June 2019 - NEST Users - NEST Initiative Mail

[stdp_dopamine] Different concentrations for different number of threads
by Guilherme Miotto 22 Jul '19

22 Jul '19

Hi everyone, I'm getting strangely different results if I use stdp_dopamine_synapse with more than 1 local thread. For instance, the mini-code bellow creates a connection with an initial non-zero DA concentration and at t=1000 ms a spike arrives at the volume transmitter. If I run it with one thread I get an initial decay on the DA concentration and then a bump at t=1000 ms. Which is the expected behavior. But if I run the same thing with 2 threads, then I get just the decay. As if the spike hasn't arrived at the volume transmitter. Is this the expected behavior or is it maybe a bug? Best, Gui [image: Screenshot from 2019-06-25 18-32-58.png] [image: 1thread.png] [image: 2threads.png]

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Recording from synapses
by Guilherme Miotto 08 Jul '19

08 Jul '19

Hi everyone, Is there a generic way of recording from connections? I know that for weights we can use a weight_recorder, but what about other parameters? For instance, right now I would like to record the dopamine concentration (aka "n") from stdp_dopamine_synapse connections. Is this possible? Best, -- Gui Miotto

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Installation of Nest Simulator with csa
by yannicknodem＠gmail.com 27 Jun '19

27 Jun '19

Hi, I try to install csa package with libneurosim to use with nest simulator. The installation of libneurosim with python support take place without any issues. When I try to install csa with these commands: ./autogen.sh ./configure ./configure --prefix=$HOME/opt/csa --with-libneurosim=$HOME/opt/libneurosim make The installation fails at the make step with these output errors: _/home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:189: undefined reference to PyGILState_Ensure' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:190: undefined reference to PyList_New' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:197: undefined reference to PyObject_CallFunctionObjArgs' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:198: undefined reference to PyList_SetItem' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:202: undefined reference to PyLong_FromLong' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:202: undefined reference to PyObject_CallFunctionObjArgs' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:209: undefined reference to PyGILState_Release' .libs/libpycsa_la-pycsa.o: In function error(std::_cxx11::basic_string<char, std::char_traits, std::allocator >)': /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:53: undefined reference to PyGILState_Release' .libs/libpycsa_la-pycsa.o: In function PyCSA::PyCSAGenerator::setMask(std::vector<ConnectionGenerator::Mask, std::allocatorConnectionGenerator::Mask >&, int)': /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:214: undefined reference to `PyGILState_Release' collect2: error: ld returned 1 exit status Makefile:444: recipe for target 'libpycsa.la' failed make[2]: *** [libpycsa.la] Error 1 make[2]: Leaving directory '/home/yannick/Downloads/csa-master/libpycsa' Makefile:420: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/yannick/Downloads/csa-master' Makefile:350: recipe for target 'all' failed make: *** [all] Error 2 I work on ubuntu 18.04 with python 3.7.3 Thank you

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Open NEST Developer *real* Conference Monday 24-25 June 2019
by Dennis Terhorst 21 Jun '19

21 Jun '19

Dear NEST Developers! Our next meeting will be the _real_ Open NEST User and Developer Conference (non-video!) in Ås, Norway. This will of course replace the usual video meeting. Looking forward to seeing you all there! best, Dennis Terhorst -- 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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Options for plotting simulated data
by TOM BUGNON 21 Jun '19

21 Jun '19

Hi all, I was wondering if the community had any suggestions of toolboxes to plot the output of simulations (ideally in python) and make publication-quality figures. I am mostly thinking of eg spike rasterplots or heatmaps (time x variable) with large datasets. Ideally in such a way that those can be aligned with other figures easily (spike histograms, LFP, you name it) This is a very general problem that I suppose a lot of us have been confronted with, and I actually haven't found so far a good solution: -matplotlib (python) is robust and can handle large datasets but looks bad and is a nightmare to deal with when trying to make figures with multiple subplots of specific sizes etc - altair (python) looked promising and versatile but is actually struggling with large datasets - The existing projects for (analysis and) visualization of neural data that I have checked (elephant spykes etc) are either quite specific/limited or not very active. Additionally they are focused on real ePhys data: either multiunit spike data or single neuron continuous data, while simulations provide both. Happy to get any suggestions and share some code ! Thanks, Tom

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AdEx gap junctions
by domenico.guarino＠cnrs.fr 19 Jun '19

19 Jun '19

Hello, from the NEST docs(https://www.nest-simulator.org/simulations-with-gap-junctions/), I see that only the cell model 'hh_psc_alpha_gap' can use gap junctions. Is it true? If true, are there any plans (or hacks) to have it also for the AdEx model? Thanks!

