netcdf4 and hdf5 and such

its1louder · Posted: Mon May 25, 2009 3:29 am Post subject: netcdf4 and hdf5 and such

I find HDF and netcdf to be building blocks for a lot of other software I need. I find the versions in portage to be too old - hdf5 is only at 1.6.7 and the current is 1.8.3. There is a lot of difference between 1.6*-1.8*. netcdf4 is not supported at all. Interestingly netcdf4 seems to be re-architected with hdf5 as its foundation so the one depends on the other.

Anyway up until now I have been building these things by hand and installing to /usr/local. But it would be nice if there were real up to date ebuilds. I found this one on the bugzilla which kinda worked for me as long as I used USE="fortran -tools -threads".
https://bugs.gentoo.org/233297
basically to make it work you have to get the 1.8.2 ebuild, patch it and change the name to 1.8.3.

but I haven't found anything for netcdf4 or python-netcdf4 that works. I might have to learn how to make them myself but before I do anything hasty I thought I'd see if anyone else has done it first. Thanks!
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its1louder · Posted: Mon May 25, 2009 11:31 pm Post subject:

https://bugs.gentoo.org/264757

this patch works, kinda, but not with the above hdf5 1.8.3. Had to turn of hdf5 support in octave to make it work. This breaks the most recent matlab datafile types.
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its1louder · Posted: Wed Jun 10, 2009 9:12 pm Post subject:

In the end it doesn't work. Not sure why. Compiling by hand to /usr/local prefix works fine and leverages the portage installed szip and zlib.
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shabbychef · n00b Joined: 08 Jun 2005 Posts: 43

I was having problems emerging the 'stable' hdf5-1.6.4 on amd64; I found I had to use gcc-4.1.2 instead of 4.3.*, otherwise emerge would bonk with an uninformative error. fiddling with -fortran and -cxx did not help me. as an experiment, I tried to emerge hdf5-1.8.4-r1, which is ~amd64; it emerged fine under gcc-4.1.2, but gave me the following:

its1louder · Posted: Wed Jan 27, 2010 6:03 am Post subject:

right now I am bringing up a new workstation with unstable funtoo. We'll see if the hdf5 and netcd4 ebuilds work, I have no reason to doubt it other than your post. The portage stable hdf5 is more recent than I need but the netcdf4 is a little stale. Anyway the situation is much better than it was back in the summer when I started this thread. We'll see how they compile on a ~amd64 system.

I'm not using these libs with matlab at all, I do all my scientific programming in python. The python netcdf lib wants netcdf4.1 and HDF5 1.8.3. The next older python lib uses netcdf4.0 so the portage builds will satisfy that. A very satisfactory situation compared to last summer, if it all builds.
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shabbychef · n00b Joined: 08 Jun 2005 Posts: 43

FWIW, I am now able to get hdf5-1.8.4-r1 (marked stable) to emerge on amd64, even under gcc-4.3.4; this is a relatively recent phenomenon.

I only mention Matlab b/c you had mentioned 'octave' in your previous post. To keep compatibility with mathworks .mat file format, I would guess that octave has to use the same hdf5 version as Matlab, which is 1.6.5 for Matlab versions up to R2008b.

cheers,
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shabby