matplotlib-devel

[matplotlib-devel] Strange bug when saving animations (with streamplot)

[Tony Yu <ts...@gm...>]

I'm having a tough time figuring this out: Saving an animation seems to
hang when using `streamplot`. The exact same animation runs without issue
when calling show.

On my system, the example below hangs consistently at frame 173. However,
the number of saved frames (before hanging) varies with density of stream
lines (i.e. number of line segments in streamplot): More frames saved for
lower density.

Seems to be a memory or file-size issue, but

   * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
frames to disk as opposed to memory.)
   * Saving the animation up to the frame just before it hangs gives modest
(~1MB) videos.
Maybe this is a limitation of `ffmpeg`?

Can someone confirm that the example hangs on their system? (Somehow, I
often run into bugs that are not reproducible.)

In case this is system dependent:
* OSX 10.6
* Python 2.6.1 (system install)
* matplotlib master
* ffmpeg 0.10

Simple plots seem to work fine, but I should probably try to reproduce
using something other than streamplot (maybe create the equivalent number
of line and arrow collections).

-Tony

#~~~ Example
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation

fig, ax = plt.subplots()

# do nothing function that prints frame
def update(frame_num):
    print frame_num
    return []

Y, X = np.mgrid[:1:100j, :1:100j]
U = np.ones_like(X)
V = np.ones_like(X)
ax.streamplot(X, Y, U, V, density=1)

ani = animation.FuncAnimation(fig, update, save_count=500)

# save hangs at frame 173 (this probably varies by system, if it's
reproducible).
ani.save('animation.avi')
# show animates all frames w/o issue.
#plt.show()

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Tony Yu <ts...@gm...>]

On Sun, Jun 24, 2012 at 10:02 AM, Tony Yu <ts...@gm...> wrote:

> I'm having a tough time figuring this out: Saving an animation seems to
> hang when using `streamplot`. The exact same animation runs without issue
> when calling show.
>
> On my system, the example below hangs consistently at frame 173. However,
> the number of saved frames (before hanging) varies with density of stream
> lines (i.e. number of line segments in streamplot): More frames saved for
> lower density.
>
> Seems to be a memory or file-size issue, but
>
>    * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
> frames to disk as opposed to memory.)
>    * Saving the animation up to the frame just before it hangs gives
> modest (~1MB) videos.
> Maybe this is a limitation of `ffmpeg`?
>
> Can someone confirm that the example hangs on their system? (Somehow, I
> often run into bugs that are not reproducible.)
>
> In case this is system dependent:
> * OSX 10.6
> * Python 2.6.1 (system install)
> * matplotlib master
> * ffmpeg 0.10
>
> Simple plots seem to work fine, but I should probably try to reproduce
> using something other than streamplot (maybe create the equivalent number
> of line and arrow collections).
>
> -Tony
>
> #~~~ Example
> import numpy as np
> import matplotlib.pyplot as plt
> import matplotlib.animation as animation
>
> fig, ax = plt.subplots()
>
> # do nothing function that prints frame
> def update(frame_num):
>     print frame_num
>     return []
>
> Y, X = np.mgrid[:1:100j, :1:100j]
> U = np.ones_like(X)
> V = np.ones_like(X)
> ax.streamplot(X, Y, U, V, density=1)
>
> ani = animation.FuncAnimation(fig, update, save_count=500)
>
> # save hangs at frame 173 (this probably varies by system, if it's
> reproducible).
> ani.save('animation.avi')
> # show animates all frames w/o issue.
> #plt.show()
>
>
>
I finally had some time to revisit this issue. It seems that subprocess
PIPEs have fairly limited buffers [1] (also see docs for
`subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a decent
amount of output to stderr. A simple solution is to redirect stderr to a
temporary file. This change fixes the issue on my system.

If this bug is reproducible, I can submit a PR. The temporary file here
could be created using tempfile so it gets cleaned up automatically, or
maybe a more permanent log file for debugging. Thoughts?

