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
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
Hi,
I'm trying to port to NEST this "conductance-based" network from Brian:
https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_…
I'm unable to reproduce their results (qualitatively - I'm not expecting
identical results since I assume RNGs, solvers and other implementation
details differ in many ways). Is there any publicly available example of a
random balanced network with conductance based synapses? From what I've
seen, all the brunel-style example networks are current based (as in the
original paper).
Thanks in advance,
Adam
Hi NEST users,
I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development.
To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor.
By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor.
At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron
which I hope it will solve the error with the receptor.
From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming
through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting
two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron."
My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ?
If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ?
Thank you very much,
Kind regards,
Nikolas
Dear NEST Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference today (please excuse the late invitation)
Monday 28 October, 11.30-12.30 CET (UTC+1).
See below for information about how to log into the meeting.
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-…
Agenda
1. Welcome
2. Planning of HBP High-Level Support Event in Heidelberg
<https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…>
next month
3. Review of NEST User Mailing List
<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…>
4. Review of open Github Pull Request
<https://github.com/nest/nest-simulator/pulls>
5. Review of open Github Issues
<https://github.com/nest/nest-simulator/issues>
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
Log-in information
------------------
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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
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Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
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* 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.
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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
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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
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)
Hello,
I would like to make a suggestion for future development. Now there is
a Python interface, but some of us have been working with C/C++ for
many years (and we have a lot of data processing software developed in
this language).
Please, could you include a C/C++ interface for NEST?
Thanks a lot in advance!
Xavier
Hi all,
I have a question regarding random number generator.
I am intend to randomly choose neuron population but keep this same across
multiple processes. (see attached)
mpirun -np 4 python network_population.py
However, seemingly I am missing something.
Also, in case I try to use different population count I am getting error
while connecting nodes with input or probes. (see mpi_example)
--
Thanks and Regards
*Maryada*
