September 2022 - NEST Users - NEST Initiative Mail

Assertion error during connection when using CopyModel and own neuron model

by Barna Zajzon

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

1 year, 12 months

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using mpi4py with nest | parallel write to a file

by Aadhar Sharma

Hi there! I am using the structural plasticity module to simulate large-scale networks on HPC. The way I run these simulations with MPI creates a large number of small data files (.npy) which I organize into a HDF5 file in a post hoc manner. This has hitherto not been a problem, however, I recently increased the size of my simulations and the number of files that I create exceeds my HPCinode quota. So, I have to come up with a way of handling all these files or the way I export them. Ideally, I would like to concurrently write to a file (like zarr) with multiple processes. However, parallel zarr writes are only optimal when the chunk size are uniform. For me, they are not uniform---so, I abandoned the idea of using zarr. Currently, I am trying to use mpi4py to gather the data I want and save it through a mother MPI process. I ran some test simulations and all was fine (see attached script). However, when I use structural plasticity with mpi4py I get an error that: "nest.lib.hl_api_exceptions.DimensionMismatch: ('DimensionMismatch in SetStatus_id: Expected dimension size: 1\nProvided dimension size: 20', 'DimensionMismatch', <SLILiteral: SetStatus_id>, ': Expected dimension size: 1\nProvided dimension size: 20". I believe that mpi4py somehow interferes with nest's internal mpi mechanism. Perhaps it signals nest kernel to use 1 process rather than the mentioned 20. If I remove the mpi4py import call, all works fine. So, I cannot run the simulation using this mpi4py hack. Do you notice something wrong with my approach? I'm just beginning to use mpi4py, so I may be missing something here. Alternatively, could you recommend a way to reduce the number of exported files. For example, through zarr or other file formats which support parallel writes. I'd appreciate any suggestions. Thanks! pyNEST version: 2.20.2 python version: Python 3.7.10 mpiexec/mpirun version: MPI Library for Linux* OS, Version 2021.3 Best, Ady

2 years

2
1
0 0

[Precise Spikes]small bug in ./pynest/examples/hpc_benchmark.py (nest-3.3)

by Tianxiang Lyu

Hi, all! I try to replace "iaf_psc_alpha" with "iaf_psc_alpha_ps" and "poisson_generator" with "poisson_generator_ps" for using precise spikes neuron template in the simulation However, there are somethings wrong with the logs related to SLI with which I hadn't been familiar: (If the randomizing of membrane potentials is removed, hpc_benchmark.py could run as usual) Traceback (most recent call last): File "./hpc_benchmark.py", line 456, in <module> run_simulation() File "./hpc_benchmark.py", line 362, in run_simulation sr = build_network(logger) File "./hpc_benchmark.py", line 227, in build_network nest.GetLocalNodeCollection(E_neurons).V_m = random_vm File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 543, in __setattr__ self.set({attr: value}) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 477, in set sli_func('SetStatus', self._datum, params) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 165, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 115, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype How could I fix that? Or another way to implement randomizing of membrane potentials? Tianxiang Lyu Department of Mechanic Sun Yet-Sen University No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, P. R. China

2 years

2
2
0 0

Open NEST Developer Video Conference Monday Sep 26 2022 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 26, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-09-26-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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

2 years

1
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0 0

How to save and reload an already trained network created with Nest Simulator?

by salvatore.taffara＠phd.unict.it

Hi, can anyone answer to my question in subject? I am using Nest 3.3. Thanks in advance, Salvo

2 years

3
2
0 0

which neuron model supports shunting inhibition

by Aadhar Sharma

Hi all! I want to use investigate the effects of shunting inhibition in one of my experiments. I tried iaf_cond_alpha, but couldn't reproduce the shunting effect. Could someone please suggest which neuron model to use? There should be a way to also change the V_th, V_rest, C_m, tau_m or g_L for this model. I am working with NEST 2.20.2 Best, Ady

2 years

2
1
0 0

Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-08-15-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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

2 years

2
1
0 0

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NEST Users September 2022