- NEST Users - NEST Initiative Mail

Open NEST Developer Video Conference Monday 14 September 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 14 Sep '20

14 Sep '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 14 September, 11.30-12.30 CEST (UTC+2). 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. The ongoing hackathon this week will be one of the topics and a quick overview will be discussed. 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/2020-09-14-Open-NEST-Developer-… 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

1 0

error when making
by Carlos Gutierrez 05 Sep '20

05 Sep '20

Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos. [ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2 ######## -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) Use threading : Yes (OpenMP: -fopenmp) Use GSL : Yes (GSL 2.5) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so Use Readline : Yes (GNU Readline 8.0) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so Use libltdl : Yes (LTDL ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so Use MUSIC : No Use libneurosim : No Use Boost : No --------------------------------------------------------------------------------

2 3

Open NEST Developer Video Conference Monday 31 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 31 Aug '20

31 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 31 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-31-Open-NEST-Developer-… 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

1 0

Re: Issue with NEST Live Media 2.20
by Steffen Graber 27 Aug '20

27 Aug '20

Hi Maryada I just tested the VM with Windows 10 Home (Version 1903) and with Virtualbox 6.12. No problems at startup. The network does not seem to start in your installation. If not done yet I would first delete the VM completely and reinstall it. Then deactivate the network in the settings of the VM and restart it again. Hope this helps. Best Steffen Am 26.08.20 um 11:08 schrieb Maryada Maryada: > Sorry for the late reply. > Here you go. I hope this helps. > > On Tue, Aug 25, 2020 at 2:16 PM Steffen Graber <s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de>> wrote: > > Hi, > > That's ok. Could you send me the log of the VM? > Highlight the VM in the manager and press CTRL+L. > > Best > > Steffen > > Am 25.08.20 um 13:01 schrieb Maryada Maryada: > > Hey, > > The latest one, 6.1.12 > > > > On Tue, Aug 25, 2020 at 12:52 PM Steffen Graber > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > wrote: > > > > Hi, > > > > Do you have the ExtensionPack installed? In which version? > > > > Best > > > > Steffen > > > > Am 25.08.20 um 12:39 schrieb Maryada Maryada: > > > Hi Steffen, > > > I am using Windows 10 as my host OS and Oracle Virtual Box 6.1 > > > > > > On Tue, Aug 25, 2020 at 12:34 PM Steffen Graber > > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > > <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>>>> > > wrote: > > > > > > Hi Maryada, > > > > > > Just tried Live Media 2.20 under Ubuntu 20.04 with > Virtualbox 6.1. > > > Starting the VM worked fine for me. > > > > > > Which operating system and which version of Virtualbox > do you use? > > > > > > Best > > > > > > Steffen > > > > > > Am 25.08.20 um 11:40 schrieb Maryada Maryada: > > > > Hi, > > > > I am trying to import Live Media 2.20 however the VM > > virtualbox is > > > > always get stuck immediately > > > > as it starts (see attachment). I also tried to import the > > 2.18 version > > > > just to be sure if it's an issue on my side. However, > that's > > working > > > > perfectly fine. > > > > > > > > Is there an additional requirement that I might be > missing? > > > > -- > > > > Thanks and Regards > > > > > > > > *Maryada* > > > > > > > > > > > > _______________________________________________ > > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>>> > > > > To unsubscribe send an email to > > users-leave(a)nest-simulator.org > <mailto:users-leave@nest-simulator.org> > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>>> > > > > > > > > > > -- > > > > > > ------------------------------------------------------------------------------------- > > > Steffen Graber > > > SimLab Neuroscience > > > Division HPC in Neuroscience > > > Jülich Supercomputing Centre > > > Institute for Advanced Simulation > > > Forschungszentrum Jülich GmbH > > > E-mail: s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > > > Phone: +49 2461 61 85457 > > > http://www.fz-juelich.de/ias/jsc > > > > > > Institute of Neuroscience and Medicine (INM-6) > > > Computational and Systems Neuroscience & > > > Institute for Advanced Simulation (IAS-6) > > > Theoretical Neuroscience & > > > JARA Institute Brain Structure-Function Relationships > (INM-10) > > > Forschungszentrum Jülich GmbH > > > http://www.csn.fz-juelich.de > > > > > > > > > ------------------------------------------------------------------------------------- > > > Forschungszentrum Juelich GmbH > > > 52425 Juelich > > > Sitz der Gesellschaft: Juelich > > > Eingetragen im Handelsregister des Amtsgerichts Dueren > Nr. HR > > B 3498 > > > Vorsitzender des Aufsichtsrats: MinDir Volker Rieke > > > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt > > (Vorsitzender), > > > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. > Harald Bolt > > > > > > ------------------------------------------------------------------------------------- > > > > > > > > > > > > -- > > > Thanks and Regards > > > > > > *Maryada* > > > > > > > > > _______________________________________________ > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > To unsubscribe send an email to > users-leave(a)nest-simulator.org <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > > > > > -- > > > ------------------------------------------------------------------------------------- > > Steffen Graber > > SimLab Neuroscience > > Division HPC in Neuroscience > > Jülich Supercomputing Centre > > Institute for Advanced Simulation > > Forschungszentrum Jülich GmbH > > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > Phone: +49 2461 61 85457 > > http://www.fz-juelich.de/ias/jsc > > > > Institute of Neuroscience and Medicine (INM-6) > > Computational and Systems Neuroscience & > > Institute for Advanced Simulation (IAS-6) > > Theoretical Neuroscience & > > JARA Institute Brain Structure-Function Relationships (INM-10) > > Forschungszentrum Jülich GmbH > > http://www.csn.fz-juelich.de > > > > > ------------------------------------------------------------------------------------- > > Forschungszentrum Juelich GmbH > > 52425 Juelich > > Sitz der Gesellschaft: Juelich > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR > B 3498 > > Vorsitzender des Aufsichtsrats: MinDir Volker Rieke > > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt > (Vorsitzender), > > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt > > > ------------------------------------------------------------------------------------- > > > > > > > > -- > > Thanks and Regards > > > > *Maryada* > > > > -- > ------------------------------------------------------------------------------------- > Steffen Graber > SimLab Neuroscience > Division HPC in Neuroscience > Jülich Supercomputing Centre > Institute for Advanced Simulation > Forschungszentrum Jülich GmbH > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > Phone: +49 2461 61 85457 > http://www.fz-juelich.de/ias/jsc > > Institute of Neuroscience and Medicine (INM-6) > Computational and Systems Neuroscience & > Institute for Advanced Simulation (IAS-6) > Theoretical Neuroscience & > JARA Institute Brain Structure-Function Relationships (INM-10) > Forschungszentrum Jülich GmbH > http://www.csn.fz-juelich.de > > ------------------------------------------------------------------------------------- > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Volker Rieke > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt > ------------------------------------------------------------------------------------- > > > > -- > Thanks and Regards > > *Maryada* > -- ------------------------------------------------------------------------------------- Steffen Graber SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber(a)fz-juelich.de Phone: +49 2461 61 85457 http://www.fz-juelich.de/ias/jsc Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH http://www.csn.fz-juelich.de ------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt -------------------------------------------------------------------------------------

