<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Isolated yt environment fixed the
problem.<br>
Thanks for all the help!<br>
<br>
Best Regards,<br>
<br>
Eve<br>
<br>
On 08/06/2013 12:39 AM, Eve Lee wrote:<br>
</div>
<blockquote cite="mid:5200A827.3020909@cita.utoronto.ca" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">On 08/06/2013 12:28 AM, Nathan
Goldbaum wrote:<br>
</div>
<blockquote
cite="mid:CAJXewOmZwLeQwySq6DiVe5AOVeb4PAeDgyhigdNLGb0Z8XnSsg@mail.gmail.com"
type="cite">
<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>
</blockquote>
This seems to be the problem!<br>
'which yt' gives me the old version of yt while importing yt on
python gives me the new version.<br>
<br>
I'll fix this and see if that solves the plotting problem.<br>
<br>
Thanks for the help.<br>
<br>
Best Regards,<br>
<br>
Eve<br>
<br>
<br>
<blockquote
cite="mid:CAJXewOmZwLeQwySq6DiVe5AOVeb4PAeDgyhigdNLGb0Z8XnSsg@mail.gmail.com"
type="cite">
<div dir="ltr">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true">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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true">elee@cita.utoronto.ca</a>>
wrote:<br>
<br>
> I've uploaded the figures
here:<br>
><br>
> <a
moz-do-not-send="true"
href="http://i.imgur.com/7T5N11o.png"
target="_blank">http://i.imgur.com/7T5N11o.png</a><br>
> <a
moz-do-not-send="true"
href="http://i.imgur.com/nOsLfQ9.png"
target="_blank">http://i.imgur.com/nOsLfQ9.png</a><br>
> <a
moz-do-not-send="true"
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
moz-do-not-send="true">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
moz-do-not-send="true">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
moz-do-not-send="true">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>
_______________________________________________<br>
yt-users mailing list<br>
<a moz-do-not-send="true">yt-users@lists.spacepope.org</a><br>
<a moz-do-not-send="true"
href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
_______________________________________________<br>
yt-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:yt-users@lists.spacepope.org"
target="_blank">yt-users@lists.spacepope.org</a><br>
<a moz-do-not-send="true"
href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
yt-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a moz-do-not-send="true"
href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
yt-users mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a>
</pre>
</blockquote>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
yt-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>
<a class="moz-txt-link-freetext" href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a>
</pre>
</blockquote>
<br>
</body>
</html>