Opened 11 years ago
Last modified 6 months ago
#8290 needs_info enhancement
Support HDF5
Reported by: | magawake | Owned by: | GeorgSWeber |
---|---|---|---|
Priority: | major | Milestone: | sage-wishlist |
Component: | packages: optional | Keywords: | hdf5 h5py hdf5python |
Cc: | Merged in: | ||
Authors: | Andrzej Giniewicz | Reviewers: | |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
We would like to have hdf5 support into sage. This will include the C/C++ bindings and also should have the Java bindings.
To obtain HDF5: http://www.hdfgroup.org/HDF5/release/obtain5.html
Current version of spkg (install in order):
Change History (28)
comment:1 Changed 11 years ago by
comment:2 Changed 11 years ago by
Thanks. Couple of requirements
- Have it completely independent therefore be shipped with SAGE
- Have all the C/C++ bindings includes into the SAGE tar ball
comment:3 Changed 11 years ago by
- Keywords hdf5python added
comment:4 Changed 11 years ago by
I also made an hdf5 library spkg, but the hdf5 version is evidently too new for h5py:
http://www.hdfgroup.org/ftp/HDF5/prev-releases/hdf5-1.8.0/src/hdf5-1.8.0.tar.gz
since compiling this, then h5py does not work.
comment:5 Changed 11 years ago by
- Status changed from new to needs_review
Hi,
So if you build
http://sage.math.washington.edu/home/wstein/patches/hdf5-1.6.9.spkg
and
http://sage.math.washington.edu/home/wstein/patches/h5py-1.2.1.spkg
then it should work. Example, do:
sage -f http://sage.math.washington.edu/home/wstein/patches/hdf5-1.6.9.spkg http://sage.math.washington.edu/home/wstein/patches/h5py-1.2.1.spkg
I'm posting this for inclusion in the *experimental* repo.
comment:6 Changed 11 years ago by
Example:
Here's a trivial example showing how to create a new HDF5 file and store a 100 x 20 array of floats: >>> f = h5py.File("myfile.hdf5", 'w') >>> f["MyDataset"] = numpy.ones((100,20)) And to get your data back: >>> dset = f["MyDataset"] >>> subset = dset[20:80,:]
comment:7 Changed 11 years ago by
Is it possible to have atleast hdf 1.8.2? 1.6.x is too old. Most of our files are 1.8.x format.
comment:8 Changed 11 years ago by
pyTables might also be an option. For comparison, see http://www.pytables.org/moin/FAQ#HowdoesPyTablescomparewiththeh5pyproject.3F and http://code.google.com/p/h5py/wiki/FAQ#What%27s_the_difference_between_h5py_and_PyTables_?
comment:9 Changed 11 years ago by
Also, on the front page of the h5py project, it says "Transparently supports both HDF5 1.6 and 1.8.".
comment:10 Changed 11 years ago by
On http://code.google.com/p/h5py/wiki/FAQ, it says that Linux supports up to 1.8.3.
comment:11 Changed 11 years ago by
On http://code.google.com/p/h5py/wiki/FAQ, it says that Linux supports up to 1.8.3.
comment:12 Changed 11 years ago by
actually h5py should support hdf5 up to 1.8.4 an PyTables? up to 1.8.3. I'd say sage should use hdf5 1.8, it's first version to introduce external links and utf8 encoded strings so two things that seems to be quite important, right?
comment:13 Changed 11 years ago by
comment:14 Changed 10 years ago by
I made quick update of those to hdf5 1.8, also this version of h5py works with hdf5 from spkg (at least it works for me - only had to specify "--hdf=$SAGE_LOCAL" to build script).
http://lab15.im.pwr.wroc.pl/~giniew/h5py-1.3.0.spkg
http://lab15.im.pwr.wroc.pl/~giniew/hdf5-1.8.4.spkg (actually, it's 1.8.4 patch 1, latest supported by h5py at time of writing - wasn't sure if I should add the patch1 to name here).
They are based on packages posted here earlier - just updated the src to pointed h5py to local hdf5 copy.
comment:15 Changed 9 years ago by
- Status changed from needs_review to needs_info
Ping. These spkgs no longer exist.
comment:16 Changed 9 years ago by
- Status changed from needs_info to needs_review
Well, after a year I forgot about it - the files are present, but url changed. For now I don't have time to update them though (h5py is now 2.0.1 and hdf5 is 1.8.8). Anyway, working links:
http://im.pwr.wroc.pl/~giniew/h5py-1.3.0.spkg
and
comment:17 Changed 8 years ago by
- Description modified (diff)
I've updated spkgs with latest versions. Also, those spkgs now contains repositories and better descriptions in SPKG.txt files (description, license, dependencies, changelog - usual stuff). I've also added links to description to not hunt for them in comments
comment:18 Changed 8 years ago by
Please fill in your real name as Author.
comment:19 Changed 8 years ago by
comment:20 Changed 8 years ago by
- Component changed from build to packages
- Status changed from needs_review to needs_info
Are these supposed to be standard packages, optional packages or experimental packages?
comment:21 Changed 8 years ago by
In its current state (i.e. only hdf5+h5py) it might be not that useful to include in standard spkg. I believe it could be optional package. But if some other packages would be compiled with hdf5 support (especially R, which is standard package) situation might change. This is of course only my opinion and it might be not mirror others opinion.
Anyway, I got e-mail that h5py package got broken during upload to github. I had to recreate and reupload it (now, I will not trust github any more and keep other copy around) - it should work now.
comment:22 Changed 8 years ago by
This would be really useful for making data interchangeable with other computing platforms. I look forward to seeing this included in Sage by default :).
comment:23 Changed 7 years ago by
- Milestone changed from sage-5.11 to sage-5.12
comment:24 Changed 7 years ago by
- Milestone changed from sage-6.1 to sage-6.2
comment:25 Changed 7 years ago by
- Milestone changed from sage-6.2 to sage-6.3
comment:26 Changed 6 years ago by
- Milestone changed from sage-6.3 to sage-6.4
comment:27 Changed 6 years ago by
- Component changed from packages: standard to packages: optional
comment:28 Changed 6 months ago by
- Milestone changed from sage-6.4 to sage-wishlist
Setting spkg proposals that have not seen recent activity to "sage-wishlist".
Here is a quick spkg that works if you have libhdf5 devel packages installed on your computer:
http://sage.math.washington.edu/home/wstein/patches/h5py-1.2.1.spkg
Install it with