1 0

Issue with NEST Live Media 2.20
by Maryada Maryada 25 Aug '20

25 Aug '20

Hi, I am trying to import Live Media 2.20 however the VM virtualbox is always get stuck immediately as it starts (see attachment). I also tried to import the 2.18 version just to be sure if it's an issue on my side. However, that's working perfectly fine. Is there an additional requirement that I might be missing? -- Thanks and Regards *Maryada*

2 5

Random refractory period
by giovannidisarra 18 Aug '20

18 Aug '20

How can I set a random refractory period (different for every neuron) in a population with SetDefaults()?

2 1

Open NEST Developer Video Conference Monday 17 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 17 Aug '20

17 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 17 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-17-Open-NEST-Developer-… 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

1 0

Saving and loading entire network
by LOW, SOCK CHING 05 Aug '20

05 Aug '20

Hi, I am new to pynest and am using it to implement a liquid state machine. It works marvelously for generating the network. My workflow is as follows: - Initialise kernel - Get stimulation episodes - Create neurons (including spike generators) - Connect neurons - nest.Simulate() - nest.GetStatus(recording_neurons) for readout at relevant timepoints I would like to save the network so I can run nest.Simulate() on other episodes in a real-time application, is there a straight-forward way to do so? I have tried pickling conn = nest.GetConnections() but to my knowledge that does not include a lot of details about the connection, like the weight. It also does not return where there is *no* connections, which means simply using nest.SetConnections(conn) prior to nest.Simulate() will not work to reproduce the previously generated network even if I initialise with all the same variables. I have found the functions GetNetwork() and GetNodes() but I'm not sure how I can use them, or if they are even useful for what I need. Cheers, Sock Ching

6 7

Open NEST Developer Video Conference Monday 3 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 03 Aug '20

03 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 3 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-03-Open-NEST-Developer-… 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

1 0

Open NEST Developer Video Conference Monday 20 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 20 Jul '20

20 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 20 July, 11.30-12.30 CEST (UTC+2). 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/2020-07-20-Open-NEST-Developer-… 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

1 0

Open NEST Developer Video Conference Monday 6 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 06 Jul '20

06 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 6 July, 11.30-12.30 CEST (UTC+2). 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: Hackathon Wrap-up The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-07-06-Open-NEST-Developer-… 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

