[yt-users] Making slices of Athena SMR data
Eve Lee
elee at cita.utoronto.ca
Tue Aug 6 00:39:19 PDT 2013
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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