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Multiplicity value + presynaptic spike history
by Benedikt Feldotto 27 Nov '19

27 Nov '19

Dear all, I have two questions that arise when implementing my adapted C++ synapse model. 1) Postsynaptic spikes have a "multiplicity" variable. Am I correct that if I receive a single spike object with a multiplicity value of 3, I actually receive 3 spikes? Since I do only get one time, what are the exact spike times of the other spikes? 2) For the postsynaptic spikes I can easily access the spike history and search for spikes in a certain time range, as for example done in the STDP synapse. Is it possible to also access the overall spike history of presynaptic spikes? So far I only found that in the std_dopamine synapse as an example the last spike time is stored manually. Thank you very much ! Best Regards, Benedikt Feldotto -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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NO Open NEST Developer Video Conference Monday 25 November 2019
by Dennis Terhorst 23 Nov '19

23 Nov '19

Dear NEST Developers! On Monday there will be no Open NEST Developer Video Conference, since many of the NEST users and developers are traveling at that time to join the HBP CodeJam#10 and adjoined events. As usual, if you would have something you want to add to the agenda, please don't hesitate to contact me anyway. I will then add it in the the following meeting. Looking forward to seeing you soon! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

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About the spike_detector records
by zhe.sun.vk＠riken.jp 18 Nov '19

18 Nov '19

Dear all, Recently I always have an error when I tried to keep the spike_detector information into files. ********************** Nov 18 19:22:09 RecordingDevice::calibrate() [Error]: I/O error while opening file '0-94476-15.gdf'. This may be caused by too many open files in networks with many recording devices and threads. ********************** And I also found most of the gdf files are empty. Do you have any idea to solve this issue? And do you know how to avoid to keeping empty gdf files. Best wishes Sun

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Open NEST Developer Video Conference Monday 11 November 2019 11:30 CET (UTC+1)
by Dennis Terhorst 10 Nov '19

10 Nov '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 11 November, 11.30-12.30 CET (UTC+1). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-11-11-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List3 * Review of open Github Pull Request * Review of open Github Issues Looking forward to seeing you soon! best, 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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Re: Issues with make under OSX
by Hans Ekkehard Plesser 08 Nov '19

08 Nov '19

Hi Benjamin, It is curious that MPI is not found on your system. Could you double check that you have installed open-mpi via Homebrew? What does which mpicxx return on your system? Best, Hans Ekkehard On 26 Oct 2019, at 17:04, Benjamin Staude <benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Thanks for the support, that solved one issue. But now, I get the same for OPEN_MPI: -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) (I need open_mpi because I need the MUSIC interface). This is my cmake-call: cmake \ -DCMAKE_C_COMPILER=gcc-9 \ -DCMAKE_CXX_COMPILER=g++-9 \ -Dwith-music=ON \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCMAKE_INSTALL_PREFIX=/Users/staude/.pyenv/versions/3.7.2/ \ /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0 And the output: -- The CXX compiler identification is GNU 9.2.0 -- The C compiler identification is GNU 9.2.0 -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/g++-9 -- Check for working CXX compiler: /usr/local/bin/g++-9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-9 -- Check for working C compiler: /usr/local/bin/gcc-9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - not found -- Looking for C++ include ostream -- Looking for C++ include ostream - not found -- Looking for C++ include sstream -- Looking for C++ include sstream - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp -- Found OpenMP_CXX: -fopenmp -- Found OpenMP: TRUE -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:528 (message): MUSIC requires -Dwith-mpi=ON. Call Stack (most recent call first): CMakeLists.txt:167 (nest_process_with_music) And the cmake-version: cmake --version cmake version 3.15.3 On 26. Oct 2019, at 14:11, Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, The CMake output shows that you are using the AppleClang compiler, which does not support OpenMP. If you want to use that compiler, you need to turn off OpenMP with -Dwith-openmp=OFF. If you want NEST with OpenMP on the Mac, I would recommend using the GCC compiler installed via Homebrew, see https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… for instructions. Best, Hans Ekkehard On 25 Oct 2019, at 18:12, Benjamin Staude <benjamin.staude(a)gmail.com> wrote: Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp) _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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VoIP Engineers jobs
by fieldengineer77＠gmail.com 06 Nov '19