1 0

How to normalize incoming/outgoing synaptic weights
by Keiko Fujii 29 Jun '20

29 Jun '20

Hello everyone, I would like to ask how to normalize synaptic weights during STDP learning. What I want to do is keeping the total amount of synaptic weights to/from each neuron constant. I try to describe my goal a bit more precisely: i: The index of a pre-synaptic neuron. j: The index of a post-synaptic neuron. w_ij(t): The synaptic weight from i-th neuron to j-th neuron at time=t. s_i(t): the sum of all incoming synaptic weights to i-th neuron at time=t. i.e. the sum of w_ij(t) over j. The goal is to set the sum of incoming weights (s_i(*)) to 1 by normalization (1 is just for simplicity). By STDP, we can get updated synaptic weight matrix w_ij(t+1), and the sum s_i(t+1) is not necessarily 1. So, I want to set w_ij(t+1) <- w_ij(t+1) / s_i(t+1) I briefly read the documentation for synaptic models( https://nest-simulator.readthedocs.io/en/stable/models/synapses.html). I am not very confident if my understanding is correct, but it seems that existing synaptic models handle only one synaptic weight. How can I gather data of all incoming(or outgoing as well) weights to a neuron and use the summation value inside of the STDP synapse model? Best regards, Keiko Fujii

2 1

Error: UnknownModelName
by Allen Rabayda 27 Jun '20

27 Jun '20

Dear Nest Community, Would anyone have insight into why I'm getting an UnknownModelName error? I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS). Thanks for any help. Best Regards, --Allen **** Error Message--additional details attached ****** raise exceptionCls(commandname, message) nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.', 'UnknownModelName', <SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.') ********************************************************

5 16

Install nest via homebrew
by Tammo Ippen 22 Jun '20

22 Jun '20

Hello nest users with a mac, From now on, it is possible to install nest via homebrew from the default homebrew-core tap: https://formulae.brew.sh/formula/nest#default [1] You get nest 2.20.0 with OpenMP and PyNEST bindings with python 3.8 delivered as a 'bottle' (prebuild binary package) in a couple of seconds - with all dependencies. Go to https://brew.sh/ [2] and follow the installation of homebrew. When brew is installed, just type: brew install nest And you should see something like: $ brew install nest ==> Downloading https://homebrew.bintray.com/bottles/nest-2.20.0_1.catalina.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/38/38bfd492f381cd059a495122d1c3342e8fb5095501c04… ######################################################################## 100.0% ==> Pouring nest-2.20.0_1.catalina.bottle.tar.gz Warning: nest dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. ==> Caveats The PyNEST bindings and its dependencies are installed with the python(a)3.8 formula. If you want to use PyNEST, use the Python interpreter from this path: /usr/local/opt/python(a)3.8/bin You may want to add this to your PATH. ==> Summary 🍺 /usr/local/Cellar/nest/2.20.0_1: 1,290 files, 21.2MB Now you can run nest like: $ nest -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 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 'help' to get more information. Type 'quit' or press CTRL-D to quit. SLI ] If you want to use PyNEST, you have to use the python(a)3.8 formula python - the dependencies numpy, scipy, etc. are also delivered via homebrew and they are build with the python(a)3.8 formula, which is keg-only [3]. Add the opt-bin path to your PATH variable like: export PATH=/usr/local/opt/python@3.8/bin:$PATH and you can start with: $ python3.8 -c 'import nest' -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 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. Best, Tammo Links: ------ [1] https://formulae.brew.sh/formula/nest#default [2] https://brew.sh/ [3] https://docs.brew.sh/How-to-Build-Software-Outside-Homebrew-with-Homebrew-k…

1 0

Feature discussion: STDP and delays
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST enthusiasts! In the NEST Meeting on May 25th <https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-…> [1] there was a very interesting discussion of handling of delays in networks with STDP in NEST. It became obvious, that this topic requires a more in-depth discussion and it was decided to do a separate VC for this discussion, which will happen this week on * Thursday, June 25, 2020 - 13:30 CEST with the connection details <https://github.com/nest/nest-simulator/wiki/Connection-Details> [2] as usual. Best, Dennis [1]: https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-… [2]: https://github.com/nest/nest-simulator/wiki/Connection-Details i.e. https://conf.dfn.de/webapp/conference/97938800 -- 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 ------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt -------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday 22 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 22 June, 11.30-12.30 CEST (UTC+2). 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/2020-06-22-Open-NEST-Developer-… 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

1 0

Installation on supercomputer failed
by Petia Koprinkova 19 Jun '20

19 Jun '20

Hi, We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors. Could you help to resolve it?Regards,Petia

5 10

LIF neuron with both current based and conductance based synapses
by Hartmut Schmidt 18 Jun '20

18 Jun '20

Dear all, I am trying to implement a network consisting of LIF neurons with mixed current based and conductance based synaptic connections. Eg. one LIF neuron which gets two inputs from which one is treated as current input and the other as conductance input. That means, how to treat the input should be encoded in the synapse and not in the type of the postsynaptic neuron. Is such a neuron model already implemented or is there a way to implement this? Thanks for your help. Best, Hartmut

