[yt-users] annotate_contour takes much longer time to run than expected on some machines

[Nathan Goldbaum]

Might be worth sending a message to the triton sysadmins too.

On Monday, August 10, 2015, John Wise <jwise at physics.gatech.edu> wrote:

> Thanks, Bili.  There could have been some loose ends in the system
> version.  I was confused because this shouldn't have happened with the
> install script, but this sort of clears things up.
>
> Thanks again!
> John
>
> On 08/10/2015 10:03 PM, Bili Dong wrote:
>
>> Hi John,
>>
>> Previously I was using the default mpl provided by the system. Then I
>> installed a local version using `pip install --user matplotlib` without
>> specifying -DNDEBUG explicitly, after which the slowdown was gone. I guess
>> somehow the system default version missed the -DNDEBUG flag while
>> compiling. But I don’t know the details.
>>
>> Regards,
>> Bili
>>
>> On Aug 10, 2015, at 6:54 PM, John Wise <jwise at physics.gatech.edu> wrote:
>>>
>>> Hi,
>>>
>>> I just wanted to follow-up with a question since -DNDEBUG should be
>>> specified by default from the Python installation.  Does anyone know why
>>> CPPFLAGS wasn't passed into mpl's setup.py?
>>>
>>> Bili, did you install yt with the install_script or on top of the
>>> system's or module's Python stack?
>>>
>>> Thanks,
>>> John
>>>
>>> On 08/10/2015 09:27 PM, Bili Dong wrote:
>>>
>>>> I reinstalled matplotlib and it works. Thanks Kacper! You saved my life!
>>>>
>>>> -Bili
>>>>
>>>> On Aug 10, 2015, at 4:30 PM, Kacper Kowalik <xarthisius.kk at gmail.com>
>>>>> wrote:
>>>>>
>>>>> On 08/10/2015 05:10 PM, Bili Dong wrote:
>>>>>
>>>>>> Hi yt-users,
>>>>>>
>>>>>> I’m using yt-3.2 (Changeset = 329b5039b031 stable).
>>>>>>
>>>>>> The problem is that the same script that could finish in seconds on
>>>>>> my local machine will take much  (order of magnitude) longer time to run on
>>>>>> the server I’m using. In some cases, it get stuck for hours that I don’t
>>>>>> know if it will ever finish. I’ve tracked down the bottleneck to be the
>>>>>> `annotate_contour` method. The server should be faster than my local
>>>>>> machine. (I’m not exactly sure about how to compare it. But the server is
>>>>>> generally much faster in other situations.)
>>>>>>
>>>>>> For example, for this script (http://paste.yt-project.org/show/5808/
>>>>>> <http://paste.yt-project.org/show/5808/>), on my local machine the
>>>>>> output shows:
>>>>>>
>>>>>> ```
>>>>>> yt : [INFO     ] 2015-08-10 14:48:15,401 Making a fixed resolution
>>>>>> buffer of (('gas', 'density')) 800 by 800
>>>>>> yt : [INFO     ] 2015-08-10 14:48:15,751 Saving plot
>>>>>> snapshot_200_Projection_z_density.png
>>>>>> yt : [INFO     ] 2015-08-10 14:48:16,716 Saving plot
>>>>>> snapshot_200_Projection_z_density.png
>>>>>> ```
>>>>>>
>>>>>> However, on the server the output shows:
>>>>>> ```
>>>>>> yt : [INFO     ] 2015-08-10 14:51:25,551 Making a fixed resolution
>>>>>> buffer of (('gas', 'density')) 800 by 800
>>>>>> yt : [INFO     ] 2015-08-10 14:51:25,917 Saving plot
>>>>>> snapshot_200_Projection_z_density.png
>>>>>> yt : [INFO     ] 2015-08-10 14:56:21,922 Saving plot
>>>>>> snapshot_200_Projection_z_density.png
>>>>>> ```
>>>>>>
>>>>>> That’s 296 times slower!!!
>>>>>>
>>>>>> This is likely to be a very specific problem with the server. But I’d
>>>>>> like to know if anyone else has encountered similar problems before so I
>>>>>> can learn from your experience. For now, I have no idea what could have
>>>>>> gone wrong.
>>>>>>
>>>>>> BTW, I’m using TSCC (http://idi.ucsd.edu/computing/ <
>>>>>> http://idi.ucsd.edu/computing/>) at UC San Diego, if you happen to
>>>>>> know it.
>>>>>>
>>>>>> Thanks,
>>>>>> Bili
>>>>>>
>>>>>
>>>>> Hi Bili,
>>>>> make sure you pass "-DNDEBUG" to CPPFLAGS when you compile matplotlib.
>>>>> Without it mpl is a good cpu cycle burner.
>>>>> There's a debug routine in triangulation module that's enabled by
>>>>> default.
>>>>> Cheers,
>>>>> Kacper
>>>>>
>>>>>
>>>>>>
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>>>>>>
>>>>>>
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>>>>
>>> --
>>> John Wise
>>> Assistant Professor of Physics
>>> Center for Relativistic Astrophysics, Georgia Tech
>>> http://cosmo.gatech.edu
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>>
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>>
> --
> John Wise
> Assistant Professor of Physics
> Center for Relativistic Astrophysics, Georgia Tech
> http://cosmo.gatech.edu
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