- NEST Users - NEST Initiative Mail

by Robin Gilbert De Schepper

Hi! It seems to have been a while since an invitation to the bi-weekly meeting has been sent out. Will they resume soon? I would like to discuss the topic of extension modules and feel like the meeting is great place to get informed. Best regards -- 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/

3 years, 7 months

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Open NEST Developer Video Conference Monday 14 September 2020 11:30 CEST (UTC+2)

by Dennis Terhorst

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

3 years, 7 months

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error when making

by Carlos Gutierrez

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 --------------------------------------------------------------------------------

3 years, 7 months

2
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Open NEST Developer Video Conference Monday 31 August 2020 11:30 CEST (UTC+2)

by Dennis Terhorst

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

3 years, 8 months

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Re: Issue with NEST Live Media 2.20

by Steffen Graber

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 -------------------------------------------------------------------------------------

3 years, 8 months

1
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Issue with NEST Live Media 2.20

by 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*

3 years, 8 months

2
5
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Random refractory period

by giovannidisarra

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

3 years, 8 months

2
1
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Open NEST Developer Video Conference Monday 17 August 2020 11:30 CEST (UTC+2)

by Dennis Terhorst

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

3 years, 8 months

1
0
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Saving and loading entire network

by LOW, SOCK CHING

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

3 years, 8 months

6
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Open NEST Developer Video Conference Monday 3 August 2020 11:30 CEST (UTC+2)

by Dennis Terhorst

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

3 years, 9 months

1
0
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