3 2

pipnest
by Robin Gilbert De Schepper 17 Jun '20

17 Jun '20

Hi, I created a little tool that provides packaging for NEST extension modules into python packages that can be `pip installed` on the target machine. https://pip-nest.readthedocs.io/en/latest/ First off, is this interesting to the community? It certainly seems easier to `pip install some-module` than to provide installation instructions, and I can now specify my modules as dependencies in code I distribute. Secondly, there are some shortcomings based on the fact that the pip install only reliably produces the build artifacts into python's site-packages and nest doesn't look for them there. This can probably only be elegantly solved by adding an `entry_point` to the nest python module so that these pip nest modules can announce themselves there? -- Robin De Schepper, MSc Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/

2 2

NEST Conference 2020 Program — Registration Deadline Monday 22 June 2020
by Hans Ekkehard Plesser 16 Jun '20

16 Jun '20

Dear Colleagues! The virtual NEST Conference 2020 on 29/30 June is less than two weeks away and we are happy to invite you to an exciting program of presentations and workshops, which you will find below. The conference will be single track to facilitate interactions and include virtual coffee breakouts to mix and mingle. Please don't forget to register by MONDAY, 22 June 2020 at https://www.nest-simulator.org/conference. Please note that we now also accept PayPal as a payment method. See you at the NEST Conference 2020! Hans Ekkehard Plesser & Susanne Kunkel Monday 29 June, 2020 (all times are CEST) * 09:00 — Welcome & Introduction (Susanne Kunkel) * 09:15 — NEST user-level documentation: Why, how and what’s next? (Sara Konradi) * 09:35 — Exploring new Fenix resources using NEST (Alexander Patronis) * 09:55 — Minibreak * 10:00 — Toward a possible integration of NeuronGPU in NEST (Bruno Golosio) * 10:45 — Coffee breakout * 11:15 — Workshop: NEST multiscale co-simulation (Wouter Klijn) * 12:15 — Lunch break * 13:15 — Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep-mediated noise-resilience (Chiara De Luca) * 14:00 — Minibreak * 14:05 — An Integrated Model of Visual Perception and Reinforcement(Petia Koprinkova-Hristova) * 14:25 — Partial Information Decomposition Contextual Neurons in NEST(Sepehr Mahmoudian) * 14:45 — Coffee breakout * 15:15 — deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon) * 15:35 — Primate perisylvian cortex in NEST: from reflex to small world (Harry Howard) * 15:55 — Minibreak * 16:00 — Modeling robust and efficient coding in the mouse primary visual cortex using computational perturbations (Stefan Mihalas) * 16:45 — Wrap-up (Hans Ekkehard Plesser) * 17:00 — Mingle Tuesday 30 June, 2020 (all times are CEST) * 09:00 — A spiking neural network builder for systematic data-to-model workflow(Carlos E Gutierrez) * 09:20 — Insite: A Generalized Pipeline for In-transit Visualization and Analysis(Simon Oehrl) * 09:40 — Minibreak * 09:45 — NEST Component for Modeling Spiking Neuron-Astrocyte Networks(Jugoslava Aćimović) * 10:30 — Coffee breakout * 11:00 — Atlas-mapped reconstruction and simulation of the cerebellar Lingula in NEST (Alice Geminiani) * 11:20 — Cerebro-cerebellar loops for sensorimotor adaptation (Alberto Antonietti) * 11:40 — Minibreak * 11:45 — Modeling plasticity inducing stimulation protocols in recurrent neuronal networks with homeostatic structural plasticity (Swathi Anil) * 12:30 — Lunch break * 13:30 — Dendrites in NEST (Willem Wybo) * 13:50 — Just-in-time compilation for NESTML models in NEST Simulator (Charl Linssen) * 14:10 — NEST Desktop: A web-based GUI for the NEST Simulator (Sebastian Spreizer) * 14:30 — Minibreak * 14:40 — Evolving interpretable plasticity rules using NEST (Jakob Jordan) * 15:25 — Coffee breakout * 15:45 — Workshop: deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon & William Mayner) * 16:45 — Closing Remarks -- 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

1 0

Training SNNs with PyNEST
by s.kraemer96＠gmx.net 15 Jun '20

15 Jun '20

Dear all, I´m writing a master thesis on spiking neural networks and how transparent they are. For that I need to implement a SNN network and train it. So I started with Brian but that is much to complex and I don´t need something special. So I decided to use PyNest. I did all the tutorials but I´m missing a tutorial how to train the network. I don´t know how to put in a dataset to train the model. I haven´t found anything to this topic. So my questions are: 1. Can PyNest train set up a SNN and train it trough data and if not is there another simulator who can do this? 2. How do I do it? Is there anything I missed to read or can someone send me an example? This would be very helpful. Thanks for your help. Best, Sonja

7 6

Open NEST Developer Video Conference Monday 8 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 08 Jun '20

