Trouble running examples

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Trouble running examples

bbrown
Hello, I'm have trouble getting any of the examples to work when I run "python visualize_output.py"
I've followed the installation instructions at (https://github.com/neurokernel/neurokernel/wiki/Installation) and even (https://github.com/neurokernel/neurokernel) so I have all the prerequisite software available on my system and in a virtualenv.  But no matter how I run e.g. as " ~/NK/bin/python" or just using the systems environment "python" it get errors.

For instance, using the "Introduction to Neurokernel's API" guide, I run the commands:
    %cd ~/neurokernel/examples/intro/data
    %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz generic_lpu_0_input.h5
    %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz generic_lpu_1_input.h5
And then
    %cd ~/neurokernel/examples/intro
    %python intro_demo.py
And Finially
    %python visualize_output.py
Where I get the errors
    un: [Errno 2] No such file or directory
    co: [Errno 2] No such file or directory

Pastebin of output http://pastebin.com/HK4fSGL9

I'm using Ubuntu 14.10, I'm wondering if my environment is severely different than what is expected, can anyone point me in the right direction?


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Re: Trouble running examples

Lev Givon
Administrator
Received from bbrown on Tue, Mar 31, 2015 at 05:13:27PM EDT:

> Hello, I'm have trouble getting any of the examples to work when I run
> "python visualize_output.py"
> I've followed the installation instructions at
> (https://github.com/neurokernel/neurokernel/wiki/Installation) and even
> (https://github.com/neurokernel/neurokernel) so I have all the prerequisite
> software available on my system and in a virtualenv.  But no matter how I
> run e.g. as " ~/NK/bin/python" or just using the systems environment
> "python" it get errors.
>
> For instance, using the "Introduction to Neurokernel's API" guide, I run the
> commands:
>     %cd ~/neurokernel/examples/intro/data
>     %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz
> generic_lpu_0_input.h5
>     %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz
> generic_lpu_1_input.h5
> And then
>     %cd ~/neurokernel/examples/intro
>     %python intro_demo.py
> And Finially
>     %python visualize_output.py
> Where I get the errors
>     un: [Errno 2] No such file or directory
>     co: [Errno 2] No such file or directory
>
> Pastebin of output http://pastebin.com/HK4fSGL9
>
> I'm using Ubuntu 14.10, I'm wondering if my environment is severely
> different than what is expected, can anyone point me in the right direction?

Hi, Ben.

What files are in examples/intro after you run intro_demo.py?
--
Lev Givon
Bionet Group | Neurokernel Project
http://www.columbia.edu/~lev/
http://lebedov.github.io/
http://neurokernel.github.io/

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Re: Trouble running examples

Benjamin Brown


On 03/31/2015 07:32 PM, Lev Givon wrote:

> Received from bbrown on Tue, Mar 31, 2015 at 05:13:27PM EDT:
>> Hello, I'm have trouble getting any of the examples to work when I run
>> "python visualize_output.py"
>> I've followed the installation instructions at
>> (https://github.com/neurokernel/neurokernel/wiki/Installation) and even
>> (https://github.com/neurokernel/neurokernel) so I have all the prerequisite
>> software available on my system and in a virtualenv.  But no matter how I
>> run e.g. as " ~/NK/bin/python" or just using the systems environment
>> "python" it get errors.
>>
>> For instance, using the "Introduction to Neurokernel's API" guide, I run the
>> commands:
>>      %cd ~/neurokernel/examples/intro/data
>>      %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz
>> generic_lpu_0_input.h5
>>      %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz
>> generic_lpu_1_input.h5
>> And then
>>      %cd ~/neurokernel/examples/intro
>>      %python intro_demo.py
>> And Finially
>>      %python visualize_output.py
>> Where I get the errors
>>      un: [Errno 2] No such file or directory
>>      co: [Errno 2] No such file or directory
>>
>> Pastebin of output http://pastebin.com/HK4fSGL9
>>
>> I'm using Ubuntu 14.10, I'm wondering if my environment is severely
>> different than what is expected, can anyone point me in the right direction?
> Hi, Ben.
>
> What files are in examples/intro after you run intro_demo.py?

After running intro_demo.py these files are created in the directory,

generic_lpu_0_un_output_gpot.h5
generic_lpu_0_co_output_spike.h5
generic_lpu_0_co_output_gpot.h5
generic_lpu_0_un_output_spike.h5
generic_lpu_1_un_output_gpot.h5
generic_lpu_1_co_output_spike.h5
generic_lpu_1_co_output_gpot.h5
generic_lpu_1_un_output_spike.h5

and after I run visualize_output.py the files,

co_0000000.png
un_0000000.png

are created in the directory and then I get the error above.

