[yt-users] analyze flash data with uniform grid

Ji Suoqing jisuoqing at gmail.com
Sat Jul 28 13:11:29 PDT 2012 

Hi Matt,

I'm grateful for your help.

> The fix I pushed changed line 377 in

Yes, after I modified this by hand, it works well. Thanks!

>  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 recall that before I've applied a patch provided by Nathan on the same file, which might lead to this strange things.

Thanks again!

Best wishes,
Suoqing


在 2012-7-28，下午4:01，Matthew Turk <matthewturk at gmail.com> 写道：

> 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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