08 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 8 June, 11.30-12.30 CEST (UTC+2). 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 suggested from the teams. In-depth discussions will cover updates on the ongoing discussion around #1604 (STDP and delays) and proposed refactoring of the testing framework. 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/2020-06-08-Open-NEST-Developer-… 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

1 0

[NEST users] Docker container with NEST3 and music
by Benjamin Staude 05 Jun '20

05 Jun '20

Hi NEST users, Does anyone know if there is a Docker container available that has NEST3 and the MUSIC interface installed? Best regards, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

2 4

NEST Conference 2020 Registration now open
by Dennis Terhorst 04 Jun '20

04 Jun '20

The NEST Conference organization team would like to share the following exciting news: Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- 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

1 0

NEST Conference 2020 Registration now open
by Hans Ekkehard Plesser 03 Jun '20

03 Jun '20

Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- 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

1 0

NEST Conference Abstract Submission via EMAIL
by Hans Ekkehard Plesser 02 Jun '20

02 Jun '20

Dear Colleagues, Regrettably, the website for the NEST Conference 2020 became unavailable shortly before the abstract submission deadline. We are currently working to restore the website. In the meantime, please submit your abstract BY EMAIL to conference(a)nest-initiative.org using the attached template (DOCX). Please also find an example abstract with detailed instructions attached. We extend the deadline to 2 June 2020. Best regards, Hans Ekkehard

2 1

NEST 2.20.1
by Ing Jyh Tsang 02 Jun '20

02 Jun '20

Hi, Is NEST 2.20.1<https://github.com/nest/nest-simulator/milestone/8> the installed version (when following https://nest-simulator.readthedocs.io/en/stable/installation/index.html), since it solves issue #1394<https://github.com/nest/nest-simulator/issues/1394>? it seems it is completed. If this is not, when will this happen? Thanks a lot Ing Jyh Tsang

1 0

send() function
by Itaru Kitayama 01 Jun '20

01 Jun '20

Hi, How do I check where send() function implemented in connector_base.h is generated and stored in which object file? Itaru.

1 1

NEST Conference website not reachable
by Bruno Golosio 30 May '20

30 May '20

Hello, the deadline for submission of contributions is approaching and the NEST Conference website is down since yesterday. Is there an alternative way to submit contributions? Bruno -- Bruno Golosio, PhD Associate Professor of Applied Physics Coordinator of the School of Medical Physics Department of Physics University of Cagliari (Italy) [image: image.gif]

1 0

Finding the right parameters for the balanced network
by nosratullah mohammadi 26 May '20

26 May '20

Dear Nest Users, I hope all of you be in health during these times. I want to create a balanced network as it’s the first step of my master thesis. The model I want to use is “iaf_cond_exp” which is a must for later purposes. There’s an example in Pynest folder of a balanced network, unless it’s using “iaf_psc_alpha” and it doesn’t fit my goals. When I try to change the model, and run the program, the network doesn’t get active and there’s nothing to record. I divided my question into two part: - Does anyone have a balanced network with “iaf_cond_exp” neurons and all of its necessary parameters to run? - In general, how do people find or calculate their network parameters to fit the neuron model they use and don’t get lost in the massive number of parameters. Note: I also tried to use the example of “brunel_alpha_evolution_strategies.py” example which is a genetic algorithm to find the best parameter, although it finds the parameters after 50 generation, I use those parameters afterwards. It just doesn’t work! Kind regards, Nosratullah Mohammadi

2 2

NEST Conference 2020 — Submission deadline 1 June 2020
by Anne Elfgen 26 May '20

26 May '20

Dear all, Just a little reminder that the submission deadline for the (virtual) NEST Conference 2020 is *this Monday, June 1st. *We are looking forward to your contributions. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

1 0

Open NEST Developer Video Conference Monday 25 May 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 25 May '20

25 May '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 25 May, 11.30-12.30 CEST (UTC+2). 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 suggested from 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/2020-05-25-Open-NEST-Developer-… 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