06 Nov '19

Available in the Field Engineer marketplace are experts with Voice over Internet Protocol (VoIP) skills, which is a mix of voice, video, and knowledge on one network. VoIP allows people to make telephone calls over broadband Internet connections rather than analog landlines. A VoIP engineer designs, tests, installs and maintains both local VoIP systems in business and large networks that cover entire regions. VoIP Engineers use their experience with computer science, digital audio hardware, and VoIP software to install cutting-edge technologies. They also work with information technology (IT) professionals and system administrators to explain the functionality of VoIP. Many industries employ VoIP engineers to complete telecommunications work on a full-time or contract basis. More info: https://www.fieldengineer.com/skills/voip-engineer

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Educational qualifications and other certifications for Apple Certified Technical Coordinators
by kaitlyn.kristy9494＠gmail.com 06 Nov '19

06 Nov '19

A High school diploma or equivalent along with an Apple Certified Technical Coordinator certification is necessary. An A + certification from CompTIA gives candidates an edge over other aspirants. They should be conversant with various network configurations and hardware devices. Salaries for Apple Certified Technical Coordinators Payscale.com reveals that the average salary of an Apple Certified Technical Coordinator is $65,000 per year in the United States. If they freelance, they will earn $26 per hour. Read More: https://www.fieldengineer.com/skills/apple-certified-technical-coordinator

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PC Technician
by ashaikfe＠gmail.com 06 Nov '19

06 Nov '19

A PC technician often referred to as a computer technician or PC repair technician is responsible for identifying, troubleshooting and resolving computer issues. They are experienced and knowledgeable professionals with hands-on experience with different tools of repair and maintaining computer hardware, software and network/Internet issues. Read More: https://www.fieldengineer.com/skills/what-is-a-pc-technician

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Newbie questions
by Roman Kalivoda 04 Nov '19

04 Nov '19

Hello Nest users, I recently started to work on my bachelor thesis and the first step is to find existing simulators of neural networks and analyze them. Regarding that, I have some questions about the Nest to which I cannot find answers. Is there some graphical interface for Nest? I have found a GitHub project called nest-desktop (https://github.com/babsey/nest-desktop), but I could not find it being mentioned anywhere in the nest simulator documentation. Does anyone have some experience with this? Is it reliable? What is it capable of? If there is not any official Nest GUI, how do you typically work on new simulations? Do you just write plain python scripts for PyNest interface? The last request is directed more to the developers, but maybe someone can lead me in the right way. My thesis lead would like to see some schema of the Nest architecture or some overview of how the simulator is designed. Thank you very much, Roman Kalivoda

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Re: parrot neurons PORT 1
by Charl Linssen 01 Nov '19

01 Nov '19

Dear Nikolas, Could the following example in NEST Simulator be what you're looking for? https://github.com/nest/nest-simulator/blob/f28b138f469354264f65c3b5c9d05e5… """Check STDP protocol between two parrot_neurons connected by a stdp_synapse. Exact pre- and post-synaptic spike times are set by spike_generators connected to each parrot neuron. Additional spikes sent through the stdp_synapse are explicitly ignored in the postsynaptic parrot_neuron by setting the stdp_synapse to connect to port 1. """ With kind regards, Charl On Wed, Oct 30, 2019, at 11:58, Nikolaos Chrysanthidis wrote: > Hi Charl, > I want to test the weight change of a single synapse providing stimulation at 2 parrot neurons, so for that reason, > If I excite two pre-,post- parrot neurons (parrot_A,B) using port 0, then the parrot_A will excite the parrot_B as well, so the parrot_B will end up having more spikes than expected. > I think this can be overcome by using port1 of parrot_B in order to ignore the extra excitation from parrot_A. > Please, I'd be grateful if you could provide a way to avoid extra excitation from parrot_A onto parrot_B. > > Kind regards, > Nikolas > > *From:* Charl Linssen <nest-users(a)turingbirds.com> > *Sent:* 28 October 2019 12:11 > *To:* users(a)nest-simulator.org > *Subject:* [NEST Users] Re: parrot neurons PORT 1 > > Dear Nikolaos, > > I'm a little confused as to why you wish to use port 1 for this. A synapse is not aware of incoming or outgoing ports, so if you want to test a particular synapse model, you can connect it between port 0 of a presynaptic parrot neuron, and port 0 of a postsynaptic parrot neuron. Could you otherwise please clarify your use case a bit? > > With kind regards, > Charl > > > On Thu, Oct 17, 2019, at 17:00, Nikolaos Chrysanthidis wrote: >> Hi NEST users, >> >> I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. >> >> To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. >> By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor. >> >> At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron >> which I hope it will solve the error with the receptor. >> >> From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming >> through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting >> >> two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron." >> >> My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ? >> If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ? >> >> Thank you very much, >> Kind regards, >> Nikolas >> >> >> >> >> _______________________________________________ >> NEST Users mailing list -- users(a)nest-simulator.org >> To unsubscribe send an email to users-leave(a)nest-simulator.org >> >

