[yt-svn] commit/yt-doc: 3 new changesets
Bitbucket
commits-noreply at bitbucket.org
Tue Feb 19 06:41:44 PST 2013
3 new commits in yt-doc:
https://bitbucket.org/yt_analysis/yt-doc/commits/889b59afb591/
changeset: 889b59afb591
user: MatthewTurk
date: 2013-02-19 15:39:21
summary: Removing some spectral frequency integrator docs that are not needed
affected #: 1 file
diff -r a8c617f1aee7175c1cca8f34e6e88661be73e0a7 -r 889b59afb5919532725a5f805e91f64da4dde483 source/api/api.rst
--- a/source/api/api.rst
+++ b/source/api/api.rst
@@ -300,8 +300,6 @@
:toctree: generated/
~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum
- ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.SpectralFrequencyIntegrator
- ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.create_table_from_textfiles
~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.EmissivityIntegrator
~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.add_xray_emissivity_field
~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.add_xray_luminosity_field
@@ -501,7 +499,6 @@
~yt.config.YTConfigParser
~yt.analysis_modules.hierarchy_subset.hierarchy_subset.ConstructedRootGrid
~yt.analysis_modules.hierarchy_subset.hierarchy_subset.ExtractedHierarchy
- ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.SpectralFrequencyIntegrator
~yt.utilities.parameter_file_storage.ParameterFileStore
~yt.data_objects.data_containers.FakeGridForParticles
~yt.utilities.parallel_tools.parallel_analysis_interface.ObjectIterator
https://bitbucket.org/yt_analysis/yt-doc/commits/d0ab1174bf6e/
changeset: d0ab1174bf6e
user: MatthewTurk
date: 2013-02-19 15:39:39
summary: Merge
affected #: 3 files
diff -r 889b59afb5919532725a5f805e91f64da4dde483 -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 source/advanced/parallel_computation.rst
--- a/source/advanced/parallel_computation.rst
+++ b/source/advanced/parallel_computation.rst
@@ -13,8 +13,7 @@
Capabilities
------------
-Currently, YT is able to
-perform the following actions in parallel:
+Currently, YT is able to perform the following actions in parallel:
* Projections (:ref:`projection-plots`)
* Slices (:ref:`slice-plots`)
@@ -39,10 +38,60 @@
To run scripts in parallel, you must first install
`mpi4py <http://code.google.com/p/mpi4py>`_.
-Instructions for doing so are provided on the mpi4py website. Once that has
-been accomplished, you're all done! You just need to launch your scripts with
-``mpirun`` (or equivalent) and signal to YT
-that you want to run them in parallel.
+Instructions for doing so are provided on the mpi4py website, but you may
+have luck by just running:
+
+.. code-block:: bash
+
+ $ pip install mpi4py
+
+Once that has been installed, you're all done! You just need to launch your
+scripts with ``mpirun`` (or equivalent) and signal to YT that you want to run
+them in parallel. In general, that's all it takes to get a speed benefit on a
+multi-core machine. Here is an example on an 8-core desktop:
+
+.. code-block:: bash
+
+ $ mpirun -np 8 python script.py --parallel
+
+Throughout its normal operation, yt keeps you aware of what is happening with
+regular messages to the stderr usually prefaced with:
+
+.. code-block:: bash
+
+ yt : [INFO ] YYY-MM-DD HH:MM:SS
+
+However, when operating in parallel mode, yt outputs information from each
+of your processors to this log mode, as in:
+
+.. code-block:: bash
+
+ P000 yt : [INFO ] YYY-MM-DD HH:MM:SS
+ P001 yt : [INFO ] YYY-MM-DD HH:MM:SS
+
+in the case of two cores being used.
+
+It's important to note that all of the processes listed in `capabilities` work
+-- and no additional work is necessary to parallelize those processes.
+Furthermore, the ``yt`` command itself recognizes the ``--parallel`` option, so
+those commands will work in parallel as well.
+
+The Derived Quantities and Profile objects must both have the ``lazy_reader``
+option set to ``True`` when they are instantiated. What this does is to
+operate on a grid-by-grid decomposed basis. In ``yt`` version 1.5 and the
+trunk, this has recently been set to be the default.
