[yt-users] Making slices of Athena SMR data

Eve Lee elee at cita.utoronto.ca
Tue Aug 6 02:22:57 PDT 2013


Isolated yt environment fixed the problem.
Thanks for all the help!

Best Regards,

Eve

On 08/06/2013 12:39 AM, Eve Lee wrote:
> On 08/06/2013 12:28 AM, Nathan Goldbaum wrote:
>> One last thought: Eve, if you're using yt on hyades, can you compare 
>> the output of the following script:
>>
>> import yt
>> print yt.__file__
>>
>> with the output of 'which yt' on the bash command line?  The path of 
>> the yt module should share a common base path with the `yt` command 
>> line tool.  If the paths don't share a common base, it's likely that 
>> you're unintentionally using the old version of yt that lives in the 
>> hyades yt module (in /pfs/sw/yt-x86_64/).
>>
> This seems to be the problem!
> 'which yt' gives me the old version of yt while importing yt on python 
> gives me the new version.
>
> I'll fix this and see if that solves the plotting problem.
>
> Thanks for the help.
>
> Best Regards,
>
> Eve
>
>
>> If you're not on hyades, sorry for the noise - this was a bad guess!
>>
>> However, if that ends up being the problem, I would forego the yt 
>> module on hyades and instead create an isolated yt environment by 
>> running the development version of the install script in your home 
>> folder.
>>
>>
>> On Tue, Aug 6, 2013 at 12:18 AM, John ZuHone <jzuhone at gmail.com 
>> <mailto:jzuhone at gmail.com>> wrote:
>>
>>     This is working for me for both the kh dataset and my cluster
>>     merger dataset, e.g.:
>>
>>     pf = load("id0/cluster.0100.vtk")
>>
>>     but Eve's script "as-is" worked for me as well.
>>
>>     John
>>
>>     On Aug 6, 2013, at 3:13 AM, Nathan Goldbaum
>>     <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
>>
>>>     No, parallel Athena, with a folder for each CPU.  Just to
>>>     clarify, which vtk file are you loading?
>>>
>>>     On Tuesday, August 6, 2013, John ZuHone wrote:
>>>
>>>         I'm not having any trouble loading my parallel SMR datasets
>>>         in 3D.
>>>
>>>         Or by parallel do you mean running yt in parallel?
>>>
>>>         On Aug 6, 2013, at 3:07 AM, Nathan Goldbaum
>>>         <nathan12343 at gmail.com> wrote:
>>>
>>>>         I looked at this earlier with Eve and noticed that there
>>>>         wasn't an obvious way to load a parallel SMR Athena
>>>>         dataset.  I believe Eve's failing data set was produced in
>>>>         parallel and was loaded using the path to the xtk file in
>>>>         the id0 folder.
>>>>
>>>>         It might also help to see your script, specifically the
>>>>         call to 'load()'.
>>>>
>>>>         On Tuesday, August 6, 2013, John ZuHone wrote:
>>>>
>>>>             Hi Eve,
>>>>
>>>>             This is odd. I'm actually getting it to work:
>>>>
>>>>             http://i.imgur.com/iMQttWd.png
>>>>
>>>>             I don't get it, because it looks like your yt is up to
>>>>             date.
>>>>
>>>>             Can you send your athinput.kh <http://athinput.kh/>?
>>>>
>>>>             John
>>>>
>>>>             On Aug 6, 2013, at 12:56 AM, Eve Lee
>>>>             <elee at cita.utoronto.ca> wrote:
>>>>
>>>>             > I've uploaded the figures here:
>>>>             >
>>>>             > http://i.imgur.com/7T5N11o.png
>>>>             > http://i.imgur.com/nOsLfQ9.png
>>>>             > http://i.imgur.com/BfojOOa.png
>>>>             >
>>>>             > Best Regards,
>>>>             >
>>>>             > Eve
>>>>             >
>>>>             > On 08/05/2013 08:56 PM, John ZuHone wrote:
>>>>             >> Also, could you send over some of the figures?
>>>>             >>
>>>>             >> John
