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error in making new module
by atiye nejadebrahim 21 Sep '23

21 Sep '23

Dear all, I installed nest from source according to this instruction (Install NEST from source — NEST Simulator Documentation) but when I run this code to make a module, I face with following error. Can you help me to solve it? import matplotlib as mplimport matplotlib.pyplot as pltimport nestimport numpy as npimport osfrom pynestml.frontend.pynestml_frontend import generate_nest_target NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::") generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml", target_path="/home/atiye/new_neuron2", module_name="hh_psc_alpha1_module", suffix="_nestml", logging_level="ERROR", # try "INFO" for more debug information codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION})nest.Install("hh_psc_alpha1_module") errors:cd /home/atiye/New\ folder ; /usr/bin/env /bin/python3 /home/atiye/.vscode-server/extensions/ms-python.python-2023.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher 52383 -- /home/atiye/New\ folder/hh_motor_neuron.py -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.5 Built: Jul 13 2023 04:45:54 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. -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.5 Built: Jul 13 2023 04:45:54 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 11.3.0-- Detecting CXX compiler ABI info-- Detecting CXX compiler ABI info - done-- Check for working CXX compiler: /usr/bin/g++ - skipped-- Detecting CXX compile features-- Detecting CXX compile features - done -------------------------------------------------------hh_psc_alpha1_module Configuration Summary------------------------------------------------------- C++ compiler : /usr/bin/g++Build static libs : OFFC++ compiler flags : NEST compiler flags : -g -O2 -ffile-prefix-map=/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=autoNEST include dirs : -I/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/includeNEST libraries flags : -L/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nest -lnest -lsli -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 /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 'hh_psc_alpha1_module' using make make install The library file libhh_psc_alpha1_module.so will be installed to /build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nestThe module can be loaded into NEST using (hh_psc_alpha1_module) Install (in SLI) nest.Install(hh_psc_alpha1_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: /home/atiye/new_neuron2[ 66%] Building CXX object CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o[ 66%] Building CXX object CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o/home/atiye/new_neuron2/hh_psc_alpha1_module.cpp:26:10: fatal error: connection_manager_impl.h: No such file or directory 26 | #include "connection_manager_impl.h" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~compilation terminated.make[2]: *** [CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:76: CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o] Error 1make[2]: *** Waiting for unfinished jobs..../home/atiye/new_neuron2/hh_psc_alpha1_nestml.cpp:29:10: fatal error: numerics.h: No such file or directory 29 | #include "numerics.h" | ^~~~~~~~~~~~compilation terminated.make[2]: *** [CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:90: CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o] Error 1make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/hh_psc_alpha1_module_module.dir/all] Error 2make: *** [Makefile:156: all] Error 2Traceback (most recent call last): File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 176, in build subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, File "/usr/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd)subprocess.CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/atiye/New folder/hh_motor_neuron.py", line 11, in <module> generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml", File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 229, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 198, in generate_target if not process() == 0: File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 351, in process _builder.build() File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 183, in build raise GeneratedCodeBuildException(stages_exception[current_stage])pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stderr. Thanks a lotBest, Atiyeh

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MPI launcher
by atiye nejadebrahim 20 Sep '23

20 Sep '23

Dear all, During running my network in nest, I faced with this error, can you help me how can I remove this error?you seem to be using NEST via an MPI launcher like mpirun, mpiexec or srun although NEST was not compiled with MPI support. Best, Atiyeh

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No Open NEST Developer VC today
by Hans Ekkehard Plesser 11 Sep '23

11 Sep '23

Dear Colleagues, There will be no NEST Developer Video Conference today. See you again on 25 September at 11.30! Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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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A problem running a .nestml file
by Hedyeh Rezaei 01 Sep '23

01 Sep '23

Dear all, I have installed nestml via conda and developed a code describing an LIF neuron with bi-exponential synaptic currents including NMDA, while the charge mediated by AMPA and NMDA receptors are not independent. When I try to compile the .nestml file, it gives me an error as: from pynestml.frontend.pynestml_frontend import generate_nest_target WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl' In [2]: generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml", ...: target_path="/tmp/nestml-component", ...: logging_level="ERROR") line 61:4 extraneous input 'end' expecting {DEDENT, 'function', 'state', 'parameters', 'internals', 'update', 'equations', 'input', 'output'} line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} ... r"""Generate and build code for NEST Simulator. Parameters A dictionary containing additional options for the target code generator. """ I was wondering what the reason could be. I would appreciate it if you could help. Thanks in advance. Best, Hedyeh

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OpenMP: only one thread is used
by Stefan Dvoretskii 30 Aug '23

