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Subsetting and executing a small subset of the Allen V1 model (layer23) using cpp intermediate objects where possible.
by Russell Jarvis 28 Jan '23

28 Jan '23

Hi there, I would like to subset and execute the subset of the Allen V1 model. I am also hoping to store intermediate simulation configuration files not as Python code, but if possible as cpp code. I am wondering if there is a way of storing the matrices in a cpp native way? Forinstance I have noticed the class https://github.com/nest/nest-simulator/blob/master/nestkernel/connection_ma… I think that this would class may have I acquired the config.json file from DropBox and all of the assoicated hdf5, and csv files from here: https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAB0B6OLRyLJwxCKjuWrG26pa/simula… I have found the nodes in the model pertaining to only layer 23 by wrangling data frames in Julia (see the code below). Calling the method `extract_subset` is slower than I would like. I suspect it would be faster to use the SL or /nest_kernel more directly, but I don't know what interventions I would need to do to get the PyNest instance to dump its intermediate objects in a cpp native way. I wonder if any one has any hints on how to do this? subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") For instance I would like to be able to use the nestkernel CLI to save using Pkg using Conda using PyCall ENV["PYTHON"] = $HOME/.julia/conda/3/lib/python3.10/ Pkg.build("PyCall") py""" def init_sim_to_call_from_julia():#slice_start,slice_end,nest=None,sim=None) import os, sys import math import numpy as np from bmtk.simulator import pointnet from bmtk.simulator.pointnet.pyfunction_cache import synaptic_weight from bmtk.simulator.pointnet.io_tools import io import nest import h5py try: nest.Install('glifmodule') except Exception as e: pass @synaptic_weight def DirectionRule_others(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) return syn_weight * w_multiplier_180 * nsyn @synaptic_weight def DirectionRule_EE(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values x_tar = trg_nodes['x'].values x_src = src_nodes['x'].values z_tar = trg_nodes['z'].values z_src = src_nodes['z'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) delta_x = (x_tar - x_src) * 0.07 delta_z = (z_tar - z_src) * 0.04 theta_pref = tar_tuning * (np.pi / 180.) xz = delta_x * np.cos(theta_pref) + delta_z * np.sin(theta_pref) sigma_phase = 1.0 phase_scale_ratio = np.exp(- (xz ** 2 / (2 * sigma_phase ** 2))) # To account for the 0.07 vs 0.04 dimensions. This ensures the horizontal neurons are scaled by 5.5/4 (from the # midpoint of 4 & 7). Also, ensures the vertical is scaled by 5.5/7. This was a basic linear estimate to get the # numbers (y = ax + b). theta_tar_scale = abs(abs(abs(180.0 - np.mod(np.abs(tar_tuning), 360.0)) - 90.0) - 90.0) phase_scale_ratio = phase_scale_ratio * (5.5 / 4.0 - 11.0 / 1680.0 * theta_tar_scale) return syn_weight * w_multiplier_180 * phase_scale_ratio * nsyn def main(config_file): configure = pointnet.Config.from_json(config_file) configure.build_env() graph = pointnet.PointNetwork.from_config(configure) sim = pointnet.PointSimulator.from_config(configure, graph) node_info = list(graph.get_node_populations()) dfv1 = node_info[0].nodes_df() pop_names = { k:v for k,v in zip(dfv1.index,dfv1["pop_name"].values) } dfv1e = dfv1[dfv1["ei"] == "e"].index dfv1i = dfv1[dfv1["ei"] == "i"].index dfv1e_pop = dfv1[dfv1["ei"] == "e"]["pop_name"].values dfv1i_pop = dfv1[dfv1["ei"] == "i"]["pop_name"].values lgn = node_info[1].nodes_df() lgne = lgn[lgn["ei"] == "e"].index return nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names #,lgni nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names = main('config.json') # ,lgni return (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) """ (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) = py"init_sim_to_call_from_julia"() function get_layer_sub_net(target) subset = Int64[] for (k,v) in pairs(pop_names) if v==target println(k,v) append!(subset,k) end end subset end subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") layer_23_ids = [] layer_23_ids = vcat(layer_23_ids,subset0) layer_23_ids = vcat(layer_23_ids,subset1) layer_23_ids = vcat(layer_23_ids,subset2) layer_23_ids = vcat(layer_23_ids,subset3) py"""def get_conns_from_py_nest(nest,sim,slice_start,nodes=None): conns = nest.GetConnections(nest.NodeCollection([slice_start])) nodes = nest.NodeCollection([slice_start]) node_ = nodes.get() dict_ = conns.get() return (dict_["source"],dict_["target"],dict_["weight"]) """ function extract_subset(nest,sim,subset) N = 230924+1#+17400#230901 exc_matrix = spzeros(N,N) @inbounds for srcv in ProgressBars.ProgressBar(subset) result = py"get_conns_from_py_nest"(nest,sim,srcv) @inbounds for (x,y,z) in zip(Vector{Int64}(result[1]),Vector{Int64}(result[2]),Vector{Float64}(result[3])) exc_matrix[y,x] = z end end exc_matrix end exc_matrix = extract_subset(nest,sim,layer_23_ids) Thanks for your help :) Russell.

