November 2019 - NEST Users - NEST Initiative Mail

NEST network object
by alehr 20 Nov '20

20 Nov '20

Dear NEST developer, I would like to initialize a network with neurons and connections and then run many simulations with it. It would be great if I could build the network one time and then deepcopy (or something similar) for each simulation. Is something like this possible? Thanks, Andrew Lehr

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Realtime access to spikes in simulation
by Benjamin Staude 04 Feb '20

04 Feb '20

Hi NEST-Team, To use the NEST-Simluator in an interactive installation, I would need to 1) have access to the spike in the network in realtime, and 2) send signals (spikes) to neurons in the simulation in realtime. For 1), I could imagine writing the spike-times to a file and then reading that file while the simulation is running. However, I currently don’t see an option for 2). Then I heard that you are actually working on module that would enable realtime I/O-access. Is that the case? And, if so, is there a timeline? Best, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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Hackathon on CEREBELLUM MODELLING
by Dennis Terhorst 17 Dec '19

17 Dec '19

Dear simulation enthusiasts, The group in Pavia is preparing an event around CEREBELLUM MODELLING, in which you can see NEST and other simulators put to use on larger scale. It will be a nice occasion to meet with many other users, exchange experience and learn about model construction. Egidio, Claudia, Simona and team are organising this as a hackathon: Hackathon on CEREBELLUM MODELLING 13-15 January 2020, in Pavia. If you are interested in joining, please drop Simona Tritto an email:simona.tritto@unipv.it<mailto:simona.tritto@unipv.it> You can find the program attached. best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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

27 Nov '19

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

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

23 Nov '19

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

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

18 Nov '19

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

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

10 Nov '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 11 November, 11.30-12.30 CET (UTC+1). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-11-11-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List3 * Review of open Github Pull Request * Review of open Github Issues Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Re: Issues with make under OSX
by Hans Ekkehard Plesser 08 Nov '19

08 Nov '19

Hi Benjamin, It is curious that MPI is not found on your system. Could you double check that you have installed open-mpi via Homebrew? What does which mpicxx return on your system? Best, Hans Ekkehard On 26 Oct 2019, at 17:04, Benjamin Staude <benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Thanks for the support, that solved one issue. But now, I get the same for OPEN_MPI: -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) (I need open_mpi because I need the MUSIC interface). This is my cmake-call: cmake \ -DCMAKE_C_COMPILER=gcc-9 \ -DCMAKE_CXX_COMPILER=g++-9 \ -Dwith-music=ON \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCMAKE_INSTALL_PREFIX=/Users/staude/.pyenv/versions/3.7.2/ \ /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0 And the output: -- The CXX compiler identification is GNU 9.2.0 -- The C compiler identification is GNU 9.2.0 -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/g++-9 -- Check for working CXX compiler: /usr/local/bin/g++-9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-9 -- Check for working C compiler: /usr/local/bin/gcc-9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - not found -- Looking for C++ include ostream -- Looking for C++ include ostream - not found -- Looking for C++ include sstream -- Looking for C++ include sstream - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp -- Found OpenMP_CXX: -fopenmp -- Found OpenMP: TRUE -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:528 (message): MUSIC requires -Dwith-mpi=ON. Call Stack (most recent call first): CMakeLists.txt:167 (nest_process_with_music) And the cmake-version: cmake --version cmake version 3.15.3 On 26. Oct 2019, at 14:11, Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, The CMake output shows that you are using the AppleClang compiler, which does not support OpenMP. If you want to use that compiler, you need to turn off OpenMP with -Dwith-openmp=OFF. If you want NEST with OpenMP on the Mac, I would recommend using the GCC compiler installed via Homebrew, see https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… for instructions. Best, Hans Ekkehard On 25 Oct 2019, at 18:12, Benjamin Staude <benjamin.staude(a)gmail.com> wrote: Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp) _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser

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

06 Nov '19

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

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

06 Nov '19

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

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NEST Users November 2019