30 Aug '23

Hello all, I am trying to use as much parallelism as possible on my computing grid. In this sense, I combine MPI+OpenMP. MPI processes are spawned fine, but OpenMP threads always amount to 1, no matter that I set local_num_threads correctly ( https://nest-simulator.readthedocs.io/en/latest/hpc/slurm_script.html#set-l…) as well as all SLURM variables. I am sure I have compiled nest with OpenMP too. I use slightly modified izhikevich neurons with stdp synapses. Can the model specifics be the cause of underutilizing available threads? Or is there something else in the system that could be the reason for that? Best regards, -- Stefan Dvoretskii

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Network simulation of Hanuschkin (2010) - precise spike times
by Evgenia Kartsaki 28 Aug '23

28 Aug '23

Hello, I am trying to simulate the network of a model with precise spike times as in Hanuschkin (2010), which is based on the balanced random network of Brunel (2000). As far as I understand the model of Hanuschkin exists already in NEST here: https://nest-simulator.readthedocs.io/en/v3.5/models/iaf_psc_exp_ps.html . However, I haven't found an example of the network simulation. I have tried using the Brunel network (https://nest-simulator.readthedocs.io/en/stable/auto_examples/brunel_delta_…) with the iaf_psc_exp_ps model, but I got a firing rate (excitatory or inhibitory) of 0 Hz. I would appreciate any advice on that! Thanks in advance, Jenny

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Open NEST Developer Video Conference Monday August 28 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 28 Aug '23

28 Aug '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 28, 11.30-12.30 CEST (UTC+2). Also 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. 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. 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/2023-08-28-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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Finalization of release procedure: NEST 3.5
by Dennis Terhorst 24 Aug '23

24 Aug '23

Dear all, After the quite silent NEST 3.5 release on GitHub in July we have waited a bit to publish the DOI record. Now we have completed the last step of the release process and I am happy to announce the completed NEST Simulator 3.5. When using this version of NEST in your work you can cite it as Haug et al. (2023). NEST 3.5. Zenodo. https://doi.org/10.5281/zenodo.8069926 As usual the full citation record and other citation formats for this and other versions are available on Zenodo. Thanks to all of you for being in this enthusiastic community and a very special thanks to everyone that contributed to this release! We're looking forward to the exciting scientific results you may produce with this tool! Best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine Computational and Systems Neuroscience (INM-6) & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA (INM-10) Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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GetConnections is too slow- can i obtain connection ids as I connect the neurons? (nest v2.20)
by Angeliki Papadimitriou 24 Aug '23

24 Aug '23

Hello, I have a serious bottleneck in terms of runtime in my simulations. I have a modular cortical network and i need to 'manually' change weights in some specific connections before i start the simulation. The modularity means that this happens inside a for loop for all populations pairs. so, before simulation starts i have a function that goes over all population pairs and does this: AMPA_conns = nest.GetConnections(source=pre_pop,target=post_pop, synapse_model='AMPA_synapse_longrange') # RETRIEVE ALL AMPA CONNECTIONS BETWEEN SOURCE AND TARGET POPULATION nest.SetStatus(AMPA_conns, {'weight': pattern_weight}) # CHANGE CONNECTION WEIGHT NMDA_conns = nest.GetConnections(source=pre_pop,target=post_pop, synapse_model='NMDA_synapse_longrange') # RETRIEVE ALL NMDA CONNECTIONS BETWEEN SOURCE AND TARGET POPULATION nest.SetStatus(NMDA_conns, {'weight': pattern_weight * nmda2ampa_ratio}) # CHANGE CONNECTION WEIGHT commenting out these 4 lines reduces my runtime by 8 hours. for reference, the model consists of ~27000neurons, is created in 20 minutes (nodes generated and connections drawn) and the actual simulation runs for about 15 minutes. so my question is: is there a way to obtain the connection ids as i draw the connections (right after the nest.Connect() function) so that i can store them in a data structure and avoid this expensive operation of searching? or perhaps it is the setstatus that makes it expensive? *I havent yet migrated to nest v3, this concerns version 2.20. thank you for your time! angeliki

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asynchronicity between spikes and firing pattern
by atiye nejadebrahim 24 Aug '23

24 Aug '23

Dear All, I made a HH neuron model and I can get an action potential from it. but it seems there is a problem in spikes. Action potential shape show one spike, but spike recorder shows several spikes and there is not any synchronicity between them. can you help me why? my second question is about spike generation, when I use I_e current for injecting current to the neuron, I can record spikes, but when I use step current generators, no spike shows. can you help me why?Thank you for your consideration. Best, Atiyeh Dear All, I made a HH neuron model and I can get an action potential from it. but it seems there is a problem in spikes. Action potential shape show one spike, but spike recorder shows several spikes and there is not any synchronicity between them. can you help me why? my second question is about spike generation, when I use I_e current for injecting current to the neuron, I can record spikes, but when I use step current generators, no spike shows. can you help me why?Thank you for your consideration. Best, Atiyeh

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