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Open NEST Developer Video Conference Monday March 14 2022 11:30 CET (UTC+1)
by Dennis Terhorst 14 Mar '22

14 Mar '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday March 14, 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/2022-03-14-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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INCF/OCNS Software working group survey on software usage
by Ankur Sinha 11 Mar '22

11 Mar '22

Dear all, Apologies for the cross-posts. We, the INCF/OCNS Software working group, are conducting a short anonymous survey to collect information on the usage of common software tools in comp-neuro. Could we please request you to spend 2 minutes of your time to fill it out here: https://forms.gle/NXWv2CwtWBSB9BXv9 The information gathered in the survey will be used to organise sessions/workshops related to the software, and improve awareness about them and their maintenance. On behalf of the Software WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

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NESTML, error in the generate_nest_target function
by Salvo T 03 Mar '22

03 Mar '22

Dear NESTML Users, when I try the NESTML Izhikevich tutorial, I have a problem in the generate_nest_target function. The output in the terminal is the following: *** -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: UNKNOWN Built: Jan 18 2022 13:53:41 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. -- The CXX compiler identification is GNU 9.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done ------------------------------------------------------- nestml_izhikevich_module Configuration Summary ------------------------------------------------------- C++ compiler : /usr/bin/c++ Build static libs : OFF C++ compiler flags : NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto NEST include dirs : -I/opt/nest/include/nest -I/usr/include -I/usr/include -I/usr/include -I/opt/music-install/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/include NEST libraries flags : -L/opt/nest/lib/nest -lnestutil -lnest -lsli -lnestkernel -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so /usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so /opt/music-install/lib/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so ------------------------------------------------------- You can now build and install 'nestml_izhikevich_module' using make make install The library file libnestml_izhikevich_module.so will be installed to /opt/nest/lib/nest The module can be loaded into NEST using (nestml_izhikevich_module) Install (in SLI) nest.Install(nestml_izhikevich_module) (in PyNEST) CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.22) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done -- Build files have been written to: /tmp/nestml-component [ 16%] Building CXX object CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o In file included from /opt/nest/include/nest/connector_base.h:35, from /opt/nest/include/nest/connection_manager.h:36, from /opt/nest/include/nest/connection_manager_impl.h:26, from /tmp/nestml-component/nestml_izhikevich_module.cpp:26: /opt/nest/include/nest/sort.h:36:10: fatal error: boost/sort/spreadsort/spreadsort.hpp: No such file or directory 36 | #include <boost/sort/spreadsort/spreadsort.hpp> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [CMakeFiles/nestml_izhikevich_module_module.dir/build.make:76: CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:112: CMakeFiles/nestml_izhikevich_module_module.dir/all] Error 2 make: *** [Makefile:156: all] Error 2 *** While the Jupyter notebook output is the following: *** 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-f7696df63255> 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. *** I installed Boost with 'sudo apt-get install libboost-all-dev' from the terminal. Can you 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

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.

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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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