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Re: Trouble running examples

Lev Givon
Administrator
Received from Benjamin Brown on Wed, Apr 01, 2015 at 02:42:23AM EDT:

>
>
> On 03/31/2015 07:32 PM, Lev Givon wrote:
> >Received from bbrown on Tue, Mar 31, 2015 at 05:13:27PM EDT:
> >>Hello, I'm have trouble getting any of the examples to work when I run
> >>"python visualize_output.py"
> >>I've followed the installation instructions at
> >>(https://github.com/neurokernel/neurokernel/wiki/Installation) and even
> >>(https://github.com/neurokernel/neurokernel) so I have all the prerequisite
> >>software available on my system and in a virtualenv.  But no matter how I
> >>run e.g. as " ~/NK/bin/python" or just using the systems environment
> >>"python" it get errors.
> >>
> >>For instance, using the "Introduction to Neurokernel's API" guide, I run the
> >>commands:
> >>     %cd ~/neurokernel/examples/intro/data
> >>     %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz
> >>generic_lpu_0_input.h5
> >>     %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz
> >>generic_lpu_1_input.h5
> >>And then
> >>     %cd ~/neurokernel/examples/intro
> >>     %python intro_demo.py
> >>And Finially
> >>     %python visualize_output.py
> >>Where I get the errors
> >>     un: [Errno 2] No such file or directory
> >>     co: [Errno 2] No such file or directory
> >>
> >>Pastebin of output http://pastebin.com/HK4fSGL9
> >>
> >>I'm using Ubuntu 14.10, I'm wondering if my environment is severely
> >>different than what is expected, can anyone point me in the right direction?
> >Hi, Ben.
> >
> >What files are in examples/intro after you run intro_demo.py?
>
> After running intro_demo.py these files are created in the directory,
>
> generic_lpu_0_un_output_gpot.h5
> generic_lpu_0_co_output_spike.h5
> generic_lpu_0_co_output_gpot.h5
> generic_lpu_0_un_output_spike.h5
> generic_lpu_1_un_output_gpot.h5
> generic_lpu_1_co_output_spike.h5
> generic_lpu_1_co_output_gpot.h5
> generic_lpu_1_un_output_spike.h5
>
> and after I run visualize_output.py the files,
>
> co_0000000.png
> un_0000000.png
>
> are created in the directory and then I get the error above.

Try commenting out the lines in visualize_output.py starting with

with futures.ProcessPoolExecutor...

and replace with

run('un')

Run the script again and post whatever exception message you observe.
--
Lev Givon
Bionet Group | Neurokernel Project
http://www.columbia.edu/~lev/
http://lebedov.github.io/
http://neurokernel.github.io/

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Re: Trouble running examples

Benjamin Brown


On 04/08/2015 03:50 PM, Lev Givon wrote:

> Received from Benjamin Brown on Wed, Apr 01, 2015 at 02:42:23AM EDT:
>>
>> On 03/31/2015 07:32 PM, Lev Givon wrote:
>>> Received from bbrown on Tue, Mar 31, 2015 at 05:13:27PM EDT:
>>>> Hello, I'm have trouble getting any of the examples to work when I run
>>>> "python visualize_output.py"
>>>> I've followed the installation instructions at
>>>> (https://github.com/neurokernel/neurokernel/wiki/Installation) and even
>>>> (https://github.com/neurokernel/neurokernel) so I have all the prerequisite
>>>> software available on my system and in a virtualenv.  But no matter how I
>>>> run e.g. as " ~/NK/bin/python" or just using the systems environment
>>>> "python" it get errors.
>>>>
>>>> For instance, using the "Introduction to Neurokernel's API" guide, I run the
>>>> commands:
>>>>      %cd ~/neurokernel/examples/intro/data
>>>>      %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz
>>>> generic_lpu_0_input.h5
>>>>      %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz
>>>> generic_lpu_1_input.h5
>>>> And then
>>>>      %cd ~/neurokernel/examples/intro
>>>>      %python intro_demo.py
>>>> And Finially
>>>>      %python visualize_output.py
>>>> Where I get the errors
>>>>      un: [Errno 2] No such file or directory
>>>>      co: [Errno 2] No such file or directory
>>>>
>>>> Pastebin of output http://pastebin.com/HK4fSGL9
>>>>
>>>> I'm using Ubuntu 14.10, I'm wondering if my environment is severely
>>>> different than what is expected, can anyone point me in the right direction?
>>> Hi, Ben.
>>>
>>> What files are in examples/intro after you run intro_demo.py?
>> After running intro_demo.py these files are created in the directory,
>>
>> generic_lpu_0_un_output_gpot.h5
>> generic_lpu_0_co_output_spike.h5
>> generic_lpu_0_co_output_gpot.h5
>> generic_lpu_0_un_output_spike.h5
>> generic_lpu_1_un_output_gpot.h5
>> generic_lpu_1_co_output_spike.h5
>> generic_lpu_1_co_output_gpot.h5
>> generic_lpu_1_un_output_spike.h5
>>
>> and after I run visualize_output.py the files,
>>
>> co_0000000.png
>> un_0000000.png
>>
>> are created in the directory and then I get the error above.
> Try commenting out the lines in visualize_output.py starting with
>
> with futures.ProcessPoolExecutor...
>
> and replace with
>
> run('un')
>
> Run the script again and post whatever exception message you observe.

