Dear NEST Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference today (please excuse the late invitation)
Monday 28 October, 11.30-12.30 CET (UTC+1).
See below for information about how to log into the meeting.
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-…
Agenda
1. Welcome
2. Planning of HBP High-Level Support Event in Heidelberg
<https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…>
next month
3. Review of NEST User Mailing List
<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…>
4. Review of open Github Pull Request
<https://github.com/nest/nest-simulator/pulls>
5. Review of open Github Issues
<https://github.com/nest/nest-simulator/issues>
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
Log-in information
------------------
We use a virtual conference room provided by DFN (Deutsches Forschungsnetz).
You can use the web client to connect. We however encourage everyone to
use a headset for better audio quality or even a proper video
conferencing system (see below) or software when available.
Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
* Enter your name and allow your browser to use camera and microphone
* The conference does not need a PIN to join, just click join and you're in.
In case you see a dfnconf logo and the phrase "Auf den
Meetingveranstalter warten", just be patient, the meeting host needs to
join first (a voice will tell you).
VC system/software
How to log in with a video conferencing system, depends on you VC system
or software.
- Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or
194.95.240.2##97938800
- Using the SIP protocol:97938800@vc.dfn.de
- By telephone: +49-30-200-97938800
For those who do not have a video conference system or suitable
software, Polycom provides a pretty good free app for iOS and Android,
so you can join from your tablet (Polycom RealPresence Mobile, available
from AppStore/PlayStore). Note that firewalls may interfere with
videoconferencing in various and sometimes confusing ways.
For more technical information on logging in from various VC systems,
please see
http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4
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*
Dear NEST colleagues,
We like to inform you all about an event of the Human Brain Project,
that will take place in Heidelberg on November 25-28. It will be
comprised of introductory sessions on different types of infrastructure
that is being built for the neuroscience community. Among these will be
several NEST related sessions which may be of interest to you (see
attached file).
This is a combined event with a CodeJam and infrastructure trainings,
which will take place in close space-time proximity:
* 25 Nov: [Public event] EBRAINS - New enabling infrastructure for
neuroscience
* 26 Nov: How to increase the FAIRness of your research - an HBP
training course about data sharing
* *26-28 Nov: 2nd HPAC Platform Training *
* *26-28 Nov: CodeJam#10 *
The 2nd HPAC Platform Training will introduce the tools and services of
the High-Performance Analysis and Computing Platform and Fenix,
including an interactive session on how to apply for those resources.
There will also be several sessions about the simulators with different
resolutions being (co)developed in the HBP (Arbor, NEST and TVB).
More info and registration can be found here:
https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…
The registration is already open but requires an account to register. If
you would like join the event please send an email to Maren Frings
<m.frings(a)fz-juelich.de> so we can create a guest account for you. Then
you can*register e.g. for the HPAC Training*. The events will have joint
breaks and it will be possible to switch to another event for the one or
the other session. You need to register only for the event you are most
interested in.
It would be great to see you there! :-)
Best regards,
Dennis & Maren
Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi… <https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi…> in the docker environment of NEST (https://github.com/nest/nest-docker <https://github.com/nest/nest-docker>) on my OSX host.
To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank.
MUSIC: Did you launch music using mpirun?
MUSIC: If so, check the comments about porting in README.
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
MUSIC: Unable to determine process rank.
MUSIC: Did you launch music using mpirun?
MUSIC: If so, check the comments about porting in README.
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[46746,1],0]
Exit code: 1
Can anyone help?
Thanks in advance,
Benjamin
-- -- --
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com
Dear HBP-NEST users!
// This mail only regards people involved in the Human Brain Project
(HBP). //
For making your usage of NEST more visible to the HBP internal
reporting, we would be happy to see you in the list of the so called
/component users/.
For this you just need to go to the NEST component page
https://plus.humanbrainproject.org/components/209/ and do *three clicks*:
1. click the green [edit] button
2. click [+me] at "Component User Group", and finally
3. click [Save] at the bottom of the page.
This ensures the continued support of many developers and helps to show
the multitude of research using NEST simulations, and is highly appreciated.
If you use or intend to use any number of the following specific NEST
features, please feel free to also add yourself there, to show your
appreciation to the respective developers:
* optimizations for simulations on high-performance computing platforms
https://plus.humanbrainproject.org/components/1666/ and
https://plus.humanbrainproject.org/components/1667/
* models with continuous dynamics / gap-junctions
https://plus.humanbrainproject.org/components/510/
* models with 3rd factor plasticity
https://plus.humanbrainproject.org/components/2696/
* the NEST modeling language (NESTML)
https://plus.humanbrainproject.org/components/2679/
* connection generation in very large networks
https://plus.humanbrainproject.org/components/2678/
There are many other related components that you may also want to add
yourself, like simulator-simulator interactions (e.g. 2693),
visualization (e.g. 2697), and many more. Please contact me if you feel
like you can't find something that you would like to "+me".
best,
Dennis
--
Dipl.-Phys. Dennis Terhorst
Coordinator Software Development
Institute of Neuroscience and Medicine (INM-6)
Computational and Systems Neuroscience &
Theoretical Neuroscience,
Institute for Advanced Simulation (IAS-6)
Jülich Research Centre, Member of the Helmholz Association and JARA
52425 Jülich, Germany
Building 15.22 Room 4004
Phone +49 2461 61-85062
Fax +49 2461 61- 9460
d.terhorst(a)fz-juelich.de
Dear NEST Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference today (please excuse the late invitation)
Monday 14 October, 11.30-12.30 CEST (UTC+2).
See below for information about how to log into the meeting.
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-…
Agenda
• Welcome
• Python 2 support in NEST3?
• Review of NEST User Mailing List
• Review of open Github Pull Request
• Review of open Github Issues
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
Log-in information
------------------
We use a virtual conference room provided by DFN (Deutsches Forschungsnetz).
You can use the web client to connect. We however encourage everyone to
use a headset for better audio quality or even a proper video
conferencing system (see below) or software when available.
Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
* Enter your name and allow your browser to use camera and microphone
* The conference does not need a PIN to join, just click join and you're in.
In case you see a dfnconf logo and the phrase "Auf den
Meetingveranstalter warten", just be patient, the meeting host needs to
join first (a voice will tell you).
VC system/software
How to log in with a video conferencing system, depends on you VC system
or software.
- Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or
194.95.240.2##97938800
- Using the SIP protocol:97938800@vc.dfn.de
- By telephone: +49-30-200-97938800
For those who do not have a video conference system or suitable
software, Polycom provides a pretty good free app for iOS and Android,
so you can join from your tablet (Polycom RealPresence Mobile, available
from AppStore/PlayStore). Note that firewalls may interfere with
videoconferencing in various and sometimes confusing ways.
For more technical information on logging in from various VC systems,
please see
http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4
