[yt-users] analyze flash data with uniform grid

[Ji Suoqing]

Hi Matt,

It is:

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.
Updated successfully.

Best wishes,
Suoqing

在 2012-7-28，下午3:54，Matthew Turk <matthewturk at gmail.com> 写道：

> 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
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