[yt-users] analyze flash data with uniform grid

Matthew Turk matthewturk at gmail.com
Sat Jul 28 12:54:11 PDT 2012 

Hi Suoqing,

What is the current output of "yt instinfo"?  It should read
2ace6373d8a3 .  If it doesn't, you'll need to manually pull again:

hg pull https://bitbucket.org/yt_analysis/yt
hg up
python2.7 setup.py develop

-Matt

On Sat, Jul 28, 2012 at 3:52 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
> Hi Matt,
>
> Thanks for your prompt response!
>
> I'm not quite sure whether my update is successful or not, but it shows:
>
> ----------------------------------------------------------------------------
> yt module located at:
>     /aphelion/jisuoqing/yt-x86_64/src/yt-hg
> The supplemental repositories are located at:
>     /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
>
> The current version of the code is:
>
> ---
> 2ace6373d8a3+ (yt) tip
> ---
>
> This installation CAN be automatically updated.
> Reading configuration from  /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc
> searching for changes
> no changes found
> Can't rebuild modules by myself.
> You will have to do this yourself.  Here's a sample commands:
>
>     $ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg
>     $ hg up
>     $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop
> Updated successfully.
> ----------------------------------------------------------------------------
>
> And I've also rebuilt the modules as what the sample tells.
>
>
> ----------------------------------------------------------------------------
> (yt-x86_64)[jisuoqing at hpcmanage yt-hg]$ hg up
> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved
> (yt-x86_64)[jisuoqing at hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop
> PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
> FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
> HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
> running develop
> running build_scripts
> running egg_info
> running build_src
> build_src
> building py_modules sources
> building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources
> building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources
> building extension "yt.frontends.ramses._ramses_reader" sources
> building extension "yt.utilities.delaunay._delaunay" sources
> building extension "yt.utilities.spatial.ckdtree" sources
> building extension "yt.utilities.spatial._distance_wrap" sources
> building extension "yt.utilities.lib.CICDeposit" sources
> building extension "yt.utilities.lib.ContourFinding" sources
> building extension "yt.utilities.lib.DepthFirstOctree" sources
> building extension "yt.utilities.lib.fortran_reader" sources
> building extension "yt.utilities.lib.freetype_writer" sources
> building extension "yt.utilities.lib.geometry_utils" sources
> building extension "yt.utilities.lib.Interpolators" sources
> building extension "yt.utilities.lib.marching_cubes" sources
> building extension "yt.utilities.lib.misc_utilities" sources
> building extension "yt.utilities.lib.Octree" sources
> building extension "yt.utilities.lib.png_writer" sources
> building extension "yt.utilities.lib.PointsInVolume" sources
> building extension "yt.utilities.lib.QuadTree" sources
> building extension "yt.utilities.lib.RayIntegrators" sources
> building extension "yt.utilities.lib.VolumeIntegrator" sources
> building extension "yt.utilities.lib.grid_traversal" sources
> building extension "yt.utilities.data_point_utilities" sources
> building extension "yt.utilities.hdf5_light_reader" sources
> building extension "yt.utilities.libconfig_wrapper" sources
> building extension "yt.visualization._MPL" sources
> building data_files sources
> build_src: building npy-pkg config files
> writing yt.egg-info/PKG-INFO
> writing top-level names to yt.egg-info/top_level.txt
> writing dependency_links to yt.egg-info/dependency_links.txt
> writing entry points to yt.egg-info/entry_points.txt
> reading manifest file 'yt.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> writing manifest file 'yt.egg-info/SOURCES.txt'
> running build_ext
> customize UnixCCompiler
> customize UnixCCompiler using build_ext
> customize UnixCCompiler
> customize UnixCCompiler using build_ext
> running scons
> Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .)
> yt 2.4dev is already the active version in easy-install.pth
> Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin
> Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin
> Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin
> Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin
>
> Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg
> Processing dependencies for yt==2.4dev
> Finished processing dependencies for yt==2.4dev
> ----------------------------------------------------------------------------
>
> But the file-load error still remains.
>
> Best wishes,
> Suoqing
>
>
> 在 2012-7-28，下午3:35，Matthew Turk <matthewturk at gmail.com> 写道：
>
>> Hi Suoqing,
>>
>> On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
>>> Hi all,
>>>
>>> Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
>>>
>>>>>> pf=load('relax_hdf5_chk_0000')
>>> Traceback (most recent call last):
>>>  File "<stdin>", line 1, in <module>
>>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load
>>>    return output_type_registry[candidates[0]](*args, **kwargs)
>>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__
>>>    StaticOutput.__init__(self, filename, data_style)
>>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__
>>>    self._parse_parameter_file()
>>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file
>>>    self.min_level = self.parameters["lrefine_min"] -1
>>> KeyError: 'lrefine_min'
>>>
>>> So, does YT provides a way to deal with the uniform grid?
>>
>> If FLASH4 either doesn't set that parameter anymore or had conditional
>> parameter setting, that will need to be taken into account in the
>> future.  I've checked and it looks like this parameter is optional (it
>> will default to L0) and so I've added a check for it.  If it's not
>> present, it sets it to be the most lenient.  This was done in the
>> current development branch, in changeset 2ace6373d8a3, so you will
>> need to update with "yt update".
>>
>> Thanks,
>>
>> Matt
>>
>>>
>>> Thanks for your care and consideration.
>>>
>>> Best wishes,
>>> Suoqing
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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