>>>>             >>
>>>>             >> On Aug 5, 2013, at 11:30 PM, Eve Lee
>>>>             <elee at cita.utoronto.ca> wrote:
>>>>             >>
>>>>             >>> Hi John,
>>>>             >>>
>>>>             >>> Yes, it is. Thank you for your help.
>>>>             >>>
>>>>             >>> Best Regards,
>>>>             >>>
>>>>             >>> Eve
>>>>             >>>
>>>>             >>> On 08/05/2013 08:29 PM, John ZuHone wrote:
>>>>             >>>> Hi Eve,
>>>>             >>>>
>>>>             >>>> Is this just the 2-D K-H test simulation with SMR?
>>>>             If I could run it myself it would make it easier to debug.
>>>>             >>>>
>>>>             >>>> Best,
>>>>             >>>>
>>>>             >>>> John
>>>>             >>>>
>>>>             >>>> On Aug 5, 2013, at 5:28 PM, Eve Lee
>>>>             <elee at cita.utoronto.ca> wrote:
>>>>             >>>>
>>>>             >>>>> Hi John,
>>>>             >>>>>
>>>>             >>>>> Following is the output from yt instinfo
>>>>             >>>>>
>>>>             >>>>> yt module located at:
>>>>             >>>>>
>>>>             /home/evejlee/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg
>>>>             >>>>> The supplemental repositories are located at:
>>>>             >>>>>  /pfs/sw/yt-x86_64/src/yt-supplemental
>>>>             >>>>>
>>>>             >>>>> The current version of the code is:
>>>>             >>>>>
>>>>             >>>>> ---
>>>>             >>>>> f936432ed45d yt
>>>>             >>>>> ---
>>>>             >>>>>
>>>>             >>>>> Best Regards,
>>>>             >>>>>
>>>>             >>>>> Eve
>>>>             >>>>>
>>>>             >>>>> On 08/05/2013 02:22 PM, John ZuHone wrote:
>>>>             >>>>>> Hi Eve,
>>>>             >>>>>>
>>>>             >>>>>> Sorry that you're having trouble!
>>>>             >>>>>>
>>>>             >>>>>> Just wanted to check real quick before anything
>>>>             else--which version of yt are you using? Also, are you
>>>>             using the stable branch or the development branch?
>>>>             Support for Athena SMR exists in yt versions 2.5.3 and
>>>>             later.
>>>>             >>>>>>
>>>>             >>>>>> Best,
>>>>             >>>>>>
>>>>             >>>>>> John
>>>>             >>>>>>
>>>>             >>>>>> On Aug 5, 2013, at 5:13 PM, Eve Lee
>>>>             <elee at cita.utoronto.ca> wrote:
>>>>             >>>>>>
>>>>             >>>>>>> Hello,
>>>>             >>>>>>>
>>>>             >>>>>>> I'm trying to make a slice plot of Athena MPI
>>>>             SMR data using TimeSeriesData, and I find that the code
>>>>             only make slices out of the base level and blanks out
>>>>             deeper level regions.
>>>>             >>>>>>>
>>>>             >>>>>>> Following is how I read in the Athena vtk files:
>>>>             >>>>>>>
>>>>             >>>>>>> ts =
>>>>             TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True)
>>>>             >>>>>>> my_storage={}
>>>>             >>>>>>> for sto,pf in ts.piter(storage=my_storage):
>>>>             >>>>>>> slc = SlicePlot(pf, 'z', 'Density')
>>>>             >>>>>>> slc.set_zlim('Density', 0.0, 3.0)
>>>>             >>>>>>> num = (pf.h.hierarchy_filename).split('.')[1]
>>>>             >>>>>>> slc.save('./slice/'+num)
>>>>             >>>>>>>
>>>>             >>>>>>> all my vtk files are in id0, ..., idn where
>>>>             n=number of processors I used, and I'm only using 1
>>>>             more level of refinement.
>>>>             >>>
>>>>
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>>>
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