[yt-users] analyze flash data with uniform grid

Matthew Turk matthewturk at gmail.com
Sat Jul 28 13:01:40 PDT 2012 

Hi Suoqing,

The fix I pushed changed line 377 in
yt/frontends/flash/data_structures.py from its original value (seen in
your traceback) of:

self.min_level = self.parameters["lrefine_min"] -1

to:

self.min_level = self.parameters.get("lrefine_min", 1) - 1

If your traceback still indicates that the old line is present,
something strange is going on.  I note that you've modified the source
(the "+" at the end of the hash) -- is it possible that the change
you've made has somehow interfered?

I have checked that my fix should work in the case of the parameter
"lrefine_min" not existing.  What's the output of:

grep lrefine_min /aphelion/jisuoqing/yt-x86_64/include,
/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py

thanks,


-Matt



On Sat, Jul 28, 2012 at 3:57 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
> 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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