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NEST 3.3 installation error
by Petia Koprinkova 16 Jan '23

16 Jan '23

Dear NEST Developers, We are trying to install NEST 3.3 on a Linux machine in Windows 11 desktop computer and the following error report was obtained: -- Docs:https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /nest-3.3.0-build/reports/07_pynesttests.xml - =========================== short testsummary info ============================ FAILED share/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing_bools FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_slice_with_unsorted_raisesFAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_array_list FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_additional_synspec_params FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_different_weights_delays FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_differnt_alpha FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_float_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_delays FAILED share/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_weights FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique_dict_conn_spec FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_receptor_type FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_threaded =========== 15 failed, 669 passed, 15skipped, 27 warnings in 43.13s =========== make[3]: *** [CMakeFiles/installcheck.dir/build.make:71:CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:465:CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:472:CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:179: installcheck]Error 2 Could you please help to resolve it?Best regards,Petia Koprinkova-Hristova

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Open NEST Developer Video Conference Monday Jan 16 2023 11:30 CET (UTC+1)
by Dennis Terhorst 16 Jan '23

16 Jan '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 16, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2023-01-16-Open-NEST-Developer-… Looking forward to seeing you! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Error installing extension module
by bstrohmer＠gmail.com 13 Jan '23

13 Jan '23

I would like to install a custom neuron model in NEST so I followed the instructions for the nest-extension-module. It is able to build the .so files but it errors during the final install of the project as seen in the below message. Install the project... -- Install configuration: "" -- Installing: /home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py", line 444 err = AttributeError(f"Cannot set attribute '{attr}' on module 'nest'") I am trying to install one of the example neurons provided first (pif_psc_alpha) so I do not expect that it is an issue within the source files. Thanks for any advice in correcting this issue!

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stdp_dopamine_synapse model
by Behnam Ghazinouri 05 Jan '23

05 Jan '23

Hi all, Happy new year! I have a question about the "stdp_dopamine_synapse" model. In the documentation, they mentioned that they used it as a benchmark the model in [1], based on [2]. In [1], in the section "2.2 Benchmark Network Models", they have C_1 and C_2. They just mentioned these two parameters are constant coefficients. My question is: Does NEST implement these equations? If yes, how can I find the values of C_1 and C_2? (they are not listed under the nest.GetValues() and are not in the table of the documentation). If not, what is the exact model that the NEST implemented for "stdp_dopamine_synapse"? Best regards, Behnam [1] Potjans W, Morrison A, Diesmann M (2010). Enabling functional neural circuit simulations with distributed computing of neuromodulated plasticity. Frontiers in Computational Neuroscience, 4:141. DOI: https://doi.org/10.3389/fncom.2010.00141 <https://doi.org/10.3389/fncom.2010.00141> [2] Izhikevich EM (2007). Solving the distal reward problem through linkage of STDP and dopamine signaling. Cerebral Cortex, 17(10):2443-2452. DOI: https://doi.org/10.1093/cercor/bhl152 <https://doi.org/10.1093/cercor/bhl152>

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Open NEST Developer Video Conference Monday Dec 19 2022 11:30 CET (UTC+1)
by Dennis Terhorst 19 Dec '22

19 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 19, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-12-19-Open-NEST-Developer-… As I will not be joining today, I delegated chairing the meeting. Looking forward to seeing you again next year! Merry Christmas and a happy new year! Cheers, Dennis Terhorst :*) ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
by 王梓瑞 08 Dec '22

08 Dec '22

Dear nest community, I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml. I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding. Is there any way to acquire the .nestml file of the cm_default neuron model? Thank you. Best, Zirui

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Open NEST Developer Video Conference Monday Dec 5 2022 11:30 CET (UTC+1)
by Dennis Terhorst 05 Dec '22

05 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 5, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are / Hackathon Results / As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-12-05-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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docker questions
by 1538356357＠qq.com 05 Dec '22

05 Dec '22

I use Docker to create a nest environment. The version is v2.16.0 But when I execute the code as follows，vt_dummy = nest.Create("global_volume_transmitter", 1, {'deliver_interval': 10})， , I encounter an error, the error is pynestkernel.NESTError: UnknownModelName in GetDefaults_l: /global_volume_transmitter is not a known model name. Please check the modeldict for a list of available models . but after I use the nest2.16 source code to install, the same code executes successfully. I don't know why

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About Polling Algorithm
by 1538356357＠qq.com 22 Nov '22

22 Nov '22

Dear NEST community： We all know that distributed computing is carried out in Nest, and neurons are distributed to each neuron through polling. However, considering the load balancing and sparsity of communication, this is a NP hard problem. Should we adopt some other methods, such as directed graph segmentation technology. Whether this will be considered in Nest, or whether graph segmentation is helpful in SNN simulation. If you can spare time to reply, thank you very much

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