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How to output numerical array (matrix) out as hdf5 format?

asked 2013-10-08 19:26:33 -0500

chenming gravatar image

I wish to use some other tools to further processing the data generated by sage. the output format should be in hdf5 format. However, it seems very hard to install h5py because it depends on HDF5.

so when i run

./sage --python setup.py build

to install h5py, it say

sh5py/api_compat.h:21:18: fatal error: hdf5.h: No such file or directory

so how do you handle hdf5 format in sage, or do you have anyideas to get around this problem (the dataset may be huge so output into txt file may not be practical.)

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answered 2013-10-09 00:26:02 -0500

chenming gravatar image

I think this is a problem to the linux system i use (Scientifc linux)

Once I tried to compile h5py in another genoo pc, it works great

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answered 2013-10-09 00:48:42 -0500

tmonteil gravatar image

You can try with Sage SPKG still in development:

sage -i https://github.com/downloads/aginiewicz/spkgs/hdf5-1.8.9.spkg
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I tried to install that in my scientific linux but still the same error occurs. It may caused by low version of gcc, not the problem of sage.

chenming gravatar imagechenming ( 2013-10-09 13:35:40 -0500 )edit

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Asked: 2013-10-08 19:26:33 -0500

Seen: 145 times

Last updated: Oct 09 '13