1 0

Reset Kernel + STDP Performance
by Benedikt S. Vogler 22 May '20

22 May '20

Hello everyone! I am writing to you regarding two matters: Reset Network/Kernel in nest2->nest 3 In the last developer conference, Daphne Cornelisse talked about that she used ResetNetwork() to solve her problem. ResetNetwork() is marked as deprecated. No one said anything, so I got confused why this is apparently the recommended way or at least approved. She showed me, that it works (in her case). It is deprecated, so there is probably some good reasoning behind it. The documentation says: "ResetNetwork is deprecated and will be removed in NEST 3, because this function is not fully able to reset network and simulator state. What are the edge cases where the use causes problems? In this ticket, it is stated that the feature is just removed with any replacement. https://github.com/nest/nest-simulator/issues/525 Thus, in nest3 there is only ResetKernel(). This means that you have to rebuild the network for any application where you do multiple simulations with different input or parameter changes. I am using nest3 for reinforcement learning and in each training episode, I have to extract all the weights and save them, reset the kernel, reconstruct the net, then load all the weights. This adds a lot of overhead in performance and bloats my code. I basically have another front-end storing the net and talking to the nest back-end. Therefore, the update to nest3 is a downgrade for many applications. I don’t have a solution for this issue, but I want to spark some discussion as I learned that I am not the only nest user to stumble into this issue. STDP Performance boost by manual computation in python In the paper "Demonstrating Advantages of Neuromorphic Computation: A Pilot Study“ by Wunderlich et al. (https://www.frontiersin.org/articles/10.3389/fnins.2019.00260/full) some performance improvement on STDP was reported. "The synaptic weight updates in each iteration were restricted to those synapses which transmitted spikes, i.e., the synapses from the active input unit to all output units (32 out of the 1,024 synapses), as the correlation a+ of all other synapses is zero in a perfect simulation without fixed-pattern noise. This has the effect of reducing the overall time required to simulate one iteration[…]“ The provided source code (https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4… <https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4…>) indeed contains a manual computation of STDP. When using the nest library I don’t expect to do some computation in python to be faster. It appears to me that the nest implementation is computing STDP every time, even without spikes? Maybe someone can comment on this whether this can be improved in nest? Kind regards, Benedikt S. Vogler -- Benedikt S. Vogler benedikt.s.vogler(a)tum.de Student M.Sc. Robotics, Cognition, Intelligence

3 3

Inhibitory plasticity with current based neurons
by Julia Gallinaro 11 May '20

11 May '20

Dear all, I would like to simulate a network of current based LIF ('iaf_psc_delta') with inhibitory plasticity. I tried using the model vogels_sprekeler_synapse, but the resulting weights are positive (and they increase when firing rate is high). I guess it is because when used with conductance based neurons, the resulting weights would be multiplied by a gI<0? And with current based neurons, this is not the case. The weight is directly used as the synaptic weight. Do I understand it right? Is there a way to implement inhibitory plasticity using the vogels_sprekeler_synapse and current based LIF? Best, Júlia

3 5

Open NEST Developer Video Conference Monday 27 April 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 11 May '20

11 May '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 11 May, 11.30-12.30 CEST (UTC+2). 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 suggested from 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/2020-05-11-Open-NEST-Developer-… 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

2 2

Spike Train Frequencies Inspection
by Benedikt Feldotto 08 May '20

08 May '20

Dear all, I am working with frequency encoded spike trains and therefore like to observe the changing spike frequencies between different individual connections in my network (if possible in real time). While I can record the spike events with time using 'spike_detector' units, I couldn't find a direct method to calculate the frequency. Is there any method implemented or a preferred way to calculate frequencies from spike trains over time or would this calculation be up to the user? I am also thinking about using an indirect way by attaching a leaky integrate and fire neuron with infinite threshold. Thanks! Best, Benedikt -- 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

2 2

Control over the synaptic weight and synaptic decay time
by Nosratullah M 08 May '20

08 May '20

Dear all, I hope you are in staying safe. I'm working on a balanced network consisting of "iaf_cond_exp" neurone model. I want to have the control over these parameters at the same time: - increasing the synaptic decay time. - reducing the synaptic weight. The goal is to make the area under the synaptic current, constant. So that we know that the only parameter that is affecting on the network, is synaptic delay. I wonder if you know of any furmula in mathematics or any algorithm, that can help me, making this process automatic. And keeping the area under the curve, a constant value. Best wishes, Nosratullah

3 3

local_num_threads, multiprocessing and topology.ConnectLayers
by Juan Manuel Vicente 06 May '20

06 May '20

Hi all, I'm trying to understand some inner workings of Nest. Rigth now I'm running simulations with close half millons elements, using mpirun in a cluster with 25 nodes. The problem I am having is that the "setup" (layer creation and connections) phase takes close to 8min and the simulation only takes 1min. So I tried to use python's multiprocessing package to speed it up, with the following code: nest.ResetKernel() nest.SetKernelStatus({"local_num_threads": 1}) #... connections = [ (layer1, layer1, conn_ee_dict, 1), (layer1, layer2, conn_ee_dict, 2), (layer2, layer2, conn_ee_dict, 3), (layer2, layer1, conn_ee_dict, 4) ] # Process the connections. def parallel_topology_connect(parameters): [pre, post, projection, number] = parameters print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) pool = multiprocessing.Pool(processes=4) pool.map(parallel_topology_connect, connections) The above example takes around 0.9s, but if the last two to lines are changed for a sequential call, it takes 2.1s: for [pre, post, projection, number] in connections: print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) So far the multiprocessing works great, the problem comes when the "local_num_threads" parameters is changed from 1 to 2 or more, in the cluster it could be 32. The code gets stuck in the topology.Connect without any error, after a while I just stopped it. Also I realised that the tolopoly.ConnectLayers just spawn one thread to connects layers despite the local_num_threads is setted more than one. Any idea what is going on? Thanks in advance Juan Manuel PD: The full example code is attached (60 lines of code). The local_num_threads and multiprocessing_flag variables change the behaviors of the code.

