4 Aug
2020
4 Aug
'20
8:59 a.m.
Dear Sock Ching,
When you say "I would like to save the network", could you elaborate on what
exact part of the state you want to save and recall? For instance, in case of simulating
plasticity, all the weights can be (re)set by calling SetStatus() on each connection
object. The same goes for neuronal state variables. There are a few things that cannot be
reset at the time of writing, such at the random number generators, but this is only an
issue if you try to reproduce the same run *exactly*, multiple times in a row. The biggest
issue might be that spike buffers (spikes in transit) cannot be reset. Potentially, you
could work around this by allowing a small "startup transient", i.e. ignoring
whatever your network produces in the first few hundred or so milliseconds after starting
simulation. If this startup transient is causing you trouble, however, please feel invited
to submit a feature request on our GitHub repository for spike buffer reset functionality.
(Please provide as much technical detail as possible.)
There is already some prior discussion on this topic at
https://github.com/nest/nest-simulator/issues/1618, where it was decided that just having
a global "ResetNetwork()" function was not feasible, because it is not clear for
the general case what this function would do. So in case you open a new GitHub issue,
please try to specify as precisely as possible what parts of your network state need to be
(re)set.
Hope this helps, please don't hesitate to share your further experiences.
Best regards,
Charl
On Mon, Aug 3, 2020, at 19:19, LOW, SOCK CHING wrote:
Hi,
I am new to pynest and am using it to implement a liquid state machine. It works
marvelously for generating the network. My workflow is as follows:
- Initialise kernel
- Get stimulation episodes
- Create neurons (including spike generators)
- Connect neurons
- nest.Simulate()
- nest.GetStatus(recording_neurons) for readout at relevant timepoints
I would like to save the network so I can run nest.Simulate() on other episodes in a
real-time application, is there a straight-forward way to do so?
I have tried pickling
conn = nest.GetConnections()
but to my knowledge that does not include a lot of details about the connection, like the
weight. It also does not return where there is *no* connections, which means simply using
nest.SetConnections(conn)
prior to nest.Simulate() will not work to reproduce the previously generated network even
if I initialise with all the same variables. I have found the functions GetNetwork() and
GetNodes() but I'm not sure how I can use them, or if they are even useful for what I
need.
Cheers,
Sock Ching
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org