[yt-users] Making slices of Athena SMR data

[Nathan Goldbaum]

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<javascript:_e({}, 'cvml', '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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