<div dir="ltr">One last thought: Eve, if you're using yt on hyades, can you compare the output of the following script:<div><br></div><div>import yt</div><div>print yt.__file__</div><div><br></div><div>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/).</div>
<div><br></div><div>If you're not on hyades, sorry for the noise - this was a bad guess!</div><div><br></div><div>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.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 6, 2013 at 12:18 AM, John ZuHone <span dir="ltr"><<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">This is working for me for both the kh dataset and my cluster merger dataset, e.g.:<div>
<br></div><div>pf = load("id0/cluster.0100.vtk")</div><div><br></div><div>but Eve's script "as-is" worked for me as well.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>John</div>
</font></span><div><div class="h5"><div><br><div><div>On Aug 6, 2013, at 3:13 AM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><blockquote type="cite">
No, parallel Athena, with a folder for each CPU. Just to clarify, which vtk file are you loading?<span></span><br><br>On Tuesday, August 6, 2013, John ZuHone wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">I'm not having any trouble loading my parallel SMR datasets in 3D. <div><br></div><div>Or by parallel do you mean running yt in parallel?</div><div><br><div><div>On Aug 6, 2013, at 3:07 AM, Nathan Goldbaum <<a>nathan12343@gmail.com</a>> wrote:</div>
<br><blockquote type="cite">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.<span></span><div>
<br></div><div>It might also help to see your script, specifically the call to 'load()'.<br><div><br>On Tuesday, August 6, 2013, John ZuHone wrote:<br><blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Eve,<br>
<br>
This is odd. I'm actually getting it to work:<br>
<br>
<a href="http://i.imgur.com/iMQttWd.png" target="_blank">http://i.imgur.com/iMQttWd.png</a><br>
<br>
I don't get it, because it looks like your yt is up to date.<br>
<br>
Can you send your <a href="http://athinput.kh/" target="_blank">athinput.kh</a>?<br>
<br>
John<br>
<br>
On Aug 6, 2013, at 12:56 AM, Eve Lee <<a>elee@cita.utoronto.ca</a>> wrote:<br>
<br>
> I've uploaded the figures here:<br>
><br>
> <a href="http://i.imgur.com/7T5N11o.png" target="_blank">http://i.imgur.com/7T5N11o.png</a><br>
> <a href="http://i.imgur.com/nOsLfQ9.png" target="_blank">http://i.imgur.com/nOsLfQ9.png</a><br>
> <a href="http://i.imgur.com/BfojOOa.png" target="_blank">http://i.imgur.com/BfojOOa.png</a><br>
><br>
> Best Regards,<br>
><br>
> Eve<br>
><br>
> On 08/05/2013 08:56 PM, John ZuHone wrote:<br>
>> Also, could you send over some of the figures?<br>
>><br>
>> John<br>
>><br>
>> On Aug 5, 2013, at 11:30 PM, Eve Lee <<a>elee@cita.utoronto.ca</a>> wrote:<br>
>><br>
>>> Hi John,<br>
>>><br>
>>> Yes, it is. Thank you for your help.<br>
>>><br>
>>> Best Regards,<br>
>>><br>
>>> Eve<br>
>>><br>
>>> On 08/05/2013 08:29 PM, John ZuHone wrote:<br>
>>>> Hi Eve,<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> Best,<br>
>>>><br>
>>>> John<br>
>>>><br>
>>>> On Aug 5, 2013, at 5:28 PM, Eve Lee <<a>elee@cita.utoronto.ca</a>> wrote:<br>
>>>><br>
>>>>> Hi John,<br>
>>>>><br>
>>>>> Following is the output from yt instinfo<br>
>>>>><br>
>>>>> yt module located at:<br>
>>>>> /home/evejlee/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg<br>
>>>>> The supplemental repositories are located at:<br>
>>>>> /pfs/sw/yt-x86_64/src/yt-supplemental<br>
>>>>><br>
>>>>> The current version of the code is:<br>
>>>>><br>
>>>>> ---<br>
>>>>> f936432ed45d yt<br>
>>>>> ---<br>
>>>>><br>
>>>>> Best Regards,<br>
>>>>><br>
>>>>> Eve<br>
>>>>><br>
>>>>> On 08/05/2013 02:22 PM, John ZuHone wrote:<br>
>>>>>> Hi Eve,<br>
>>>>>><br>
>>>>>> Sorry that you're having trouble!<br>
>>>>>><br>
>>>>>> 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.<br>
>>>>>><br>
>>>>>> Best,<br>
>>>>>><br>
>>>>>> John<br>
>>>>>><br>
>>>>>> On Aug 5, 2013, at 5:13 PM, Eve Lee <<a>elee@cita.utoronto.ca</a>> wrote:<br>
>>>>>><br>
>>>>>>> Hello,<br>
>>>>>>><br>
>>>>>>> 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.<br>
>>>>>>><br>
>>>>>>> Following is how I read in the Athena vtk files:<br>
>>>>>>><br>
>>>>>>> ts = TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True)<br>
>>>>>>> my_storage={}<br>
>>>>>>> for sto,pf in ts.piter(storage=my_storage):<br>
>>>>>>> slc = SlicePlot(pf, 'z', 'Density')<br>
>>>>>>> slc.set_zlim('Density', 0.0, 3.0)<br>
>>>>>>> num = (pf.h.hierarchy_filename).split('.')[1]<br>
>>>>>>> slc.save('./slice/'+num)<br>
>>>>>>><br>
>>>>>>> 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.<br>
>>></blockquote></div></div>
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