+
+.. warning:: If you manually interact with the filesystem, not through YT, you
+ will have to ensure that you only execute your functions on the root
+ processor. You can do this with the function :func:`only_on_root`.
+
+yt.pmods
+--------
+
+yt.pmods is a replacement module for yt.mods, which can be enabled in
+the ``from yt.mods import *`` calls in yt scripts. It should enable
+more efficient use of parallel filesystems, if you are running on such a
+system.
For instance, the following script, which we'll save as ``my_script.py``:
@@ -55,35 +104,19 @@
p = ProjectionPlot(pf, "x", "Density")
p.save()
-Will execute the finding of the maximum density and the projection in parallel
-if launched in parallel.
-Note that the usual ``from yt.mods import *`` has been replaced by
-``from yt.pmods import *``.
-The pmods option gives the same result as reglar mods, but it can speed up
-the initialization process when running in parallel.
-To do so, at the command line you would execute
+will execute the finding of the maximum density and the projection in parallel
+if launched in parallel. Note that the usual ``from yt.mods import *`` has
+been replaced by ``from yt.pmods import *``.
+To run this script at the command line you would execute:
.. code-block:: bash
$ mpirun -np 16 python2.7 my_script.py --parallel
-if you wanted it to run in parallel. If you run into problems, the you can use
+if you wanted it to run in parallel on 16 cores (you can always the number of
+cores you want to run on). If you run into problems, the you can use
:ref:`remote-debugging` to examine what went wrong.
-.. warning:: If you manually interact with the filesystem, not through YT, you
- will have to ensure that you only execute your functions on the root
- processor. You can do this with the function :func:`only_on_root`.
-
-It's important to note that all of the processes listed in `capabilities` work
--- and no additional work is necessary to parallelize those processes.
-Furthermore, the ``yt`` command itself recognizes the ``--parallel`` option, so
-those commands will work in parallel as well.
-
-The Derived Quantities and Profile objects must both have the ``lazy_reader``
-option set to ``True`` when they are instantiated. What this does is to
-operate on a grid-by-grid decomposed basis. In ``yt`` version 1.5 and the
-trunk, this has recently been set to be the default.
-
Types of Parallelism
--------------------
diff -r 889b59afb5919532725a5f805e91f64da4dde483 -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 source/changelog.rst
--- a/source/changelog.rst
+++ b/source/changelog.rst
@@ -138,6 +138,7 @@
* Particles can now be created ex nihilo with CICSample_3.
* Rockstar halo finding is now a targeted goal. Support for using Rockstar
has improved dramatically.
+ * Increased support for tracking halos across time using the FOF halo finder.
* The command ``yt notebook`` has been added to spawn an IPython notebook
server, and the ``yt.imods`` module can replace ``yt.mods`` in the IPython
Notebook to enable better integration.
diff -r 889b59afb5919532725a5f805e91f64da4dde483 -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 source/cookbook/rendering_with_box_and_grids.py
--- a/source/cookbook/rendering_with_box_and_grids.py
+++ b/source/cookbook/rendering_with_box_and_grids.py
@@ -48,10 +48,10 @@
# Add the domain edges, with an alpha blending of 0.3:
cam.draw_domain(im, alpha=0.3)
-write_bitmap('%s_vr_domain.png' % pf)
+write_image(im, '%s_vr_domain.png' % pf)
# Add the grids, colored by the grid level with the algae colormap
cam.draw_grids(im, alpha=0.3, cmap='algae')
-write_bitmap('%s_vr_grids.png' % pf)
+write_image(im, '%s_vr_grids.png' % pf)
https://bitbucket.org/yt_analysis/yt-doc/commits/2bc0ca9761b8/
changeset: 2bc0ca9761b8
user: MatthewTurk
date: 2013-02-19 15:41:31
summary: Merge
affected #: 4 files
diff -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 -r 2bc0ca9761b86d84964955f5d080bd09932f879d source/advanced/installing.rst
--- a/source/advanced/installing.rst
+++ b/source/advanced/installing.rst
@@ -48,24 +48,29 @@
numbers are those used by the installation script -- ``yt`` may work with lower
versions or higher versions, but these are known to work.
