On Tue, Oct 2, 2018 at 7:38 AM Wise, John H <jwise@physics.gatech.edu> wrote:

Hi Stephanie,

I actually ran into this bug in the past week. I fixed in for my case
by making this change in clump_handling.py

- elif (child._validate()):
+ elif ((child.children is not None) and child._validate()):

I haven't had the time to submit a PR. If this works for you, let me
know, and I can I create one this week.

Thanks,
John

On 10/01/2018 09:48 PM, Stephanie Tonnesen wrote:
> Hi,
>
> Sorry about the crazy delay, here is a script that reproduces the error
> with the IsolatedGalaxy dataset!
>
> The script is attached. I am happy to help someone look into it, or
> look more myself with a bit of extra guidance.
>
> Thanks!!
>
> Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
>
>
> On Fri, Sep 14, 2018 at 6:51 AM Stephanie Tonnesen <stonnes@gmail.com
> <mailto:stonnes@gmail.com>> wrote:
>
> Hi Britton!
>
> No, I have not resolved the issue, unfortunately. I will try and
> get a script that reproduces the problem up soon.
>
> Best,
> Stephanie
>
> On Thu, Sep 13, 2018 at 7:45 PM Britton Smith
> <brittonsmith@gmail.com <mailto:brittonsmith@gmail.com>> wrote:
>
> HI Stephanie,
>
> Have you managed to resolve this issue? If so, would you be
> willing to submit a pull request to get this fix in the main
> repo? If not, could you post a script that could be used to
> reproduce this error with some of the public data?
>
> Britton
>
> On Fri, Sep 7, 2018 at 1:05 PM Nathan Goldbaum
> <nathan12343@gmail.com <mailto:nathan12343@gmail.com>> wrote:
>
> Generally an error like this is due to a bug in yt. I don't
> know enough about the code you're using to provide useful
> advice, but perhaps we should be checking if `children` is
> `None` and doing something else. The "workaround" is likely
> to fix whatever bug you've run into.
>
> On Fri, Sep 7, 2018 at 2:56 PM, Stephanie Tonnesen
> <stonnes@gmail.com <mailto:stonnes@gmail.com>> wrote:
>
> Hi yt-users!
>
> I have been fiddling some more with yt's clump finder
> and have another question. I want to use density to
> find clumps, but want my maximum threshold value to be
> below the fiducial setting--instead of above the maximum
> possible density in the code I just want the finder to
> stop searching at, say 3.2e-24.
>
> The code was working but running out of memory until I
> set the max threshold, and I now get this error:
>
> ....lots of pleasant looking output messages....
> Updating joins ... : 0%| | 0/7 [00:00<?, ?it/s]
> Updating joins ... : 100%|██████████| 7/7 [00:00<00:00,
> 48933.55it/s]
> yt : [INFO ] 2018-09-07 14:08:55,007 Investigating 2
> children.
> yt : [INFO ] 2018-09-07 14:08:55,007 Finding clumps:
> min: 3.200000e-24, max: 3.200000e-24, step: 2.000000
> yt : [INFO ] 2018-09-07 14:08:55,041 Finding clumps:
> min: 3.200000e-24, max: 3.200000e-24, step: 2.000000
> yt : [INFO ] 2018-09-07 14:08:55,042 Eliminating
> invalid, childless clump with 2 cells.
> yt : [INFO ] 2018-09-07 14:08:55,042 1 of 2 children
> survived, linking its children to parent.
> Traceback (most recent call last):
> File "yt_clump_fingert.py", line 59, in <module>
> find_clumps(master_clump, c_min, c_max, step)
> File
> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
> line 444, in find_clumps
> find_clumps(child, min_val*d_clump, max_val, d_clump)
> File
> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
> line 438, in find_clumps
> find_clumps(clump, min_val*d_clump, max_val, d_clump)
> File
> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
> line 438, in find_clumps
> find_clumps(clump, min_val*d_clump, max_val, d_clump)
> File
> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
> line 438, in find_clumps
> find_clumps(clump, min_val*d_clump, max_val, d_clump)
> File
> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
> line 461, in find_clumps
> for child in clump.children:
> TypeError: 'NoneType' object is not iterable
>
> I tried to circumvent this error by changing my max to
> 2e-24 (not a multiple of 2 of 1e-25), and got the same
> error when the min was 3.2e-24 and the max was 2e-24 (!).
>
> Is there any way I can get around this error and have
> the clumpfinder stop looking once it has clump edges at
> my maximum density?
>
> Thanks!
> Stephanie
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
>
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> --
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
>
>
>
> _______________________________________________
> yt-users mailing list -- yt-users@python.org
> To unsubscribe send an email to yt-users-leave@python.org
>

--
John Wise
Associate Professor of Physics
Center for Relativistic Astrophysics, Georgia Tech
http://cosmo.gatech.edu
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