August 2019 - NEST Users - NEST Initiative Mail

by Xavier Otazu

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

5 years, 1 month

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problem loading pynn nest installed from live media

by Julian Martin Leslie Budd

Hi After installing NEST ubuntu 18.04 live media (lubuntu-18.04_nest-2.18.0.ova downloaded a few days ago), I get the following error message but a m able to import nest in python3 ok: nest@nestvm:~$ python3 Python 3.6.8 (default, Jan 14 2019, 11:02:34) [GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import pyNN.nest as sim [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.18.0 Built: Jul 2 2019 15:09:55 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. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 257, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 59, in __init__ self.verbosity = "warning" File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 120, in _set_verbosity nest.sli_run("M_%s setverbosity" % verbosity.upper()) AttributeError: module 'nest' has no attribute 'sli_run' >>> Any suggestions? Thanks.

5 years, 3 months

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installation issue: make installcheck fail pynest tests

by Julian Martin Leslie Budd

Hi Please could someone suggest the most likely reason why current NEST (v2.16.0) appears to install ok (tutorials tested work) but fails during make installcheck for pynest tests: $ make installcheck ... Phase 7: Running PyNEST tests. ------------------------------ Using nosetests. [cajal:07463] Failing at address: 0x44000099 [cajal:07463] *** End of error message *** Segmentation fault (core dumped) PyNEST tests: Passed: 0 Skipped: 0 Failed: 0 /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: 790: /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: arithmetic expression: expecting primary: " 363 + " 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:208: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 $ Current setup: ubuntu 16.04, python 2.7.12, and nose 1.3.7. Thanks.

5 years, 3 months

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weigth recorder does not record recorded eligibility trace and neuromodulator concentration.

by anduls＠web.de

5 years, 3 months

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stdp_dopamine_synapse weight_recorder eligibility trace and neuromodulator concentration.

by anduls＠web.de

5 years, 4 months

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cannot "import nest" in virtual box installation?

by r.doursat＠mmu.ac.uk

Hello, I followed the NEST LIVE MEDIA Installation instructions, and the NEST 2.18.0 VirtualBox lubuntu 18.04_1 seems to be running fine. But then in a terminal window in the home directory, and whether running from inside ipython or python, after I type "import nest" at the prompt, I get an error message: "ImportError: dynamic module does not define init function (initpynestkernel)" (line 74 of ll_api.py). There is also another error message just before it: "Import kernel in __init__ after initializing low-level APIs" (line 28 of __init__.py) How can this be fixed? Thanks! -Rene

5 years, 4 months

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Save all weights, set new weights and update to the simulation.

by zhe.sun.vk＠riken.jp

Hi everyone, I am SUN, working in RIKEN, Japan. I am working on one issue. I am useing the GetConnections to get the weights and keep it in the text. connections = nest.GetConnections(source, target) When I want to update the weight with the new information. I am using this: conn=nest.GetConnections(gid,gid) nest.SetStatus(conn, newweight) But it is not working, do you have any ideas? Best wishes, Sun

5 years, 4 months

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Open NEST Developer Video Conference Monday 19 August 2019 11.30 CEST (UTC+2)

by Hans Ekkehard Plesser

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 19 August, 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 https://github.com/nest/nest-simulator/wiki/2019-08-19-Open-NEST-Developer-… • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues See you soon! Hans Ekkehard Plesser ------------------ 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 -- 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

5 years, 4 months

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NEST 2.18.0 (and 2.16.0) now available in NeuroFedora

by Ankur Sinha

Hello, On behalf of the NeuroFedora team, I'm happy to report that NEST 2.18.0 and 2.16.0 are both available for use on Fedora. Information on using NEST on NeuroFedora is documented here: https://docs.fedoraproject.org/en-US/neurofedora/nest/ Here are a few quick FAQs for your convenience: Q. How do I use NEST on NeuroFedora? A. It only takes two steps to install NEST using `dnf` (the default package manager): - Download and run (optionally install) a "live" Fedora Workstation image from https://getfedora.org - Install NEST 2.18.0: Run `sudo dnf install python3-nest` in a terminal. Q. How do I use version 2.16.0? A. 2.16.0 is provided as a "module". To install the 2.16.0 version: - Download and run (optionally install) a "live" Fedora Workstation image from https://getfedora.org - Install NEST 2.16.0: Run `sudo dnf module install nest:2.16.0` in a terminal. Please note that only one version of NEST can be installed at once. Q. Does NEST in NeuroFedora include MPI support? A. Yes---variants built with both MPICH and OpenMPI are available to use. Q. Does NEST in NeuroFedora include libneurosim/MUSIC/CSA support? A. Not all of them yet. - libneurosim: Yes - MUSIC: No (under review: https://pagure.io/neuro-sig/NeuroFedora/issue/28) - CSA: No (WIP: https://pagure.io/neuro-sig/NeuroFedora/issue/33) Q. Where do I get help? A. The NeuroFedora team maintains multiple communication channels for support and general discussion: https://docs.fedoraproject.org/en-US/neurofedora/communicating/ Q. What other tools does NeuroFedora provide? A. The complete list includes neuron, auryn, PyLEMS, NineML and lots more: https://src.fedoraproject.org/group/neuro-sig Fedora also includes more software that is not specific to computational neuroscience---such as productivity and development tools, a variety of desktop environments, server and container focussed editions, and other science related software: - https://getfedora.org/ - https://labs.fedoraproject.org/ - https://spins.fedoraproject.org/ Q. How can I help? A. The NeuroFedora team is made up of volunteers that believe in Free Software and Open Science. Information on how you can join us and help is summarised here: https://docs.fedoraproject.org/en-US/neurofedora/contributing/ -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in PhD candidate in computational neuroscience at UH Biocomputation | http://biocomputation.herts.ac.uk/ Free/Open source community volunteer at the Fedora project | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