4 5

Implementing Synaptic Failure Rate
by Joshua Stern 04 May '20

04 May '20

Hello, I hope everyone is well. I am working on replicating some results from Teremae et al 2012 <https://www.nature.com/articles/srep00485#Sec4> and have run into an area of uncertainty. The paper calls for there to be a synaptic weight-dependent failure rate of synaptic transmission: [image: image.png] Is there any way to implement this in Nest? If it would help, I am working on a custom neuron model built in Nestml. I can also write some C++ if it seems that there would be an easy way to add this functionality with a short function. Alternatively, are there canonical ways to alter network structure to account for such a failure rate if it cannot be implemented in Nest? Thank you and best wishes, Josh Stern

2 2

NEST3 / Some thoughts on NodeCollections and Connect
by Hans Ekkehard Plesser 01 May '20

01 May '20

Dear Colleagues, This mail is mostly relevant for developers, but I would also like interested users to take a look and comment. In https://github.com/nest/nest-simulator/issues/1570#issuecomment-622380622 I have attempted to summarize a number of thoughts about the details of node representation and Connect() semantics. While a lot is in place, we still need to clarify some details in the near future, before we can release NEST 3. Your input is therefore welcome! If you haven't looked at NEST 3 yet, you may want to take a look at https://nest-simulator.readthedocs.io/en/latest/guides/nest2_to_nest3/nest2… first. Best regards, Hans Ekkehard -- 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

1 0

NEST Conference 2020 goes virtual — Call for Contributions
by Anne Elfgen 30 Apr '20

30 Apr '20

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2020. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are now inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

1 0

error at installing nest2.20 from source code
by Abolfazl Ziaeemehr 29 Apr '20

29 Apr '20

Hello everyone, I used the source code to install nest simulator 2.20 from here <https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.…> and did the following steps (I used to do the same steps for version 2.18 without error.) cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path> </path/to/NEST/src> make make install make installcheck I got this error from "make installcheck": Phase 1: Testing if SLI can execute scripts and report errors ------------------------------------------------------------- Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found Failed: unexpected exit code 127 Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found *** *** An unexpected exit code usually hints at a bug in the test suite! *** *** Please report the problem at *** https://github.com/nest/nest-simulator/issues *** *** To help us diagnose the problem, please attach the archived content *** of these directories to the issue: *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports' *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi' *** CMakeFiles/installcheck.dir/build.make:57: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 2 CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:188: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 -- regards, Abolfazl Ziaeemehr Department of Physics, PhD student in Computational Physics Institute for Advanced Studies in Basic Sciences (IASBS) Tel: 0919 607 4296 Page: iasbs.ac.ir/~a.ziaeemehr

3 11

Reset while keeping network connections
by Daphne Cornelisse 27 Apr '20

27 Apr '20

Dear Nest community, I have a network of LIF neurons ('iaf_cond_alpha') and I would like to implement STDP synapses, rather than the standard 'static_synapse'. I would like to be able to set a subset of the network to STDP synapses (e.g. all excitatory ones) and leave the rest static. This is how have implemented that currently (see code). I am using a for loop because I want to see how STDP changes the activity over time (over many iterations), which leaves me with the following two questions: *1. Is this a correct way to implement STDP in nest? * *2. Is there a way to reset the network such that the connections are not lost? *ResetNetwork() and ResetKernel() both seem to destroy all the network connections. While I would like to keep them, so that the network becomes less and less randomly connected per simulation. Thank you! Best, Daphne *CODE* # define network connectivity conn_dict = {'rule': 'pairwise_bernoulli', 'p': 0.1} # define dicts for static synapses static_ex_params = {'model':'static_synapse','weight': 6.0, 'delay': 1.5} static_in_params = {'model':'static_synapse','weight': -96.0, 'delay': 1.5} if self.STDP == 'ALL': # all synapses should be stdp ones, make connections between the two populations: # from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, self.syn_params_in) elif self.STDP == 'EXC': # keep the inhibitory synapses static # connections from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # connections from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, static_in_params) where synapse_params_in = { 'model':'stdp_synapse', 'lambda': 0.01, 'alpha': 1.0, 'delay': 1.5, 'weight':-95.0 }