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Nest installation
by gerlach.mi＠gmx.de 13 Jun '19

13 Jun '19

Hello, I am using Anaconda on a Mac OS X platform. I installed nest using homebrew by following the instructions on this page: https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… After finishing the installation, IPython first could not find the nest module, so I manually copied the nest folder that was created in /Users/name/opt/nest/lib/python3.7/site-packages/nest into /anaconda/lib/python3.7/site-packages/nest Now IPython can import the nest module, but returns an error message when I try to run a basic nest example: "module 'nest' has no attribute 'Create' ". I am sorry for failing at a very basic level here, but I tried for quite some time and could not get it running despite trying different instructions. I would greatly appreciate it if anyone could help me or give me a hint into the right direction, thanks in advance!

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Where are the archive questions?
by Abolfazl Ziaeemehr 12 Jun '19

12 Jun '19

I remember before the new mailing list I had access to the archived questions and some times by digging into them I could find some answers to simple questions. Now I can not find them. Thank you let me know if there are still available. One more silly question. Do we have access to synaptic current in iaf psc alpha model. We can simply plot the post synaptic potential for two couple neuron (in tutorial <https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>), how about the I_syn? Excuse me if seems easy, and thanks for guide.

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parallel computing on a shared cluster
by Jimmy Mulder 03 Jun '19

03 Jun '19

Hi everyone, For my masters thesis I'm using (py)NEST for the first time. I have some questions about parallel computing. first a short intro to give you the context: My research group has access to 4 clusters; 2 with a focus on RAM/CPU on 2 with focus on GPU. These are shared systems; resources are dynamically allocated depending on the number of users doing calculations. The way these clusters are set up allows me to simply set "local_num_threads" to a value of 10, and if no one else is using it the cluster manager will say I get 1000% CPU power, and the speed will increase about 8-fold as expected. (in case you find that number confusing: the manager rates 1 core as 100%, so 56 cores translates to 5600% CPU power) However, problems start to occur when others are using the cluster as well. I might get 500% CPU power one moment, and just 300% the next. At this point it is actually FASTER to only request 1 thread and get the full 100% power. I'm guessing this is due to the architecture; something with nodes A and B waiting on node C which has been temporarily allocated to my colleague? *So, the questions:* 1. Does NEST prefer CPU or GPU? Is it RAM intensive? I couldn't find this on your website, or anywhere really. Are there ballpark numbers for the memory required for 10^9 connections? 2. Am I abusing the "local_num_threads" mechanic by applying it to a cluster like this? Why is 1 thread sometimes faster than 10 threads? 3. Would switching to MPI help? 4. If so: the documentation says I need to run $NEST_SOURCE_DIR/configure -- with-mpi, but there is no "configure" folder or command to be found anywhere, and this line fails. What and where is this "configure"? Any help would be greatly appreciated. Thank you for your time. Kind regards, Jimmy Mulder

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Open NEST Developer Video Conference Monday 3 June 2019 11.30 CET (UTC+2)
by Dennis Terhorst 02 Jun '19

02 Jun '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 3 June, 11.30-12.30 CET (UTC+2). This is the substitute for the postponed meeting from last week and the missing meeting next week (pentecost). 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/2019-06-03-Open-NEST-Developer-… 1. Welcome 2. New features in NEST3 / current developments 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/postorius/lists/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> See 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 * Enter your name and allow your browser to use camera and microphone * Click green video-call button to open the call panel * In the "Search to call" box at the top right enter *97938800* and connect * 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 -- 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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NEST Users June 2019