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Random balanced network with conductance based synapses
by Adam Haber 31 Oct '19

31 Oct '19

Hi, I'm trying to port to NEST this "conductance-based" network from Brian: https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_… I'm unable to reproduce their results (qualitatively - I'm not expecting identical results since I assume RNGs, solvers and other implementation details differ in many ways). Is there any publicly available example of a random balanced network with conductance based synapses? From what I've seen, all the brunel-style example networks are current based (as in the original paper). Thanks in advance, Adam

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parrot neurons PORT 1
by Nikolaos Chrysanthidis 28 Oct '19

28 Oct '19

Hi NEST users, I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor. At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron which I hope it will solve the error with the receptor. From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron." My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ? If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ? Thank you very much, Kind regards, Nikolas

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Open NEST Developer Video Conference Monday 28 October 2019 11.30 CET (UTC+1)
by Dennis Terhorst 28 Oct '19

28 Oct '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today (please excuse the late invitation) Monday 28 October, 11.30-12.30 CET (UTC+1). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-… Agenda 1. Welcome 2. Planning of HBP High-Level Support Event in Heidelberg <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> next month 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> Looking forward to seeing you soon! best, 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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ok
by 岳训 26 Oct '19

26 Oct '19

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Issues with make under OSX
by Benjamin Staude 25 Oct '19

25 Oct '19

Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp)

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C/C++ interface
by Xavier Otazu 24 Oct '19

24 Oct '19

Hello, I would like to make a suggestion for future development. Now there is a Python interface, but some of us have been working with C/C++ for many years (and we have a lot of data processing software developed in this language). Please, could you include a C/C++ interface for NEST? Thanks a lot in advance! Xavier

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RGN
by Maryada Maryada 22 Oct '19

22 Oct '19

Hi all, I have a question regarding random number generator. I am intend to randomly choose neuron population but keep this same across multiple processes. (see attached) mpirun -np 4 python network_population.py However, seemingly I am missing something. Also, in case I try to use different population count I am getting error while connecting nodes with input or probes. (see mpi_example) -- Thanks and Regards *Maryada*

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precise firing events
by Nikolaos Chrysanthidis 22 Oct '19

22 Oct '19

Dear NEST users, I would like to ask you if there is any way to have an AdEx neuron model firing at specific times (ms) in NEST. Kind regards,

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HBP event in Heidelberg
by Dennis Terhorst 17 Oct '19

17 Oct '19

Dear NEST colleagues, We like to inform you all about an event of the Human Brain Project, that will take place in Heidelberg on November 25-28. It will be comprised of introductory sessions on different types of infrastructure that is being built for the neuroscience community. Among these will be several NEST related sessions which may be of interest to you (see attached file). This is a combined event with a CodeJam and infrastructure trainings, which will take place in close space-time proximity: * 25 Nov: [Public event] EBRAINS - New enabling infrastructure for neuroscience * 26 Nov: How to increase the FAIRness of your research - an HBP training course about data sharing * *26-28 Nov: 2nd HPAC Platform Training * * *26-28 Nov: CodeJam#10 * The 2nd HPAC Platform Training will introduce the tools and services of the High-Performance Analysis and Computing Platform and Fenix, including an interactive session on how to apply for those resources. There will also be several sessions about the simulators with different resolutions being (co)developed in the HBP (Arbor, NEST and TVB). More info and registration can be found here: https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… The registration is already open but requires an account to register. If you would like join the event please send an email to Maren Frings <m.frings(a)fz-juelich.de> so we can create a guest account for you. Then you can*register e.g. for the HPAC Training*. The events will have joint breaks and it will be possible to switch to another event for the one or the other session. You need to register only for the event you are most interested in. It would be great to see you there! :-) Best regards, Dennis & Maren