Like this?
~~~~~~~~~~visualize_output.py~~~~~~~~~

     V.xlim = [0, 1.0]

     V.run()

run('un')

# Run the visualizations in parallel:

#with futures.ProcessPoolExecutor() as executor:

#    fs_dict = {}

#    for out_name in ['un', 'co']:

#        res = executor.submit(run, out_name)

#        fs_dict[out_name] = res

#    futures.wait(fs_dict.values())

     # Report any exceptions that may have occurred:

#    for k in fs_dict:

#        e = fs_dict[k].exception()

#        if e:

#            print '%s: %s' % (k, e)

Output of "python visualize_output.py" follows;

Traceback (most recent call last):

   File "visualize_output.py", line 59, in <module>

     run('un')

   File "visualize_output.py", line 56, in run

     V.run()

   File "/usr/local/lib/python2.7/dist-packages/neurokernel-0.1-py2.7.egg/neurokernel/LPU/utils/visualizer.py", line 168, in run

     self._close()

   File "/usr/local/lib/python2.7/dist-packages/neurokernel-0.1-py2.7.egg/neurokernel/LPU/utils/visualizer.py", line 593, in _close

     self.writer.finish()

   File "/usr/local/lib/python2.7/dist-packages/matplotlib/animation.py", line 370, in finish

     self._run()

   File "/usr/local/lib/python2.7/dist-packages/matplotlib/animation.py", line 204, in _run

     creationflags=subprocess_creation_flags)

   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__

     errread, errwrite)

   File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child

     raise child_exception

OSError: [Errno 2] No such file or directory



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Re: Trouble running examples

Nikul Ukani
Hi Ben,

Please try adding the following line before V.run()  (line 56)

V.FFMpeg = True

Let us know what error, if any, you get after adding the above line.

Nikul

On Thu, Apr 9, 2015 at 7:54 PM, Benjamin Brown <[hidden email]> wrote:


On 04/08/2015 03:50 PM, Lev Givon wrote:
Received from Benjamin Brown on Wed, Apr 01, 2015 at 02:42:23AM EDT:

On 03/31/2015 07:32 PM, Lev Givon wrote:
Received from bbrown on Tue, Mar 31, 2015 at 05:13:27PM EDT:
Hello, I'm have trouble getting any of the examples to work when I run
"python visualize_output.py"
I've followed the installation instructions at
(https://github.com/neurokernel/neurokernel/wiki/Installation) and even
(https://github.com/neurokernel/neurokernel) so I have all the prerequisite
software available on my system and in a virtualenv.  But no matter how I
run e.g. as " ~/NK/bin/python" or just using the systems environment
"python" it get errors.

For instance, using the "Introduction to Neurokernel's API" guide, I run the
commands:
     %cd ~/neurokernel/examples/intro/data
     %python gen_generic_lpu.py -s 0 -l lpu_0 generic_lpu_0.gexf.gz
generic_lpu_0_input.h5
     %python gen_generic_lpu.py -s 1 -l lpu_1 generic_lpu_1.gexf.gz
generic_lpu_1_input.h5
And then
     %cd ~/neurokernel/examples/intro
     %python intro_demo.py
And Finially
     %python visualize_output.py
Where I get the errors
     un: [Errno 2] No such file or directory
     co: [Errno 2] No such file or directory

Pastebin of output http://pastebin.com/HK4fSGL9

I'm using Ubuntu 14.10, I'm wondering if my environment is severely
different than what is expected, can anyone point me in the right direction?
Hi, Ben.

What files are in examples/intro after you run intro_demo.py?
After running intro_demo.py these files are created in the directory,

generic_lpu_0_un_output_gpot.h5
generic_lpu_0_co_output_spike.h5
generic_lpu_0_co_output_gpot.h5
generic_lpu_0_un_output_spike.h5
generic_lpu_1_un_output_gpot.h5
generic_lpu_1_co_output_spike.h5
generic_lpu_1_co_output_gpot.h5
generic_lpu_1_un_output_spike.h5

and after I run visualize_output.py the files,

co_0000000.png
un_0000000.png

are created in the directory and then I get the error above.
Try commenting out the lines in visualize_output.py starting with

with futures.ProcessPoolExecutor...

and replace with

run('un')

Run the script again and post whatever exception message you observe.

Like this?
~~~~~~~~~~visualize_output.py~~~~~~~~~

    V.xlim = [0, 1.0]