-Tony

[1]
http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/

[2]
http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Tony Yu <ts...@gm...>]

On Mon, Jul 2, 2012 at 11:42 PM, Tony Yu <ts...@gm...> wrote:

>
>
> On Sun, Jun 24, 2012 at 10:02 AM, Tony Yu <ts...@gm...> wrote:
>
>> I'm having a tough time figuring this out: Saving an animation seems to
>> hang when using `streamplot`. The exact same animation runs without issue
>> when calling show.
>>
>> On my system, the example below hangs consistently at frame 173. However,
>> the number of saved frames (before hanging) varies with density of stream
>> lines (i.e. number of line segments in streamplot): More frames saved for
>> lower density.
>>
>> Seems to be a memory or file-size issue, but
>>
>>    * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
>> frames to disk as opposed to memory.)
>>    * Saving the animation up to the frame just before it hangs gives
>> modest (~1MB) videos.
>> Maybe this is a limitation of `ffmpeg`?
>>
>> Can someone confirm that the example hangs on their system? (Somehow, I
>> often run into bugs that are not reproducible.)
>>
>> In case this is system dependent:
>> * OSX 10.6
>> * Python 2.6.1 (system install)
>> * matplotlib master
>> * ffmpeg 0.10
>>
>> Simple plots seem to work fine, but I should probably try to reproduce
>> using something other than streamplot (maybe create the equivalent number
>> of line and arrow collections).
>>
>> -Tony
>>
>> #~~~ Example
>> import numpy as np
>> import matplotlib.pyplot as plt
>> import matplotlib.animation as animation
>>
>> fig, ax = plt.subplots()
>>
>> # do nothing function that prints frame
>> def update(frame_num):
>>     print frame_num
>>     return []
>>
>> Y, X = np.mgrid[:1:100j, :1:100j]
>> U = np.ones_like(X)
>> V = np.ones_like(X)
>> ax.streamplot(X, Y, U, V, density=1)
>>
>> ani = animation.FuncAnimation(fig, update, save_count=500)
>>
>> # save hangs at frame 173 (this probably varies by system, if it's
>> reproducible).
>> ani.save('animation.avi')
>> # show animates all frames w/o issue.
>> #plt.show()
>>
>>
>>
> I finally had some time to revisit this issue. It seems that subprocess
> PIPEs have fairly limited buffers [1] (also see docs for
> `subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a decent
> amount of output to stderr. A simple solution is to redirect stderr to a
> temporary file. This change fixes the issue on my system.
>
> If this bug is reproducible, I can submit a PR. The temporary file here
> could be created using tempfile so it gets cleaned up automatically, or
> maybe a more permanent log file for debugging. Thoughts?
>
> -Tony
>
> [1]
> http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/
>
> [2]
> http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate
>
>
And just to clarify: My original email mentioned that saving would hang
only when `streamplot` was used to create the figure. It turns out that
ffmpeg prints more output (keyframes?) for more complex images, so when I
ran simpler plots, they didn't produce enough output to fill the subprocess
`PIPE` (although they would eventually).

Also, theres's a simpler fix than piping ffmpeg output to a file: Just
set `-loglevel quiet` in the ffmpeg command.

-Tony

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Ryan M. <rm...@gm...>]

