[yt-users] problem with slices in non-unitary volumes

Brian O'Shea bwoshea at gmail.com
Wed Dec 23 14:57:02 PST 2015


Actually, interesting followup here - I have to take it back.  When I do a
projection plot:

    yt.ProjectionPlot(ds,'x',("gas",
"temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()

the behavior is perfectly fine and I get projections that look sensible.
 *however*, when I do a slice plot:

   yt.SlicePlot(ds,'x',("gas",
"temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()

I get a malloc error:

yt : [INFO     ] 2015-12-23 17:50:59,082 Gathering a field list (this may
take a moment.)
yt : [INFO     ] 2015-12-23 17:50:59,155 Loading field plugins.
yt : [INFO     ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new
fields)
yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded local (112 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new
fields)
yt : [INFO     ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields)
yt : [INFO     ] 2015-12-23 17:50:59,158 Loaded species (122 new fields)
python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008:
incorrect checksum for freed object - object was probably modified after
being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux
machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get
a seg fault instead of the malloc stuff.  Using pdb (python -m pdb
crashing_script.py) gives me the same error with no additional information.


On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <bwoshea at gmail.com> wrote:

> Bugfix confirmed; this works for me as well.  Thank you very much!
>
> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> I've opened a pull request that allows me to load your dataset:
>>
>>
>> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
>>
>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>
>>> Oh, interesting.  Is there a way to circumvent auto-detection of fields?
>>>
>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> It looks like field detection is breaking for this Enzo-3.0 active
>>>> particle dataset. StoredEnergy is available on-disk as ('AGNParticle,
>>>> 'StoredEnergy'), but for some reason the field detection system isn't able
>>>> to guess that.
>>>>
>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>>> > wrote:
>>>>
>>>>>
>>>>>
>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <bwoshea at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear yt-users,
>>>>>>
>>>>>> I'm having a problem with making slices in non-unitary volumes.  I
>>>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every
>>>>>> dimension (units of megaparsecs), and after I updated to the tip of yt-3
>>>>>> (changeset d9502d848029) from a fairly old version of the code I suddenly
>>>>>> have problems with making simple projections.  If I run this set of
>>>>>> commands:
>>>>>>
>>>>>>
>>>>> Any idea which version you updated from? I tried on yt-3.1 and get the
>>>>> same error. This is just so we can bisect and find the change that
>>>>> introduced the regression.
>>>>>
>>>>>
>>>>>> import yt
>>>>>> ds = yt.load("DD0400/DD0400")
>>>>>> proj =
>>>>>> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>>>>>>
>>>>>> I get this error:
>>>>>>
>>>>>> http://paste.yt-project.org/show/6115/
>>>>>>
>>>>>> This seems to work fine on an Enzo cosmological dataset (domain
>>>>>> bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a
>>>>>> version of the code from a couple of months ago).
>>>>>>
>>>>>> is this a bug, or am I doing something dumb?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> --Brian
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>
>>>>>>
>>>>>
>>>>
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