3 2

Open NEST Video Conference Satellite Event: A declarative front-end for network and simulation specifications
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! Additionally to the Open NEST Developers VC on Monday, we would like to announce a user contributed presentation of *A declarative front-end for network and simulation specifications* by /Tom Bugnon/ (Paris) and /Will Mayner/ (Wisconsin). on Monday 27 April, 16.00-17.00 CEST (UTC+2) / 9.00am CDT (UTC-5). This frontend to NEST allows to define the structure of more-or-less arbitrary simulations in a set of parameter files. Those let the user define network parameters (layers, neuron/synapse models, connections and nest.Topo "connection models", "input" layers etc.) and simulation parameters (set-up recorders, set-up "sessions", or units of simulations, for which the user can define specific inputs, changes in the state of some units, etc). This approach makes it easier to version-control the network and simulation specifications, share parameter files, perform parameter exploration, or run the same network in different conditions. We will meet in the same VC room, but due to the timezone difference of the presenters this had to be detached from the meeting in the morning. Connection details are given below. 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 -- 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 ------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt -------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday 27 April 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 27 April, 11.30-12.30 CEST (UTC+2). This VC will be in the updated format and we may do some more explanation than I'd expect in future meetings. 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 suggested from the teams. Agenda Welcome Review of NEST User Mailing List Short introduction to Github project usage Project team round In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-04-27-Open-NEST-Developer-… 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

1 0

Re: SARS-CoV face mask sanitizing gels
by ywjingqing 23 Apr '20

23 Apr '20

1 0

Question about MPI and multithreading
by kusch lionel 15 Apr '20

15 Apr '20

Dear all, I am actually working on the I/O for Nest with MPI. I am not aware of the solution of Nest for managing the communication between process and thread. I would like to learn more about it for adapting the interface with the actual solution. If someone can answer some of my questions : 1) By looking at the initialization of the MPI, I saw Nest use the /MPI_THREAD_FUNNELED /for the level of thread support. What is the reason for it? 2) This level of thread support surprise me because I suppose that it will overload one thread with all the MPI calls. Why do you do not choose the level /MPI_THREAD_SERIALIZED/? 3) I would like to have different levels for thread support. Do you think it's possible ? Thank you in advance for your answer, Kusch Lionel PS: The reference to the different MPI thread support : http://mpi.deino.net/mpi_functions/MPI_Init_thread.html

2 1

GitHub Projects
by Dennis Terhorst 14 Apr '20

14 Apr '20

Dear NEST users and developers, some of you may already have noticed, that we recently updated a lot of issues and pull-requests in our repository. The changes are completely organizational and aim to provide a better overview and service to our community. In particular, we removed the "C:" category labels (Model, Kernel, PyNEST, Documentation, ...) and instead now make use of corresponding GitHub projects. There, issues and pull-requests are represented as "cards" on a Kanban-like board, which gives a comprehensive view on the current topics and enables dedicated discussions to focus more easily. For each project we assigned a contact person that will take care of organizing work for that subset of cards. You notice that also the "P:" progress labels have mostly been removed (except "blocked" and "won't fix"), as this is automatically tracked in the columns of the projects and is much easier to manage there. The change to GitHub projects enables us to discuss topics in a more focused fashion than detailed issue-by-issue, which will also be reflected in the Open NEST Developer Video Conference. Projects will give a general status update and can raise overarching questions into the discussion. The detailed issue-by-issue work on the other hand, is organized by the project groups separately and each group may decide to do separate meetings to discuss details. Besides the long-running projects corresponding to the category labels, larger short/mid-term activities are organized in "Feature-Projects". These projects aim to help developers to work on special or cross-cutting topics and are expected to be "finished" at some point. The open VC will cover them similar to the long-term projects if required. We hope these changes improve the overview over the work ongoing in all the many areas for users and developers, facilitate detailed discussions between relevant and interested people and make the work on the simulator more transparent. Best, Dennis

1 0

Open NEST Developer Video Conference Monday 13 April 2020 SKIPPED (Easter Monday)
by Dennis Terhorst 13 Apr '20

13 Apr '20

Dear NEST Users & Developers! I would like to wish you all a happy Easter time and I hope you are all well despite the current circumstances. Since it is Easter Monday in some parts of the world, we will skip this meeting. I am looking forward to seeing you again in our next Open NEST Developer Video Conference on April 27th. Stay safe, best, Dennis Terhorst

1 0

Custom input for neurons
by Nicolas Martorell 06 Apr '20

06 Apr '20

Dear all, I'm new at NEST, and I've been trying to recreate a neural system from my work. This involves an IAF neuron which receives two different stimuli (they would be represented by inputs to the neuron - increases in post-synaptic potential). Since these are stimuli I control in my experiments, I need to be able to control their dynamics as the simulation progresses (for example, one of the stimuli has an exponentially larger effect as time progresses). Therefore, it's important for me to be able to control the dynamic of these inputs. However, I have not been able to find a way to do this. One idea I've had is to set the amplitude of a noise-generator to change according to a function of my choosing (going back to the previous example, it would be an exponential function). But this would require for this parameter to be changed mid-simulation, or to be assigned to a function and interpreted by NEST. Is any of this possible? Or alternatively, do you know of another way of accomplishing this? Thank you! Nicolas

2 1

2025

2024

2023

2022

2021

2020

2019

NEST Users