February 2022 - NEST Users - NEST Initiative Mail

Assertion error during connection when using CopyModel and own neuron model
by Barna Zajzon 07 Oct '22

07 Oct '22

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

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Nest 3.0 conda installation issue using source code
by Maryada Maryada 13 Apr '22

13 Apr '22

Dear NEST users, After trying multiple ideas, I am still facing the issue where my installation is successful with an error message: -- Configuring done CMake Warning at cmake/UseCython.cmake:100 (add_library): Cannot generate a safe runtime search path for target pynestkernel because files in some directories may conflict with libraries in implicit directories: runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/9 may be hidden by files in: /home/<user>/miniconda3/envs/nestConda/lib Some of these libraries may not be found correctly. Call Stack (most recent call first): cmake/UseCython.cmake:283 (python_add_module) pynest/CMakeLists.txt:28 (cython_add_module) ------------------------------------------------------------------------------------------------ This leads to the failure of multiple tests. The summary of the tests and logs for the failed tests is attached. I must mention that I tested the installation by creating a neuron and it works fine. It would be nice to get rid of the error, please see error_msg file to see where it fails. -- Thanks and Regards *Maryada*

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Error in NESTML when I run the 'NESTML Izhikevich tutorial'
by Salvo T 28 Feb '22

28 Feb '22

Dear NESTML Users, In the last post I fixed a problem that was related to the fact that in the 'izhikevich_solution.nestml' the first line was commented. Now, after following the guide in "https://nestml.readthedocs.io/en/latest/installation.html" related to the NESTML installation, I tried to follow the NESTML Izhikevich tutorial in "https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…". After installing the cmake with "pip install cmake", when I execute the following part of the tutorial: generate_nest_target(input_path="izhikevich_solution.nestml", target_path="/tmp/nestml-component", logging_level="ERROR", codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) I obtain the following error: Warning: PyGSL is not available. The stiffness test will be skipped. Warning: No module named 'pygsl' Option "nest_path" does not exist in builder --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 149 try: --> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell, 151 cwd=str(os.path.join(target_path))) /usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs) 363 cmd = popenargs[0] --> 364 raise CalledProcessError(retcode, cmd) 365 return 0 CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) <ipython-input-2-f0909be085f4> in <module> ----> 1 generate_nest_target(input_path="izhikevich_solution.nestml", 2 target_path="/tmp/nestml-component", 3 module_name="nestml_izhikevich_module", 4 suffix="_nestml", 5 logging_level="ERROR", /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 181 A dictionary containing additional options for the target code generator. 182 """ --> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, 184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path, 185 dev=dev, codegen_opts=codegen_opts) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 150 FrontendConfiguration.set_codegen_opts(codegen_opts) 151 --> 152 if not process() == 0: 153 raise Exception("Error(s) occurred while processing the model") 154 /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process() 278 options=FrontendConfiguration.get_codegen_opts()) 279 if _builder is not None: --> 280 _builder.build() 281 282 if FrontendConfiguration.store_log: /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 151 cwd=str(os.path.join(target_path))) 152 except subprocess.CalledProcessError as e: --> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') 154 155 # finally execute make install GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout. So, the "nest_path" keyword does not exist. Can anyone help me? Best, Salvo

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Error in NESTML when I run the 'NESTML Izhikevich tutorial'
by Salvo T 28 Feb '22

