ASKSAGE: Sage Q&A Forum - Individual question feedhttp://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Wed, 09 Oct 2013 13:35:40 -0500How to output numerical array (matrix) out as hdf5 format?http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/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.)Tue, 08 Oct 2013 19:26:33 -0500http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/Answer by chenming for <p>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.</p>
<p>so when i run </p>
<pre><code>./sage --python setup.py build
</code></pre>
<p>to install h5py, it say</p>
<pre><code>sh5py/api_compat.h:21:18: fatal error: hdf5.h: No such file or directory
</code></pre>
<p>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.)</p>
http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?answer=15530#post-id-15530I 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 greatWed, 09 Oct 2013 00:26:02 -0500http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?answer=15530#post-id-15530Answer by tmonteil for <p>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.</p>
<p>so when i run </p>
<pre><code>./sage --python setup.py build
</code></pre>
<p>to install h5py, it say</p>
<pre><code>sh5py/api_compat.h:21:18: fatal error: hdf5.h: No such file or directory
</code></pre>
<p>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.)</p>
http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?answer=15507#post-id-15507You can try with Sage SPKG [still in development](http://trac.sagemath.org/ticket/8290):
sage -i https://github.com/downloads/aginiewicz/spkgs/hdf5-1.8.9.spkg
Wed, 09 Oct 2013 00:48:42 -0500http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?answer=15507#post-id-15507Comment by chenming for <p>You can try with Sage SPKG <a href="http://trac.sagemath.org/ticket/8290">still in development</a>:</p>
<pre><code>sage -i https://github.com/downloads/aginiewicz/spkgs/hdf5-1.8.9.spkg
</code></pre>
http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?comment=16943#post-id-16943I 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. Wed, 09 Oct 2013 13:35:40 -0500http://ask.sagemath.org/question/10600/how-to-output-numerical-array-matrix-out-as-hdf5-format/?comment=16943#post-id-16943