5 years, 4 months

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Error running tutorial notebook

by Filip Vercruysse

(CNS2019_NEST) Filips-MacBook-Pro:CNS2019_NEST_Tutorial filip$ jupyter-notebook [I 11:01:50.427 NotebookApp] The port 8888 is already in use, trying another port. [I 11:01:50.439 NotebookApp] Serving notebooks from local directory: /Users/filip/Desktop/Research/Conferences/CNS Barcelona/NEST tutorial/CNS2019_NEST_Tutorial [I 11:01:50.439 NotebookApp] The Jupyter Notebook is running at: [I 11:01:50.439 NotebookApp] http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4… [I 11:01:50.439 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 11:01:50.445 NotebookApp] To access the notebook, open this file in a browser: file:///Users/filip/Library/Jupyter/runtime/nbserver-31158-open.html Or copy and paste one of these URLs: http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4… [I 11:01:57.768 NotebookApp] Kernel started: 103ab68f-95af-4961-8f9d-3756f2192fd2 [I 11:01:58.401 NotebookApp] Adapting to protocol v5.1 for kernel 103ab68f-95af-4961-8f9d-3756f2192fd2 [INFO] [2019.7.13 11:2:4 /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2019.7.13 11:2:4 /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG Assertion failed: (out != NULL), function execute, file /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/sli/sli_io.cc, line 422. [Filips-MacBook-Pro:31166] *** Process received signal *** [Filips-MacBook-Pro:31166] Signal: Abort trap: 6 (6) [Filips-MacBook-Pro:31166] Signal code: (0) [Filips-MacBook-Pro:31166] [ 0] 0 libsystem_platform.dylib 0x00007fff791bfb3d _sigtramp + 29 [Filips-MacBook-Pro:31166] [ 1] 0 ??? 0x0000000000000001 0x0 + 1 [Filips-MacBook-Pro:31166] [ 2] 0 libsystem_c.dylib 0x00007fff7907e1c9 abort + 127 [Filips-MacBook-Pro:31166] [ 3] 0 libsystem_c.dylib 0x00007fff79046868 basename_r + 0 [Filips-MacBook-Pro:31166] [ 4] 0 libsli.dylib 0x0000000110a01077 _ZNK18StrSStreamFunction7executeEP14SLIInterpreter + 759 [Filips-MacBook-Pro:31166] [ 5] 0 libsli.dylib 0x00000001109edb2e _ZN13FunctionDatum7executeEP14SLIInterpreter + 446 [Filips-MacBook-Pro:31166] [ 6] 0 libsli.dylib 0x00000001109ebe42 _ZN14SLIInterpreter8execute_Em + 466 [Filips-MacBook-Pro:31166] [ 7] 0 libsli.dylib 0x00000001109ebc58 _ZN14SLIInterpreter7startupEv + 40 [Filips-MacBook-Pro:31166] [ 8] 0 libnest.dylib 0x0000000110031ffa _Z11neststartupPiPPPcR14SLIInterpreterNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE + 3306 [Filips-MacBook-Pro:31166] [ 9] 0 pynestkernel.so 0x000000010ffd5cb8 _ZL42__pyx_pw_12pynestkernel_10NESTEngine_5initP7_objectS0_S0_ + 3464 [Filips-MacBook-Pro:31166] [10] 0 python 0x00000001025a948a _PyCFunction_FastCallDict + 362 [Filips-MacBook-Pro:31166] [11] 0 python 0x000000010268042f call_function + 143 [Filips-MacBook-Pro:31166] [12] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [13] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [14] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [15] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [16] 0 python 0x0000000102671729 _PyEval_EvalCodeWithName + 425 [Filips-MacBook-Pro:31166] [17] 0 python 0x000000010266bf99 builtin_exec + 345 [Filips-MacBook-Pro:31166] [18] 0 python 0x00000001025a8dd2 PyCFunction_Call + 66 [Filips-MacBook-Pro:31166] [19] 0 python 0x000000010267e2b2 _PyEval_EvalFrameDefault + 47554 [Filips-MacBook-Pro:31166] [20] 0 python 0x0000000102671729 _PyEval_EvalCodeWithName + 425 [Filips-MacBook-Pro:31166] [21] 0 python 0x000000010268089a fast_function + 362 [Filips-MacBook-Pro:31166] [22] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [23] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [24] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [25] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [26] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [27] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [28] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [29] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] *** End of error message *** [I 11:02:06.763 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports WARNING:root:kernel 103ab68f-95af-4961-8f9d-3756f2192fd2 restarted [I 11:03:57.801 NotebookApp] Saving file at /part1_NEST/0_hello_world.ipynb

5 years, 4 months

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NEST Users August 2019