[yt-users] Making slices of Athena SMR data

[John ZuHone]

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> 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?
>> 
>> 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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