HDF5 - Revision history

Admin: /* Python and HDF5 */

2017-10-10T05:42:28Z

Python and HDF5

← Older revision		Revision as of 05:42, 10 October 2017
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	==Python and HDF5==		==Python and HDF5==

	Link: http://docs.h5py.org/en/latest/		Link to docs: http://docs.h5py.org/en/latest/

			Link to quickstart: http://docs.h5py.org/en/latest/quick.html

	Start by creating an HDF5 file object:		Start by creating an HDF5 file object:
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	u'/'		u'/'
	</pre>		</pre>


	=Flags=		=Flags=

	{{Programs}}		{{Programs}}

2017-10-10T02:58:58Z

Errors

← Older revision		Revision as of 02:58, 10 October 2017
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	The solution, as mentioned here http://kartadikaria.wordpress.com/2011/10/06/how-to-install-hdf5-macintosh-lion/, is to modify the configure flags for GNU compilers (the one used on Mac, if you're using gcc). Change the <code>PROD_CFLAG</code> for gcc compilers version 4 and up to use <code>-O0</code> instead of the default <code>-O3</code>.		The solution, as mentioned here http://kartadikaria.wordpress.com/2011/10/06/how-to-install-hdf5-macintosh-lion/, is to modify the configure flags for GNU compilers (the one used on Mac, if you're using gcc). Change the <code>PROD_CFLAG</code> for gcc compilers version 4 and up to use <code>-O0</code> instead of the default <code>-O3</code>.


			=Using=

			==Python and HDF5==

			Link: http://docs.h5py.org/en/latest/

			Start by creating an HDF5 file object:

			<pre>
			>>> import h5py
			>>> import numpy as np
			>>>
			>>> f = h5py.File("mytestfile.hdf5", "w")
			</pre>

			Now that you have a file object, create data sets:

			<pre>
			>>> dset = f.create_dataset("mydataset", (100,), dtype='i')
			</pre>

			(This is not a file, but a dataset object - this is similar to a Numpy array.)

			HDF5 files are stored in a hierarchical way, with a "directory"-like structure.

			<pre>
			>>> dset.name
			u'/mydataset'
			</pre>

			The file object is the root group, equivalent to <code>/</code> on a Unix system:

			<pre>
			>>> f.name
			u'/'
			</pre>


			=Flags=

	{{Programs}}		{{Programs}}

2013-10-09T04:32:11Z

Mac OS X Lion: Use Brew

← Older revision		Revision as of 04:32, 9 October 2013
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	$ brew install hdf5		$ brew install hdf5
	</pre>		</pre>

			UPDATE: HDF5 has since moved to Homebrew-Science (https://github.com/Homebrew/homebrew-science). You can "tap" into Homebrew Science to get to the HDF5 recipe.

	== Configuring ==		== Configuring ==

2013-04-27T16:36:34Z

← Older revision		Revision as of 16:36, 27 April 2013
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	= Installing =		= Installing =

			==Mac OS X Lion: Use Brew==

			If you're on Mac OS X Lion (10.7), you may run into issues. If you're less inclined to get elbow-deep in computer problems, you can just use Homebrew (http://mxcl.github.io/homebrew/), a really nice package manager for Mac OS X. MacPorts and Fink can both be nightmares, but Homebrew manages to do everything hassle-free.

			You can install HDF5 using Homebrew by running:

			<pre>
			$ brew install hdf5
			</pre>

	== Configuring ==		== Configuring ==

2013-04-27T16:30:16Z

← Older revision		Revision as of 16:30, 27 April 2013
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	</syntaxhighlight>		</syntaxhighlight>

	~~Professor James Sutherland [http://www.che.utah.edu/~sutherland/JamesHome/Home.html] also recommends adding~~ the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.		You can optionally use the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.

			==Errors==

			You may run into problems during make check, something looking like this:

			<pre>
			Testing hard normalized long double -> signed char conversions Command terminated by signal 11
			0.31user 0.04system 0:01.64elapsed 21%CPU (0avgtext+0avgdata 19936maxresident)k
			824inputs+360outputs (6major+14996minor)pagefaults 0swaps
			make[4]: *** [dt_arith.chkexe_] Error 1
			</pre>

			The solution, as mentioned here http://kartadikaria.wordpress.com/2011/10/06/how-to-install-hdf5-macintosh-lion/, is to modify the configure flags for GNU compilers (the one used on Mac, if you're using gcc). Change the <code>PROD_CFLAG</code> for gcc compilers version 4 and up to use <code>-O0</code> instead of the default <code>-O3</code>.


	{{Programs}}		{{Programs}}

2011-05-28T16:13:03Z

2010-10-18T21:23:01Z

← Older revision		Revision as of 21:23, 18 October 2010
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	</syntaxhighlight>		</syntaxhighlight>

	James Sutherland also recommends adding the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.		Professor James Sutherland [http://www.che.utah.edu/~sutherland/JamesHome/Home.html] also recommends adding the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.

2010-10-06T06:43:21Z

← Older revision		Revision as of 06:43, 6 October 2010
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	James Sutherland also recommends adding the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.		James Sutherland also recommends adding the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.





			[[Category:Computers]]
			[[Category:Programs]]

2010-10-05T07:56:16Z

← Older revision		Revision as of 07:56, 5 October 2010
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	== Configuring ==		== Configuring ==

	I am using the HDF5 libraries for various software tools available through the CRSim Software repository http://software.crsim.utah.edu/ - specifically, C++ programs using the C++ interface to HDF5:		I am using the HDF5 libraries for various software tools available through the CRSim Software repository http://software.crsim.utah.edu/ - specifically, C++ programs using the C++ interface to HDF5 - necessitating the <code>--enable-cxx</code> configure argument:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	./configure \		./configure \
	--prefix=/~~Users~~/~~charles/pkg~~/hdf5~~-1.8.4~~ \		--prefix=/path/to/hdf5 \
	--enable-cxx		--enable-cxx
	</syntaxhighlight>		</syntaxhighlight>

			James Sutherland also recommends adding the configure arguments <code>--enable-static-exe --enable-static</code>, though in my experience these aren't necessary to build (and link to) HDF5.

2010-10-05T07:51:16Z

← Older revision		Revision as of 07:51, 5 October 2010
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	== Configuring ==		== Configuring ==

	I am using the HDF5 libraries for various software tools [http://software.crsim.utah.edu/], ~~specifically through a~~ C++ interface:		I am using the HDF5 libraries for various software tools available through the CRSim Software repository http://software.crsim.utah.edu/ - specifically, C++ programs using the C++ interface to HDF5:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">