NEST Users September 2023

users@nest-simulator.org

6 participants
7 discussions

NEST 3.6 released
by Hans Ekkehard Plesser 28 Sep '23

28 Sep '23

Dear NEST Users! It is a great pleasure to inform you that we have released NEST 3.6 which brings a number of exciting enhancements in particular * Support for astrocytes and a first astrocyte model * A new glif_psc_double_alpha model * Much improved performance, especially for highly threaded simulations * Improved security for NEST Server * Minor changes to the volume transmitter syntax and to rarely used kernel attributes * Many tests ported to pytest and modernized * Lots of minor improvements and bug fixes For more information, see - https://nest-simulator.readthedocs.io/en/v3.6/whats_new/v3.6/index.html - https://github.com/nest/nest-simulator/releases/tag/v3.6 I would like to thank all NEST developers who contributed to this release and the NEST release team, especially Dennis, for making this release a reality. Best wishes straight from the Bernstein Conference in Berlin, 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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CMake error
by atiye nejadebrahim 28 Sep '23

28 Sep '23

Dear All, I am trying to install nest from source in miniconda3 (ubuntu) and following this instruction (Install from source in a conda environment — NEST Simulator Documentation),but at this step, cmake -DCMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX /home/atiye/Downloads/nest-simulator-3.5 I face with this error: CMake Error: CMake was unable to find a build program corresponding to "Unix Makefiles". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool.CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguageCMake Error: CMAKE_C_COMPILER not set, after EnableLanguage-- Configuring incomplete, errors occurred! Can you help me to remove this error and install nest?Thanks.Best, Atiyeh | | | | Install from source in a conda environment — NEST Simulator Documentation This is the documentation index for the NEST, a simulator for spiking neuronal networks. | | |

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Open NEST Developer Video Conference Monday September 25 2023 11:30 CEST (UTC+2)
by Hans Ekkehard Plesser 25 Sep '23

25 Sep '23

1. Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 25, 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 1. Welcome 2. Review of NEST User Mailing List<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Project team<https://github.com/nest/nest-simulator/projects> round 4. In-depth discussion * NEST 3.6 Release * Next steps * Two hints for productive work * Semantics of tripartite connections (https://github.com/nest/nest-simulator/pull/2955; see in particular this proposal<https://github.com/nest/nest-simulator/pull/2955#issuecomment-1733030870>) * New way of registering connections (https://github.com/nest/nest-simulator/pull/2956) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2023-09-25-Open-NEST-Developer-… Looking forward to seeing you! Cheers, Hans Ekkehard ------------------ 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<mailto:97938800@vc.dfn.de> - By telephone: +49-30-200-97938800<tel:+493020097938800> 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 -- 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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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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NEST Users September 2023