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MUSIC in nest-docker
by Benjamin Staude 17 Oct '19

17 Oct '19

Hi there, I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi… <https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi…> in the docker environment of NEST (https://github.com/nest/nest-docker <https://github.com/nest/nest-docker>) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker. The output was: MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[46746,1],0] Exit code: 1 Can anyone help? Thanks in advance, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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+me for HBP members
by Dennis Terhorst 15 Oct '19

15 Oct '19

Dear HBP-NEST users! // This mail only regards people involved in the Human Brain Project (HBP). // For making your usage of NEST more visible to the HBP internal reporting, we would be happy to see you in the list of the so called /component users/. For this you just need to go to the NEST component page https://plus.humanbrainproject.org/components/209/ and do *three clicks*: 1. click the green [edit] button 2. click [+me] at "Component User Group", and finally 3. click [Save] at the bottom of the page. This ensures the continued support of many developers and helps to show the multitude of research using NEST simulations, and is highly appreciated. If you use or intend to use any number of the following specific NEST features, please feel free to also add yourself there, to show your appreciation to the respective developers: * optimizations for simulations on high-performance computing platforms https://plus.humanbrainproject.org/components/1666/ and https://plus.humanbrainproject.org/components/1667/ * models with continuous dynamics / gap-junctions https://plus.humanbrainproject.org/components/510/ * models with 3rd factor plasticity https://plus.humanbrainproject.org/components/2696/ * the NEST modeling language (NESTML) https://plus.humanbrainproject.org/components/2679/ * connection generation in very large networks https://plus.humanbrainproject.org/components/2678/ There are many other related components that you may also want to add yourself, like simulator-simulator interactions (e.g. 2693), visualization (e.g. 2697), and many more. Please contact me if you feel like you can't find something that you would like to "+me". best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Open NEST Developer Video Conference Monday 14 October 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 14 Oct '19

14 Oct '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today (please excuse the late invitation) Monday 14 October, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-… Agenda • Welcome • Python 2 support in NEST3? • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues Looking forward to seeing you soon! best, 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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IF COND EXP Model
by vergani.aa＠gmail.com 17 Sep '19

17 Sep '19

Dear experts, do you have any suggestions where could I find the explicit model for the IF COND EXP neuron? I mean the mathematical formulation of the model. Thanks Alberto

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Poisson - crash when changing the rate and delay of rate change
by nest-simulator.org＠weinzierl.it 16 Sep '19

16 Sep '19

I use NEST (Version 2.16.0) by using PyNN. While using I came across the problem that NEST throws an error, when the rate of a SpikeSourcePoisson (in PyNN) is updated from any positive value to 0 and to any positive value again. In other words, once the rate is set to zero, it cannot be changed anymore. It seems like this issue is independant of the temporal location. The exception thrown is the following: > python2.7: /pathToNestSimulator/nest-simulator-2.16.0/nestkernel/event_delivery_manager.h:564: nest::delay nest::EventDeliveryManager::get_slice_modulo(nest::delay): Assertion `static_cast< std::vector< delay >::size_type >( d ) < slice_moduli_.size()' failed. Further, any rate change of a specific neuron is not applied before the next spike at the previous rate. This is problematic when dealing with low rates as spikes occur only rarely. For instance, with a rate of 1 it is not unlikely that there is not a spike for a few seconds. As a result, a rate change can and will be applied extremely delayed. I initially reported this at PyNN, but it seems to be a NEST issue: https://github.com/NeuralEnsemble/PyNN/issues/650 What would you advise?

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Open NEST Developer Video Conference Monday 16 September 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 15 Sep '19

15 Sep '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 16 September, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-09-16-Open-NEST-Developer-… Agenda • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues Looking forward to seeing you soon! best, 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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