18 Sep
2024
18 Sep
'24
3:55 p.m.
Ok, I got something working. I’m using the iaf_cond_exp_neuron model, not the
iaf_psc_exp_neuron. I just renamed it to chris_iaf_cond_exp_neuron. Now when I create it
in pynest, I use chris_iaf_cond_exp_neuron__with_stp_synapse. Similarly, the connect uses
stp_synapse__with_chris_iaf_cond_exp_neuron.
For completeness, I generate using
generate_target(input_path=["/home/chris/CAs/sep24/nestML8_models/chris_iaf_cond_exp_neuron.nestml","/home/chris/CAs/sep24/nestML8_models/stp_synapse.nestml"],target_platform="NEST",target_path="/home/chris/CAs/sep24/nestML8_models/targetdir",codegen_opts={"neuron_synapse_pairs":[{"neuron":"chris_iaf_cond_exp_neuron","synapse":"stp_synapse","post_ports":["post_spikes","chris_iaf_cond_exp_neuron"]}],"delay_variable":{"stp_synapse":"d"},"weight_variable":{"stp_synapse":"w"}})
Thanks for the support.
-Chris
From: Charl Linssen <nest-users(a)turingbirds.com>
Sent: 18 September 2024 14:16
To: users(a)nest-simulator.org
Subject: [NEST Users] Re: stp synapse nestml errror
Hi,
Thanks for the clarifications! This looks like it might be a naming issue. Because there
is already a NEST built-in "iaf_cond_exp" neuron, we append a suffix to it
(typically "_nestml", although you can change this in the call to
generate_code()). Additionally, when you generate the code for a neuron in combination
with a synapse, the model names will be appended to one another, resulting in somewhat
awkwardly long names, like "iaf_psc_exp_neuron_nestml__with_stp_synapse_nestml"
and "stp_synapse_nestml__with_iaf_psc_exp_neuron_nestml". You should be able to
instantiate these after generating the code, more or less as follows:
nest.Install("nestmlmodule")
n = nest.Create("iaf_psc_exp_neuron_nestml__with_stp_synapse_nestml",
2)
nest.Connect(n[0], n[1], syn_spec={"synapse_model":
"stp_synapse_nestml__with_iaf_psc_exp_neuron_nestml"})
nest.Simulate(100)
Hope this helps,
Kind regards,
Charl
On Wed, Sep 18, 2024, at 14:32, Chris Huyck wrote:
I run it from python. After I import generate_target I use
generate_target(input_path=["/home/chris/CAs/sep24/nestML8_models/iaf_cond_exp_neuron.nestml","/home/chris/CAs/sep24/nestML8_models/stp_synapse.nestml"],target_platform="NEST",target_path="/home/chris/CAs/sep24/nestML8_models/targetdir",codegen_opts={"neuron_synapse_pairs":[{"neuron":"iaf_cond_exp_neuron","synapse":"stp_synapse","post_ports":["post_spikes","iaf_cond_exp_neuron"]}],"delay_variable":{"stp_synapse":"d"},"weight_variable":{"stp_synapse":"w"}})
(I’m obliged too. Thanks for the quick response.)
-Chris
From: Charl Linssen
<nest-users@turingbirds.com<mailto:nest-users@turingbirds.com>>
Sent: 18 September 2024 13:27
To: users@nest-simulator.org<mailto:users@nest-simulator.org>
Subject: [NEST Users] Re: stp synapse nestml errror
Hi Chris,
Thank you for the report! That shouldn't be the case; could you perhaps send your
invocation to generate_code() so we can double-check the parameters? It works for me when
I use the following:
codegen_opts = {"neuron_synapse_pairs": [{"neuron":
"iaf_psc_exp_neuron",
"synapse":
"stp_synapse",
"post_ports":
["post_spikes"]}],
"delay_variable": {"stp_synapse":
"d"},
"weight_variable": {"stp_synapse":
"w"}}
input_path = [os.path.join("models", "neurons",
"iaf_psc_exp_neuron.nestml"),
os.path.join("models", "synapses",
"stp_synapse.nestml")]
generate_nest_target(input_path=input_path,
logging_level="DEBUG",
suffix="_nestml",
codegen_opts=codegen_opts)
I am looking into your PyNN issue and will try to report back on that as soon as I can.
Much obliged,
Charl
On Wed, Sep 18, 2024, at 11:46, Chris Huyck wrote:
I’m trying to make a Hebbian Short Term plasticity model. I got the stdp_synapse working,
and then tried to change that to stp. I kept getting the error stp_synapse not found in
pynest. So, I just started from the static synapse, and modified that to get an
stp_synapse that wasn’t Hebbian. When I introduced the post_synaptic neuron into the
model, the stp_synapse not found error returns. Oddly, in the generated files (.h, .cpp,
in stp_synapse__with_iaf_cond_exp_neuron and iaf_cond_exp_neuron__with_stp_synapse) there
is a function for register stdp_synapse. (If you want to duplicate this, just change the
stdp_synapse model name to stp_synapse).
-Chris
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