    V.run()

run('un')

# Run the visualizations in parallel:

#with futures.ProcessPoolExecutor() as executor:

#    fs_dict = {}

#    for out_name in ['un', 'co']:

#        res = executor.submit(run, out_name)

#        fs_dict[out_name] = res

#    futures.wait(fs_dict.values())

    # Report any exceptions that may have occurred:

#    for k in fs_dict:

#        e = fs_dict[k].exception()

#        if e:

#            print '%s: %s' % (k, e)

Output of "python visualize_output.py" follows;

Traceback (most recent call last):

  File "visualize_output.py", line 59, in <module>

    run('un')

  File "visualize_output.py", line 56, in run

    V.run()

  File "/usr/local/lib/python2.7/dist-packages/neurokernel-0.1-py2.7.egg/neurokernel/LPU/utils/visualizer.py", line 168, in run

    self._close()

  File "/usr/local/lib/python2.7/dist-packages/neurokernel-0.1-py2.7.egg/neurokernel/LPU/utils/visualizer.py", line 593, in _close

    self.writer.finish()

  File "/usr/local/lib/python2.7/dist-packages/matplotlib/animation.py", line 370, in finish

    self._run()

  File "/usr/local/lib/python2.7/dist-packages/matplotlib/animation.py", line 204, in _run

    creationflags=subprocess_creation_flags)

  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__

    errread, errwrite)

  File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory




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--
--
Nikul Ukani

Doctoral Candidate,
Electrical Engineering,
Columbia University.

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Re: Trouble running examples

Benjamin Brown


On 04/11/2015 11:26 AM, Nikul Ukani wrote:

> Hi Ben,
>
> Please try adding the following line before V.run()  (line 56)
>
> V.FFMpeg = True
>
> Let us know what error, if any, you get after adding the above line.
>
> Nikul
>
Thank you, that solved the errors I was receiving. Running "python
./visualize_output.py" now generates a file un.avi, without any error.  
Although it appears to be only one frame, and I'm not sure what the
expected result is :-\  It's at least doing something now :)

Thanks again everyone.

Ben
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Re: Trouble running examples

Lev Givon
Administrator
In reply to this post by Nikul Ukani
Received from Nikul Ukani on Sat, Apr 11, 2015 at 11:26:29AM EDT:
> Hi Ben,
>
> Please try adding the following line before V.run()  (line 56)
>
> V.FFMpeg = True
>
> Let us know what error, if any, you get after adding the above line.
>
> Nikul

If you download the latest revision (e37fb8b), the visualizer class should
automatically determine whether to use ffmpeg or avconv (depending on what is
available) to generate the output animation if visualizer.FFMpeg is set to None
(which is now the default).
--
Lev Givon
Bionet Group | Neurokernel Project
http://www.columbia.edu/~lev/
http://lebedov.github.io/
http://neurokernel.github.io/

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Re: Trouble running examples

Lev Givon
Administrator
Received from Lev Givon on Sun, Apr 12, 2015 at 03:47:51PM EDT:

> Received from Nikul Ukani on Sat, Apr 11, 2015 at 11:26:29AM EDT:
> > Hi Ben,
> >
> > Please try adding the following line before V.run()  (line 56)
> >
> > V.FFMpeg = True
> >
> > Let us know what error, if any, you get after adding the above line.
> >
> > Nikul
>
> If you download the latest revision (e37fb8b), the visualizer class should
> automatically determine whether to use ffmpeg or avconv (depending on what is
> available) to generate the output animation if visualizer.FFMpeg is set to None
> (which is now the default).

Note that this update does add an additional installation dependency to
Neurokernel (shutilwhich).
--
Lev Givon
Bionet Group | Neurokernel Project
http://www.columbia.edu/~lev/
http://lebedov.github.io/
http://neurokernel.github.io/

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Re: Trouble running examples

Lev Givon
Administrator
In reply to this post by Benjamin Brown
Received from Benjamin Brown on Sun, Apr 12, 2015 at 09:48:30AM EDT:

>
> On 04/11/2015 11:26 AM, Nikul Ukani wrote:
> >Hi Ben,
> >
> >Please try adding the following line before V.run()  (line 56)
> >
> >V.FFMpeg = True
> >
> >Let us know what error, if any, you get after adding the above line.
> >
> >Nikul
> >
> Thank you, that solved the errors I was receiving. Running "python
> ./visualize_output.py" now generates a file un.avi, without any
> error.  Although it appears to be only one frame, and I'm not sure
> what the expected result is :-\  It's at least doing something now
> :)

The generated video should look like this:

https://www.youtube.com/watch?v=5eB78fLl1AM
--
Lev Givon
Bionet Group | Neurokernel Project
http://www.columbia.edu/~lev/
http://lebedov.github.io/
http://neurokernel.github.io/

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