On Tue, Jul 3, 2012 at 9:14 AM, Tony Yu <ts...@gm...> wrote:
> On Mon, Jul 2, 2012 at 11:42 PM, Tony Yu <ts...@gm...> wrote:
>> On Sun, Jun 24, 2012 at 10:02 AM, Tony Yu <ts...@gm...> wrote:
>>>
>>> I'm having a tough time figuring this out: Saving an animation seems to
>>> hang when using `streamplot`. The exact same animation runs without issue
>>> when calling show.
>>>
>>> On my system, the example below hangs consistently at frame 173. However,
>>> the number of saved frames (before hanging) varies with density of stream
>>> lines (i.e. number of line segments in streamplot): More frames saved for
>>> lower density.
>>>
>>> Seems to be a memory or file-size issue, but
>>>
>>>    * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
>>> frames to disk as opposed to memory.)
>>>    * Saving the animation up to the frame just before it hangs gives
>>> modest (~1MB) videos.
>>> Maybe this is a limitation of `ffmpeg`?
>>>
>>> Can someone confirm that the example hangs on their system? (Somehow, I
>>> often run into bugs that are not reproducible.)
>>>
>>> In case this is system dependent:
>>> * OSX 10.6
>>> * Python 2.6.1 (system install)
>>> * matplotlib master
>>> * ffmpeg 0.10
>>>
>>> Simple plots seem to work fine, but I should probably try to reproduce
>>> using something other than streamplot (maybe create the equivalent number of
>>> line and arrow collections).
>>>
>>> -Tony
>>>
>>> #~~~ Example
>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> import matplotlib.animation as animation
>>>
>>> fig, ax = plt.subplots()
>>>
>>> # do nothing function that prints frame
>>> def update(frame_num):
>>>     print frame_num
>>>     return []
>>>
>>> Y, X = np.mgrid[:1:100j, :1:100j]
>>> U = np.ones_like(X)
>>> V = np.ones_like(X)
>>> ax.streamplot(X, Y, U, V, density=1)
>>>
>>> ani = animation.FuncAnimation(fig, update, save_count=500)
>>>
>>> # save hangs at frame 173 (this probably varies by system, if it's
>>> reproducible).
>>> ani.save('animation.avi')
>>> # show animates all frames w/o issue.
>>> #plt.show()
>>>
>>>
>>
>> I finally had some time to revisit this issue. It seems that subprocess
>> PIPEs have fairly limited buffers [1] (also see docs for
>> `subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a decent
>> amount of output to stderr. A simple solution is to redirect stderr to a
>> temporary file. This change fixes the issue on my system.
>>
>> If this bug is reproducible, I can submit a PR. The temporary file here
>> could be created using tempfile so it gets cleaned up automatically, or
>> maybe a more permanent log file for debugging. Thoughts?
>>
>> -Tony
>>
>> [1]
>> http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/
>>
>> [2]
>> http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate
>>
>
> And just to clarify: My original email mentioned that saving would hang only
> when `streamplot` was used to create the figure. It turns out that ffmpeg
> prints more output (keyframes?) for more complex images, so when I ran
> simpler plots, they didn't produce enough output to fill the subprocess
> `PIPE` (although they would eventually).
>
> Also, theres's a simpler fix than piping ffmpeg output to a file: Just set
> `-loglevel quiet` in the ffmpeg command.
>
> -Tony

It's not a bad idea to have it logged to a file in a temp directory.
We could potentially just do this if debug is set to verbose, however,
and just use -loglevel quiet otherwise. Can you manage PR for this or
do I need to?

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Tony Yu <ts...@gm...>]

On Tue, Jul 3, 2012 at 10:22 AM, Ryan May <rm...@gm...> wrote:

