LPU to LPU communication problems

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LPU to LPU communication problems

davidgr1995
Hello,

I have created my two LPU circuits using the LPU from neurodriver package.

I have defined the pattern between them: linking two spike out ports on the
1st LPU to two spike in ports on the 2nd LPU. When I use the connections
command from the pattern interface it tells me that the connections are
made. I have then defined a maximum conductance synapse connected to the in
ports. This synapse then leads to a neuron. When I put an input into the 1st
LPU, the 2nd LPU neuron has zero change in it's spike rate.

The KC_axon should be following a very similar spiking pattern to the KC as
these are connected via the ports.
<http://neurokernel.67426.x6.nabble.com/file/t24/KC-Comp_out.png>

I am running in a conda environment. The implementation builds but it's as
if there is no link when I have clearly defined one via the pattern
interface.

Any advice would be great!

David



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Re: LPU to LPU communication problems

Yiyin Zhou
Hi David,

Have you recorded from the in-port to check if the data from LPU1 is propagated to LPU2?
If you can see activity at the in-port, then one possibility is that your synapse model implementation was not found, you should have got a warning in the log saying "Ignoring Model ...: Can not find implementation".
If you cannot see activity at the in-port, something went wrong in the pattern configuration, and it would hard to tell without looking at the code. Can you please send me the relevant code portion for the pattern connection?

Yiyin


On Mon, Jul 23, 2018 at 5:33 PM davidgr1995 <[hidden email]> wrote:
Hello,

I have created my two LPU circuits using the LPU from neurodriver package.

I have defined the pattern between them: linking two spike out ports on the
1st LPU to two spike in ports on the 2nd LPU. When I use the connections
command from the pattern interface it tells me that the connections are
made. I have then defined a maximum conductance synapse connected to the in
ports. This synapse then leads to a neuron. When I put an input into the 1st
LPU, the 2nd LPU neuron has zero change in it's spike rate.

The KC_axon should be following a very similar spiking pattern to the KC as
these are connected via the ports.
<http://neurokernel.67426.x6.nabble.com/file/t24/KC-Comp_out.png>

I am running in a conda environment. The implementation builds but it's as
if there is no link when I have clearly defined one via the pattern
interface.

Any advice would be great!

David



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Yiyin Zhou
Postdoctoral Research Scientist
Department of Electrical Engineering
Columbia University


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Re: LPU to LPU communication problems

davidgr1995
Hi Yiyin,

I added a print in the LPU code for reading the in ports and it seems to
just return 0s for the whole simulation so I think there must be something
with the patterns.
I am basing my current implementation on the examples on the neurodriver
package.
Here is a copy of my LPU creation script and my run script.
run script:  run_lpus.py
<http://neurokernel.67426.x6.nabble.com/file/t24/run_lpus.py>  
lpu creation script:  BasicCompartment_lpus.py
<http://neurokernel.67426.x6.nabble.com/file/t24/BasicCompartment_lpus.py>  

I really hope I haven't made a silly mistake!

David



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Re: LPU to LPU communication problems

Yiyin Zhou
Hi David,

It appears that there are some problems with some new APIs pandas introduced since 0.23.0.
For the moment, if you downgrade pandas to 0.22.0, your code should work fine.
I will look into it further to fix the problem for pandas 0.23.0 and up.

Best,
Yiyin

On Mon, Jul 23, 2018 at 8:24 PM davidgr1995 <[hidden email]> wrote:
Hi Yiyin,

I added a print in the LPU code for reading the in ports and it seems to
just return 0s for the whole simulation so I think there must be something
with the patterns.
I am basing my current implementation on the examples on the neurodriver
package.
Here is a copy of my LPU creation script and my run script.
run script:  run_lpus.py
<http://neurokernel.67426.x6.nabble.com/file/t24/run_lpus.py
lpu creation script:  BasicCompartment_lpus.py
<http://neurokernel.67426.x6.nabble.com/file/t24/BasicCompartment_lpus.py

I really hope I haven't made a silly mistake!

David



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Department of Electrical Engineering
Columbia University


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Re: LPU to LPU communication problems

davidgr1995
Hi Yiyin,

I have downgraded my pandas version to 0.22.0 but the problem persists.

Is there any other reason that the LPUs wont communicate?
My errfile output seems to still mention pandas having issues.

errfile.txt <http://neurokernel.67426.x6.nabble.com/file/t24/errfile.txt>  


David



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Re: LPU to LPU communication problems

Yiyin Zhou
Hi David,

Please pull the latest commits on neurokernel's master branch. The problem was actually not from pandas but networkx (works fine on 1.9 but 2.0+ has problem). Thanks.

Best,
Yiyin


On Tue, Jul 24, 2018 at 7:11 AM davidgr1995 <[hidden email]> wrote:
Hi Yiyin,

I have downgraded my pandas version to 0.22.0 but the problem persists.

Is there any other reason that the LPUs wont communicate?
My errfile output seems to still mention pandas having issues.

errfile.txt <http://neurokernel.67426.x6.nabble.com/file/t24/errfile.txt


David



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Department of Electrical Engineering
Columbia University


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Re: LPU to LPU communication problems

davidgr1995
Hi Yiyin!

Thanks for the support! It seems to be passing the spikes through the ports
now!
I have a few more inquires about setting up different NDComponents but I
will start a new thread with those instead. I do not want to use too much of
your time though so I will send them later and will try to keep them short!

Thanks again!

David



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