx-10.3-i386-2.5
compile options: '-I/usr/local/include -I/usr/local/include -I/opt/local/include
-I/Library/Frameworks/Python.framework/Versions/5.0.0/lib/python2.5/site-packages/numpy/core/include
-I/Library/Frameworks/Python.framework/Versions/5.0.0/include/python2.5 -c'
gcc: netCDF4.c
In file included from /usr/include/architecture/i386/math.h:626,
from /usr/include/math.h:28,
from
/Library/Frameworks/Python.framework/Versions/5.0.0/include/python2.5/pyport.h:231,
from
/Library/Frameworks/Python.framework/Versions/5.0.0/include/python2.5/Python.h:57,
from netCDF4.c:4:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for Intel with
Mac OS X Deployment Target < 10.4 is invalid.
netCDF4.c: In function ‘__pyx_pf_7netCDF4_getlibversion’:
netCDF4.c:23811: warning: assignment discards qualifiers from pointer target type
gcc -g -arch i386 -L/usr/local/lib -L/opt/local/lib -bundle -undefined dynamic_lookup
build/temp.macosx-10.3-i386-2.5/netCDF4.o -L/usr/local/lib -L/usr/local/lib
-L/opt/local/lib -L/usr/local/lib -L/usr/local/lib -L/opt/local/lib -lnetcdf -lhdf5
-lhdf5_hl -lz -lsz -o build/lib.macosx-10.3-i386-2.5/netCDF4.so
running scons
running build_scripts
creating build/scripts.macosx-10.3-i386-2.5
copying and adjusting utils/nc3tonc4 -> build/scripts.macosx-10.3-i386-2.5
copying and adjusting utils/nc4tonc3 -> build/scripts.macosx-10.3-i386-2.5
copying and adjusting utils/grib2nc4 -> build/scripts.macosx-10.3-i386-2.5
changing mode of build/scripts.macosx-10.3-i386-2.5/nc3tonc4 from 644 to 755
changing mode of build/scripts.macosx-10.3-i386-2.5/nc4tonc3 from 644 to 755
changing mode of build/scripts.macosx-10.3-i386-2.5/grib2nc4 from 644 to 755

-Sourish

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From [email protected] on December 10, 2009 09:01:22

P.S. - I can see that the python module is linked to the correct libraries because:

$ otool -L
/Library/Frameworks/Python.framework/Versions/5.0.0/lib/python2.5/site-packages/netCDF4.so

/Library/Frameworks/Python.framework/Versions/5.0.0/lib/python2.5/site-packages/netCDF4.so:
/usr/local/lib/libnetcdf.5.dylib (compatibility version 6.0.0, current
version 6.0.0)
/usr/local/lib/libhdf5.6.dylib (compatibility version 7.0.0, current version
7.2.0)
/usr/local/lib/libhdf5_hl.6.dylib (compatibility version 7.0.0, current
version 7.2.0)
/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
/opt/local/lib/libsz.2.dylib (compatibility version 3.0.0, current version 3.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.0.0)

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From [email protected] on December 17, 2009 05:35:35

Hi,

Has this issue been resolved yet? Recently I installed netcdf-4.1-rc1, and I

still get this error.

-Sourish

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From [email protected] on December 17, 2009 08:14:29

Sourish: Unfortunately, I don't have a snow leopard machine to test on. I'm a bit
concerned about "/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building
for Intel with
Mac OS X Deployment Target < 10.4 is invalid." - but I don't know what to suggest to
get rid of that.

The function _StartCountStride is in the module netCDF4_utils, so to see if that
module was installed correctly, you could try

import netCDF4_utils
netCDF4_utils._StartCountStride
<function _StartCountStride at 0x1146b30>

If you have cython installed, you might try re-generating the C source code
(netCDF4.c) by running "cython netCDF4.pyx". Other than that, I really don't have
any ideas. I'll see if I can find someone who has snow leopard installed so I can
try it myself.

-Jeff

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From [email protected] on December 18, 2009 01:06:40

Jeff,

There is a module netCDF4_utils, but that doesn't have the function _StartCountStride.

[1]: import netCDF4_utils

2:
['builtins',
'doc',
'file',
'name',
'_buildStartCountStride',
'_find_dim',
'_quantize',
'ma',
'numpy',
'types']

I regenerated netCDF4.c using cython, but that didn't help either.

Regarding access to a machine running snow leopard, do you just need a normal user
account? If you want, I can create an account for you on my machine. Since I need the
netCDF4 module for my research, and you need a snow leopard machine to debug the
module, I think that would be a fair exchange :)

-Sourish

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From [email protected] on December 18, 2009 07:55:57

Sourish: A normal user account should do it. I'll also need to know where you
installed the hdf5 and netcdf4 libs. Thanks.

-Jeff

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From [email protected] on December 18, 2009 10:09:22

The problem's gone! For some reason, "python setup.py install" wasn't overwriting the
old netcdf4_utils.pyc. So deleting that file manually, regenerating netCDF4.c using
cython, and re-doing the "install" step solved the problem :)

-Sourish

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From [email protected] on February 25, 2014 18:04:09

Status: Fixed

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