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[Precise Spikes]small bug in ./pynest/examples/hpc_benchmark.py (nest-3.3)
by Tianxiang Lyu 26 Sep '22

26 Sep '22

Hi, all! I try to replace "iaf_psc_alpha" with "iaf_psc_alpha_ps" and "poisson_generator" with "poisson_generator_ps" for using precise spikes neuron template in the simulation However, there are somethings wrong with the logs related to SLI with which I hadn't been familiar: (If the randomizing of membrane potentials is removed, hpc_benchmark.py could run as usual) Traceback (most recent call last): File "./hpc_benchmark.py", line 456, in <module> run_simulation() File "./hpc_benchmark.py", line 362, in run_simulation sr = build_network(logger) File "./hpc_benchmark.py", line 227, in build_network nest.GetLocalNodeCollection(E_neurons).V_m = random_vm File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 543, in __setattr__ self.set({attr: value}) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 477, in set sli_func('SetStatus', self._datum, params) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 165, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 115, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype How could I fix that? Or another way to implement randomizing of membrane potentials? Tianxiang Lyu Department of Mechanic Sun Yet-Sen University No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, P. R. China

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Open NEST Developer Video Conference Monday Sep 26 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 26 Sep '22

26 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 26, 11.30-12.30 CEST (UTC+2). 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/2022-09-26-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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How to save and reload an already trained network created with Nest Simulator?
by salvatore.taffara＠phd.unict.it 21 Sep '22

21 Sep '22

Hi, can anyone answer to my question in subject? I am using Nest 3.3. Thanks in advance, Salvo

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which neuron model supports shunting inhibition
by Aadhar Sharma 14 Sep '22

14 Sep '22

Hi all! I want to use investigate the effects of shunting inhibition in one of my experiments. I tried iaf_cond_alpha, but couldn't reproduce the shunting effect. Could someone please suggest which neuron model to use? There should be a way to also change the V_th, V_rest, C_m, tau_m or g_L for this model. I am working with NEST 2.20.2 Best, Ady

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 12 Sep '22

12 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 11.30-12.30 CEST (UTC+2). 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/2022-08-15-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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Upcoming conference in Computational Neuroscience - Neuromatch 2022
by Alberto Antonietti 30 Aug '22

30 Aug '22

Dear NEST users and developers, I am glad to invite you to the upcoming fifth edition of the Neuromatch Conference (NMC), which will take place online on September 27-28! The scope of NMC 2022 includes computational neuroscience and machine learning work that has a biological link. We are excited to have a slate of excellent speakers and panelists lined up including: - Keynotes from Larry Abbott, Rosa Chan, Ida Momennejad and Mac Shine - Panel on spiking computation: Priya Panda, Katie Schuman, and Peter Suma - Panel on the future of scientific publishing: Tim Behrens, Simine Vazire, and Abeni Wickham - Bridging-the-gap with computational psychiatry: Xiaosi Gu and Quentin Huys Registration costs are set at 15 USD to cover technical costs, and if this is a difficulty, the fee can be waived without questions. **Important dates** September 5, 2022: Abstract submission deadline September 7, 2022: Abstract acceptance and live talk selection news September 22, 2022: Video submission deadline for flashtalks September 27 - 28, 2022: NMC 2022 Each of the two conference days will have two sessions, each of which is 4 hours long. Here are the hours for each of the sessions, as they would occur across five time zones from around the world: Read more at http://conference.neuromatch.io I hope to see many of you there! Best, Alberto

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Spike->Synapse->Update
by lvtx＠mail2.sysu.edu.cn 25 Aug '22

25 Aug '22

I wrote a simple python code(without nest) for a E-I random balanced network with poisson noise stimulus. Then I try to build it on nest. However, the response firing rates are changed.(not a computing error) Is there anything wrong? neurons -> spike synapse -> wait delay post_neurons -> add weight from connected synapses to corresponding input channel neurons -> update ODE each step I figured out that without connections but with poisson noise input, the firing rates of my python code is the same as the code on nest. (Seems that the ODE calculations are the same in my python code and nest) However, the firing rates show differ greatly when I add the connections on both.

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Hans Ekkehard Plesser 15 Aug '22

15 Aug '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 11.30-12.30 CEST (UTC+2). 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/2022-08-15-Open-NEST-Developer-… Looking forward to seeing you again soon! Best regards, Hans Ekkehard Plesser ------------------ 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 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 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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Compiling nest-simulator from source
by Daniel Naoumenko 11 Aug '22

11 Aug '22

Hi, I've been trying to compile the latest version on github (c1cebdc) without success. The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results. I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator make make fails at 47%. I have uploaded the make output here: https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=… As well as the output of cmake to show the build configuration: https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=… Thank you in advance for any assistance.

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Fwd: Building nest 3.3
by Mikael Lindahl 05 Aug '22

05 Aug '22

Hi, I am trying to build NEST on debian 11 with cmake 3.16.9 and conda python=3.9. I have attached my installation script asswell as the full logs for make and install steps. ( I run the script with using source to conda activate will play nice) During "make install" I get the following message error -- Set runtime path of "/home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest/pynestkernel.so" to "$ORIGIN/../lib/nest:$ORIGIN/../../lib/nest:$ORIGIN/../../../nest:/home/mikael/opt/anaconda3/envs/nest-3.3/lib" running install_egg_info /home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info creating nest_simulator.egg-info writing nest_simulator.egg-info/PKG-INFO writing dependency_links to nest_simulator.egg-info/dependency_links.txt writing requirements to nest_simulator.egg-info/requires.txt writing top-level names to nest_simulator.egg-info/top_level.txt writing manifest file 'nest_simulator.egg-info/SOURCES.txt' reading manifest file 'nest_simulator.egg-info/SOURCES.txt' writing manifest file 'nest_simulator.egg-info/SOURCES.txt' Copying nest_simulator.egg-info to /home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest_simulator-3.3-py3.9.egg-info Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 477, in get_distribution dist = get_provider(dist) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 353, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'nest-simulator' distribution was not found and is required by the application And for make installcheck i get this error Scanning dependencies of target installcheck Executing NEST's testsuite... make[3]: *** [CMakeFiles/installcheck.dir/build.make:61: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:524: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:531: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:178: installcheck] Error 2 It took 160 seconds Anyone who knows how to solve this? /Mikael -- Mikael Lindahl Phd Phone: +46735119429 Email: m <lindahlm(a)csc.kth.se>ickelindahl(a)gmail.com

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