> On Tue, Jul 3, 2012 at 9:14 AM, Tony Yu <ts...@gm...> wrote:
> > On Mon, Jul 2, 2012 at 11:42 PM, Tony Yu <ts...@gm...> wrote:
> >> On Sun, Jun 24, 2012 at 10:02 AM, Tony Yu <ts...@gm...> wrote:
> >>>
> >>> I'm having a tough time figuring this out: Saving an animation seems to
> >>> hang when using `streamplot`. The exact same animation runs without
> issue
> >>> when calling show.
> >>>
> >>> On my system, the example below hangs consistently at frame 173.
> However,
> >>> the number of saved frames (before hanging) varies with density of
> stream
> >>> lines (i.e. number of line segments in streamplot): More frames saved
> for
> >>> lower density.
> >>>
> >>> Seems to be a memory or file-size issue, but
> >>>
> >>>    * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
> >>> frames to disk as opposed to memory.)
> >>>    * Saving the animation up to the frame just before it hangs gives
> >>> modest (~1MB) videos.
> >>> Maybe this is a limitation of `ffmpeg`?
> >>>
> >>> Can someone confirm that the example hangs on their system? (Somehow, I
> >>> often run into bugs that are not reproducible.)
> >>>
> >>> In case this is system dependent:
> >>> * OSX 10.6
> >>> * Python 2.6.1 (system install)
> >>> * matplotlib master
> >>> * ffmpeg 0.10
> >>>
> >>> Simple plots seem to work fine, but I should probably try to reproduce
> >>> using something other than streamplot (maybe create the equivalent
> number of
> >>> line and arrow collections).
> >>>
> >>> -Tony
> >>>
> >>> #~~~ Example
> >>> import numpy as np
> >>> import matplotlib.pyplot as plt
> >>> import matplotlib.animation as animation
> >>>
> >>> fig, ax = plt.subplots()
> >>>
> >>> # do nothing function that prints frame
> >>> def update(frame_num):
> >>>     print frame_num
> >>>     return []
> >>>
> >>> Y, X = np.mgrid[:1:100j, :1:100j]
> >>> U = np.ones_like(X)
> >>> V = np.ones_like(X)
> >>> ax.streamplot(X, Y, U, V, density=1)
> >>>
> >>> ani = animation.FuncAnimation(fig, update, save_count=500)
> >>>
> >>> # save hangs at frame 173 (this probably varies by system, if it's
> >>> reproducible).
> >>> ani.save('animation.avi')
> >>> # show animates all frames w/o issue.
> >>> #plt.show()
> >>>
> >>>
> >>
> >> I finally had some time to revisit this issue. It seems that subprocess
> >> PIPEs have fairly limited buffers [1] (also see docs for
> >> `subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a
> decent
> >> amount of output to stderr. A simple solution is to redirect stderr to a
> >> temporary file. This change fixes the issue on my system.
> >>
> >> If this bug is reproducible, I can submit a PR. The temporary file here
> >> could be created using tempfile so it gets cleaned up automatically, or
> >> maybe a more permanent log file for debugging. Thoughts?
> >>
> >> -Tony
> >>
> >> [1]
> >>
> http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/
> >>
> >> [2]
> >>
> http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate
> >>
> >
> > And just to clarify: My original email mentioned that saving would hang
> only
> > when `streamplot` was used to create the figure. It turns out that ffmpeg
> > prints more output (keyframes?) for more complex images, so when I ran
> > simpler plots, they didn't produce enough output to fill the subprocess
> > `PIPE` (although they would eventually).
> >
> > Also, theres's a simpler fix than piping ffmpeg output to a file: Just
> set
> > `-loglevel quiet` in the ffmpeg command.
> >
> > -Tony
>
> It's not a bad idea to have it logged to a file in a temp directory.
> We could potentially just do this if debug is set to verbose, however,
> and just use -loglevel quiet otherwise. Can you manage PR for this or
> do I need to?
>
> Ryan
>
>
Hey Ryan,

If you have time, that'd be great. Otherwise, I should have some time at
the end of the week to submit a PR.

-Tony

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Ryan M. <rm...@gm...>]

