[yt-users] Issue loading data with yt

Nathan Goldbaum nathan12343 at gmail.com
Wed Nov 2 13:15:08 PDT 2016


I got it, glad it helped!

On Wed, Nov 2, 2016 at 3:06 PM, Matthew Robert Brinson <mbrinson at uwm.edu>
wrote:

> Hi,
>
> I sent this the other day but I’m not sure if it went through, so
> apologies if you get this twice. The one-liner that you gave me fixed the
> problem.
>
> Thanks so much for your help,
> Matt
>
> On Oct 31, 2016, at 2:17 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> Hi Matthew,
>
> First of all, thank you for the detailed report. That made it much easier
> to track down the issue. Just in case you run into issues in the future and
> want to share larger data files, you can use the yt curldrop for that:
>
> https://docs.hub.yt/services.html#curldrop
>
> As Ben mentioned, your issue is eerily reminiscent of Issue 1084:
>
> https://bitbucket.org/yt_analysis/yt/issues/1084
>
> This was fixed last year by Ben Keller in PR 1735:
>
> https://bitbucket.org/yt_analysis/yt/pull-requests/1735
>
> However, it turns out that the implementation in PR 1735 had a bug that
> your test script revealed. I think there's a one-liner fix:
>
> https://bitbucket.org/yt_analysis/yt/pull-requests/2430
>
> If you want to test out that fix, that would be very much appreciated. The
> easiest way to do so is to modify your current yt installation by hand (you
> can find it's location by looking at yt.__file__). That said, if you have
> time I'd recommend compiling yt from source:
>
> $ # get rid of old yt installation via conda or pip
> $ pip uninstall yt
> $ conda uninstall yt
>
> $ hg clone https://bitbucket.org/yt_analysis/yt ./yt-hg
> $ cd yt-hg
>
> $ # pull bugfix from Nathan's fork of yt and update to bugfix changeset
> $ hg pull -u -r 1a290fab65e4 https://bitbucket.org/ngoldbaum/yt
>
> $ # compile yt
> $ python setup.py develop
>
> This will build yt from source. It may take a few minutes because it will
> need to compile yt's C extensions. Once that's done, try rerunning your
> test script.
>
> -Nathan
>
> On Mon, Oct 31, 2016 at 10:27 AM, B.W. Keller <kellerbw at mcmaster.ca>
> wrote:
>
>> Hi Matt,
>>
>> This sounds similar to a bug that I (thought)  I had fixed a while back.
>> I'll take a look at your issue, see if I can reproduce it and put in a fix.
>>
>> Ben
>>
>> On Mon, Oct 31, 2016 at 11:06 AM, Matthew Robert Brinson <
>> mbrinson at uwm.edu> wrote:
>>
>>> Hi yt-users,
>>>
>>> Let’s try this again. The file I sent the first time was too large.
>>>
>>> I’m using yt version 3.3.1, and I’ve recently encountered an issue
>>> loading data correctly. I’m running SPH simulations of white dwarf mergers
>>> and want to know what the mass fractions of different elements are at
>>> different times. I have two files that contain the data: 1) a tipsy file,
>>> 2) and a text file that contains the mass fraction values of helium-4. The
>>> tipsy file loads just fine and I’m able to access the information from the
>>> helium file once the tipsy file is loaded. For some reason though, when I
>>> have more than 262144 particles in my simulation, yt does not load the
>>> helium mass fraction values correctly anymore. I’ve initialized all
>>> particles to have a 4% helium mass fraction, and all of the particles up to
>>> and including the particle indexed by 262143 have this value, but after
>>> that the particles all have 0% according to yt. I’ve checked the helium
>>> files directly and all values are at 4%. I’m confused as to why yt would
>>> stop loading values correctly after a certain point.
>>>
>>> I’ve included two tipsy files as well as their corresponding helium mass
>>> fraction files. I have also written a script called
>>> visualization_test_script.py that makes scatter plots of the white dwarfs
>>> showing particles that have correct and incorrect values of helium. I can
>>> send more tipsy files if necessary, but they are too large to send any more
>>> here.
>>>
>>> Thanks,
>>> Matt
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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