[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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