- * Python-2.7.2, but not (yet) 3.0 or higher
+ * Python-2.7.3, but not (yet) 3.0 or higher
* NumPy-1.6.1 (at least 1.4.1)
- * HDF5-1.8.7 or higher (at least 1.8.7)
- * h5py-2.0.1 (2.0 fixes a major bug)
- * Matplotlib-1.1.0 or higher
- * Mercurial-2.0 or higher (anything higher than 1.5 works)
- * Cython-0.15.1 or higher (at least 0.15.1)
+ * HDF5-1.8.9 or higher (at least 1.8.7)
+ * h5py-2.1.0 (2.0 fixes a major bug)
+ * Matplotlib-1.2.0 or higher
+ * Mercurial-2.5.1 or higher (anything higher than 1.5 works)
+ * Cython-0.17.1 or higher (at least 0.15.1)
Optional Libraries
++++++++++++++++++
These libraries are all optional, but they are highly recommended.
- * Forthon-0.8.5 or higher (for halo finding and correlation functions)
- * libpng-1.2.43 or higher (for raw image outputting)
+ * Forthon-0.8.10 or higher (for halo finding and correlation functions)
+ * libpng-1.5.12 or higher (for raw image outputting)
* FreeType-2.4.4 or higher (for text annotation on raw images)
- * IPython-0.11 (0.10 will also work)
- * ExtJS 3.3.1 and PhiloGL 1.4.2 (for Reason, the yt GUI)
+ * IPython-0.13.1 (0.10 will also work)
+ * PyX-0.11.1
+ * zeromq-2.2.0 (needed for IPython notebook)
+ * pyzmq-2.2.11 (needed for IPython notebook)
+ * tornado-2.2 (needed for IPython notebook)
+ * sympy-0.7.2
+ * nose-1.2.1
If you are attempting to install manually, and you are not installing into a
fully-isolated location, you should probably use your system's package
@@ -114,7 +119,17 @@
Ubuntu PPAs
+++++++++++
-We do not yet provide PPAs for Ubuntu, but we hope to in the near future.
+Mike Kuhlen has kindly provided PPAs for Ubuntu. If you're running Ubuntu, you
+can install these easily:
+
+.. code-block:: bash
+
+ $ sudo add-apt-repository ppa:kuhlen
+ $ sudo apt-get update
+ $ sudo apt-get install yt
+
+If you'd like a development branch of yt, you can change yt for yt-devel to get
+the most recently packaged development branch.
MacPorts
++++++++
diff -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 -r 2bc0ca9761b86d84964955f5d080bd09932f879d source/advanced/plugin_file.rst
--- a/source/advanced/plugin_file.rst
+++ b/source/advanced/plugin_file.rst
@@ -7,6 +7,8 @@
objects and so on without modifying the source code of yt. The plugin file
will be executed if it is detected, and it must be::
+.. code-block:: bash
+
$HOME/.yt/my_plugins.py
The code in this file can thus add fields, add derived quantities, add
diff -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 -r 2bc0ca9761b86d84964955f5d080bd09932f879d source/analysis_modules/radial_column_density.rst
--- a/source/analysis_modules/radial_column_density.rst
+++ b/source/analysis_modules/radial_column_density.rst
@@ -1,4 +1,4 @@
-.. _radial_column_density:
+.. _radial-column-density:
Radial Column Density
=====================
diff -r d0ab1174bf6ee02835341b2c94975e3f57e6d679 -r 2bc0ca9761b86d84964955f5d080bd09932f879d source/changelog.rst
--- a/source/changelog.rst
+++ b/source/changelog.rst
@@ -242,7 +242,7 @@
(see :ref:`within-reason`)
* Performance improvements for volume rendering
* Adaptive HEALpix support (see :ref:`adaptive_healpix_volume_rendering`)
- * Column density calculations (see :ref:`radial_column_density`)
+ * Column density calculations (see :ref:`radial-column-density`)
* Massive speedup for 1D profiles
* Lots more, bug fixes etc.
* Substantial improvements to the documentation, including
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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