28 Feb '22

Hi, after following the guide in "https://nestml.readthedocs.io/en/latest/installation.html" related to the NESTML installation, I tried to follow the NESTML Izhikevich tutorial in "https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…". After installing the cmake with "pip install cmake", when I execute the following part of the tutorial: generate_nest_target(input_path="izhikevich_solution.nestml", target_path="/tmp/nestml-component", logging_level="ERROR", codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) I obtain the following error: line 3:2 extraneous input 'state' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 4:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 8:2 extraneous input 'equations' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 9:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 10:4 extraneous input 'u' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 11:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 13:2 extraneous input 'parameters' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 14:4 extraneous input 'a' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 20:2 extraneous input 'input' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 21:4 extraneous input 'spikes' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 22:4 extraneous input 'I_e' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 23:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 25:2 extraneous input 'output' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 27:2 extraneous input 'update' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 28:4 extraneous input 'integrate_odes' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 31:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 34:4 extraneous input 'if' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 35:6 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 36:6 extraneous input 'u' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 37:6 extraneous input 'emit_spike' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 38:4 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 40:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 42:0 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} [5,GLOBAL, ERROR]: Error occurred during parsing: abort --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 149 try: --> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell, 151 cwd=str(os.path.join(target_path))) /usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs) 363 cmd = popenargs[0] --> 364 raise CalledProcessError(retcode, cmd) 365 return 0 CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) <ipython-input-5-5d459438a659> in <module> ----> 1 generate_nest_target(input_path="izhikevich_solution.nestml", 2 target_path="/tmp/nestml-component", 3 logging_level="ERROR", 4 codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 181 A dictionary containing additional options for the target code generator. 182 """ --> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, 184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path, 185 dev=dev, codegen_opts=codegen_opts) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 150 FrontendConfiguration.set_codegen_opts(codegen_opts) 151 --> 152 if not process() == 0: 153 raise Exception("Error(s) occurred while processing the model") 154 /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process() 278 options=FrontendConfiguration.get_codegen_opts()) 279 if _builder is not None: --> 280 _builder.build() 281 282 if FrontendConfiguration.store_log: /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 151 cwd=str(os.path.join(target_path))) 152 except subprocess.CalledProcessError as e: --> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') 154 155 # finally execute make install GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout. I can't solve it. Can anyone help me?

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Open NEST Developer Video Conference Monday February 28 2022 11:30 CET (UTC+1)
by Dennis Terhorst 28 Feb '22

28 Feb '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 28, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also 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/2022-02-28-Open-NEST-Developer-… Looking forward to seeing you 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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Retrieving states and parameters variables from NodeCollection
by m.benelhedi＠fz-juelich.de 28 Feb '22

28 Feb '22

Hey Nest Team, Calling "NodeCollection.get" returns a dictionary containing the user declared "States" and "Parameters" with other keys such as "global_id", "recordables", and "synaptic_elements". In this context, I want to ask if there is a function in "nest" that returns exactly only the model declared "States" or "Parameters" without having these extra keys, and of course without having a prior knowledge of the "nestml" file from which the model was originated. Best, Ayssar

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Use of std::thread in rand generators in NEST
by Itaru Kitayama 28 Feb '22

28 Feb '22

Hi, Am I correct in thinking that all rand generators provided for NEST use std::thread? If I am not mistaken, it's an extension of POSIX threads and I'd like to avoid it for my target offloading work. Thanks, Itaru.

2 1

Neuron models with Tsodyks synapse
by Alexander Kozlov 21 Feb '22

21 Feb '22

Hello, Documentation for `tsodyks_synapse` says it is only compatible with `iaf_psc_exp` or `iaf_psc_exp_htum` neuron models. Would it be possible to use it with other `_exp`-type models with postsynaptic currents or conductances with exponential decay (for example, `aeif_cond_exp`)? If not, what could be a work around? With best regards, Alexander Kozlov, CST EECS KTH.

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NEST Conference 2022 - registration is open
by Hans Ekkehard Plesser 17 Feb '22

17 Feb '22

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2022. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We particularly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual event on Thursday/Friday 23/24 June 2022. Register now! For more information please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and colleagues -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Neuron models with NMDA channels
by cagnol＠ksvi.mff.cuni.cz 15 Feb '22

15 Feb '22

Hello, We would like to use neurons models with NMDA channels in our spiking neuron model. We're still unsure whether we will use a native neuron model in Nest or whether we will implement our own one in NESTML. My understanding is that the only model in Nest which does that is the Hill - Tononi model, which seems rather complex. How fast would you roughly expect a Hill - Tononi neuron network to run compared to a network made of aeif_cond_exp neurons? Do you know by any chance any example of adex NESTML models which implement NMDA and Gaba_B channels? Also, one last question not really related to the previous ones: Is there any way to model synaptic reliability in Nest? Thanks a lot, Remy,

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NEST Users February 2022