On Tue, Jul 3, 2012 at 10:03 AM, Tony Yu <ts...@gm...> wrote:
>
>
> On Tue, Jul 3, 2012 at 10:22 AM, Ryan May <rm...@gm...> wrote:
>>
>> On Tue, Jul 3, 2012 at 9:14 AM, Tony Yu <ts...@gm...> wrote:
>> > On Mon, Jul 2, 2012 at 11:42 PM, Tony Yu <ts...@gm...> wrote:
>> >> On Sun, Jun 24, 2012 at 10:02 AM, Tony Yu <ts...@gm...> wrote:
>> >>>
>> >>> I'm having a tough time figuring this out: Saving an animation seems
>> >>> to
>> >>> hang when using `streamplot`. The exact same animation runs without
>> >>> issue
>> >>> when calling show.
>> >>>
>> >>> On my system, the example below hangs consistently at frame 173.
>> >>> However,
>> >>> the number of saved frames (before hanging) varies with density of
>> >>> stream
>> >>> lines (i.e. number of line segments in streamplot): More frames saved
>> >>> for
>> >>> lower density.
>> >>>
>> >>> Seems to be a memory or file-size issue, but
>> >>>
>> >>>    * Memory use doesn't seem to grow. (this suggests that ffmpeg adds
>> >>> frames to disk as opposed to memory.)
>> >>>    * Saving the animation up to the frame just before it hangs gives
>> >>> modest (~1MB) videos.
>> >>> Maybe this is a limitation of `ffmpeg`?
>> >>>
>> >>> Can someone confirm that the example hangs on their system? (Somehow,
>> >>> I
>> >>> often run into bugs that are not reproducible.)
>> >>>
>> >>> In case this is system dependent:
>> >>> * OSX 10.6
>> >>> * Python 2.6.1 (system install)
>> >>> * matplotlib master
>> >>> * ffmpeg 0.10
>> >>>
>> >>> Simple plots seem to work fine, but I should probably try to reproduce
>> >>> using something other than streamplot (maybe create the equivalent
>> >>> number of
>> >>> line and arrow collections).
>> >>>
>> >>> -Tony
>> >>>
>> >>> #~~~ Example
>> >>> import numpy as np
>> >>> import matplotlib.pyplot as plt
>> >>> import matplotlib.animation as animation
>> >>>
>> >>> fig, ax = plt.subplots()
>> >>>
>> >>> # do nothing function that prints frame
>> >>> def update(frame_num):
>> >>>     print frame_num
>> >>>     return []
>> >>>
>> >>> Y, X = np.mgrid[:1:100j, :1:100j]
>> >>> U = np.ones_like(X)
>> >>> V = np.ones_like(X)
>> >>> ax.streamplot(X, Y, U, V, density=1)
>> >>>
>> >>> ani = animation.FuncAnimation(fig, update, save_count=500)
>> >>>
>> >>> # save hangs at frame 173 (this probably varies by system, if it's
>> >>> reproducible).
>> >>> ani.save('animation.avi')
>> >>> # show animates all frames w/o issue.
>> >>> #plt.show()
>> >>>
>> >>>
>> >>
>> >> I finally had some time to revisit this issue. It seems that subprocess
>> >> PIPEs have fairly limited buffers [1] (also see docs for
>> >> `subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a
>> >> decent
>> >> amount of output to stderr. A simple solution is to redirect stderr to
>> >> a
>> >> temporary file. This change fixes the issue on my system.
>> >>
>> >> If this bug is reproducible, I can submit a PR. The temporary file here
>> >> could be created using tempfile so it gets cleaned up automatically, or
>> >> maybe a more permanent log file for debugging. Thoughts?
>> >>
>> >> -Tony
>> >>
>> >> [1]
>> >>
>> >> http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/
>> >>
>> >> [2]
>> >>
>> >> http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate
>> >>
>> >
>> > And just to clarify: My original email mentioned that saving would hang
>> > only
>> > when `streamplot` was used to create the figure. It turns out that
>> > ffmpeg
>> > prints more output (keyframes?) for more complex images, so when I ran
>> > simpler plots, they didn't produce enough output to fill the subprocess
>> > `PIPE` (although they would eventually).
>> >
>> > Also, theres's a simpler fix than piping ffmpeg output to a file: Just
>> > set
>> > `-loglevel quiet` in the ffmpeg command.
>> >
>> > -Tony
>>
>> It's not a bad idea to have it logged to a file in a temp directory.
>> We could potentially just do this if debug is set to verbose, however,
>> and just use -loglevel quiet otherwise. Can you manage PR for this or
>> do I need to?
>>
>> Ryan
>>
>
> Hey Ryan,
>
> If you have time, that'd be great. Otherwise, I should have some time at the
> end of the week to submit a PR.
>
> -Tony
>

I might be able to squeeze it in. If you don't see anything by the end
of the week, hit me up.

