Problem with HDF5 on install

[dopplershift]

From paul.zak...@gmail.com on August 05, 2010 03:33:21

What steps will reproduce the problem? 1. wget http://netcdf4-python.googlecode.com/files/netCDF4-0.9.1.tar.gz ; tar xvzf netCDF4-0.9.1.tar.gz ; cd netCDF4-0.9.1 ; python setup.py install 2. 3. ---------- What is the expected output? What do you see instead? Expected output : some normal installation log
Instead:
HDF5_DIR environment variable not set, checking some standard locations ..,
checking /root ...
checking /usr/local ...
checking /sw ...
checking /opt ...
checking /opt/local ...
checking /usr ...
Traceback (most recent call last):
File "setup.py", line 47, in
raise ValueError('did not find HDF5 headers and libraries')
ValueError: did not find HDF5 headers and libraries

---------- What version of the product are you using? On what operating system? Mandriva 2010.1
netcdf-python : 0.9.1

hdf5 : hdf5-1.8.4-4mdv2010.1
netcdf : netcdf-4.1.1-1mdv2010.1

---------- Please provide any additional information below. HDF5 is installed. HDF5_DIR is not defined, but HDF5 is in /usr/include so it's easy found by setup.py.
The file H5pubconf.h is present. But! There is no line "#define H5_VERSION".
So setup.py think that there is no HDF5 or it's not a good version.

Finally I installed netcdf4-python using a little hack of setup.py.

$ diff setup.py setup.py.original
40,44d39
< #hack
< hdf5_version = ' 1.8.4'
< direc = '/usr'
< #end of hack
<

After that install works and it seems installed well.
Test says it's ok.

$ cd test ; python run_all.py

.......................................

Ran 39 tests in 4.365s

OK

Original issue: http://code.google.com/p/netcdf4-python/issues/detail?id=63

[dopplershift]

From whitaker.jeffrey@gmail.com on August 07, 2010 19:01:08

I don't understand why the H5_VERSION macro isn't defined in your H5pubconf.h, unless the Mandriva package is messing with this file somehow. If you install it yourself (by building version 1.8.5 or 1.8.4-patch1 from source, outside of the Mandriva packaging system) I bet you will find that macro in there. Would you mind trying that?

-Jeff

[dopplershift]

From joaolsi...@yahoo.com on August 12, 2010 04:15:55

I've had the same problem in 64-bit Fedora 13. It happens because H5_VERSION is defined in H5pubconf-64.h but not in H5pubconf.h. The function check_hdf5version in setup.py first tries to open H5pubconf.h and uses it if it exists. Well at least on Fedora they both exist, so it will fail to find H5_VERSION in H5pubconf.h when it should be looking in H5pubconf-64.h.

[dopplershift]

From whitaker.jeffrey@gmail.com on August 12, 2010 08:48:46

Sounds like a packaging bug to me ...

I've changed the order so that it checks H5pubconf=64.h first. Hopefully that will fix it, can someone check?

-Jeff

[dopplershift]

From fullyion...@gmail.com on January 04, 2012 15:56:12

I am having this problem when building HDF5 from source:

grep VERSION H5pubconf.h
#define H5_PACKAGE_VERSION "1.8.7"
#define VERSION "1.8.7"

I had to modify the setup.py to just use define VERSION. In my build, I am only getting the H5Dpubconf.h file.

I am using the HDF5 configure instead of CMake -- I do not know if that is part of the problem.

[dopplershift]

From whitaker.jeffrey@gmail.com on February 25, 2014 18:04:10

Status: Fixed