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Re: [matplotlib-devel] Strange bug when saving animations (with streamplot)

[Tony Yu <ts...@gm...>]

On Tue, Jul 3, 2012 at 11:18 AM, Ryan May <rm...@gm...> wrote:

> On Tue, Jul 3, 2012 at 10:03 AM, Tony Yu <ts...@gm...> wrote:
> >
> >
> > On Tue, Jul 3, 2012 at 10:22 AM, Ryan May <rm...@gm...> wrote:
> >>
> >> On Tue, Jul 3, 2012 at 9:14 AM, Tony Yu <ts...@gm...> wrote:
> >> > On Mon, Jul 2, 2012 at 11:42 PM, Tony Yu <ts...@gm...> wrote:
>
> >> >> I finally had some time to revisit this issue. It seems that
> subprocess
> >> >> PIPEs have fairly limited buffers [1] (also see docs for
> >> >> `subprocess.Popen.communicate` [2]) and ffmpeg tends to generate a
> >> >> decent
> >> >> amount of output to stderr. A simple solution is to redirect stderr
> to
> >> >> a
> >> >> temporary file. This change fixes the issue on my system.
> >> >>
> >> >> If this bug is reproducible, I can submit a PR. The temporary file
> here
> >> >> could be created using tempfile so it gets cleaned up automatically,
> or
> >> >> maybe a more permanent log file for debugging. Thoughts?
> >> >>
> >> >> -Tony
> >> >>
> >> >> [1]
> >> >>
> >> >>
> http://thraxil.org/users/anders/posts/2008/03/13/Subprocess-Hanging-PIPE-is-your-enemy/
> >> >>
> >> >> [2]
> >> >>
> >> >>
> http://docs.python.org/library/subprocess.html#subprocess.Popen.communicate
> >> >>
> >> >
> >> > And just to clarify: My original email mentioned that saving would
> hang
> >> > only
> >> > when `streamplot` was used to create the figure. It turns out that
> >> > ffmpeg
> >> > prints more output (keyframes?) for more complex images, so when I ran
> >> > simpler plots, they didn't produce enough output to fill the
> subprocess
> >> > `PIPE` (although they would eventually).
> >> >
> >> > Also, theres's a simpler fix than piping ffmpeg output to a file: Just
> >> > set
> >> > `-loglevel quiet` in the ffmpeg command.
> >> >
> >> > -Tony
> >>
> >> It's not a bad idea to have it logged to a file in a temp directory.
> >> We could potentially just do this if debug is set to verbose, however,
> >> and just use -loglevel quiet otherwise. Can you manage PR for this or
> >> do I need to?
> >>
> >> Ryan
> >>
> >
> > Hey Ryan,
> >
> > If you have time, that'd be great. Otherwise, I should have some time at
> the
> > end of the week to submit a PR.
> >
> > -Tony
> >
>
> I might be able to squeeze it in. If you don't see anything by the end
> of the week, hit me up.
>
> Ryan
>
>
Hey Ryan,

I didn't see a PR for this issue, so I just added a fix:

https://github.com/matplotlib/matplotlib/pull/989

As mentioned before, the PR suppresses logging in ffmpeg under normal
circumstances. When the verbosity level is set to debug, however, the
subprocess output (stdout + stderr) are piped to `sys.stdout`. This is
where verbose reports are posted, so I figured that was the best place (oh,
actually, I guess could have piped to `verbose.fileo`).

If you feel the debug output should go to a file instead, let me know.

Cheers,
-Tony