Trouble about the spiking time will increase and get so bigger with the simulation epoch increasing.
19 Dec
2020
19 Dec
'20
4:59 a.m.
Deal all,
I am recording the spiking time of neurons after every simulation, and I find that the
time beginning of every simulation isn't all 0 except the first simulation. So how can
I set to recording spiking time beginning from 0 during all simulations? By now I am
processing that for every simulation spiking time recording by deleting all the time used
before a specific simulation epoch.
Hope for your answer,thanks!
Enguang
19 Dec
19 Dec
3:16 p.m.
Dear Enguang
How about using “nest.ResetKernel()” for each simulation?
Here you can find more information
https://nest-simulator.readthedocs.io/en/nest-2.20.1/guides/running_simulat…
<https://nest-simulator.readthedocs.io/en/nest-2.20.1/guides/running_simulations.html>
Best Wishes,
Sun
---------------------------------------------------------
Zhe Sun, PhD
Research Scientist
RIKEN Center for Advanced Photonics
Image Processing Research Team
RIKEN, Japan
国立研究開発法人 理化学研究所
光量子工学研究センター 画像情報処理研究チーム
研究員 孫 哲
E-mail： zhe.sun.vk(a)riken.jp
sunzhe839(a)gmail.com
Tel : 048-462-1111 (ext. 7828)
http://www2.riken.jp/brict/Sun/index.html
---------------------------------------------------------
2020/12/19 12:59、enguang zhou
<1240288839(a)qq.xn--com>-1e4f10b4csit;のメール:
Deal all,
I am recording the spiking time of neurons after every simulation, and I find that the
time beginning of every simulation isn't all 0 except the first simulation. So how can
I set to recording spiking time beginning from 0 during all simulations? By now I am
processing that for every simulation spiking time recording by deleting all the time used
before a specific simulation epoch.
Hope for your answer,thanks!
Enguang
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
23 Dec
23 Dec
10:09 a.m.
Dear Zhe Sun,
Thank you for your answer! I tried the 'nest.ResetKernel()' before, but it will
delete all the connections and the synapses weight data is gone which I want to keep that
during my all simulations.
Thank you again.
Best Wishes
11 Jan
11 Jan
3:17 p.m.
Dear Enguang,
I think the command you are looking for is nest.SetKernelStatus({'time': 0.0}).
This will reset the time, but leave your network intact.
Please be aware that the command will print a scary-sounding warning, but usually
everything should be fine as long as you only call Simulate() with times that fall on the
min-delay
grid<https://nest-simulator.readthedocs.io/en/latest/guides/running_simulations.html#simulation-resolution-and-update-interval>.
Best regards,
Jochen!
On 23.12.20 10:09, enguang zhou wrote:
Dear Zhe Sun,
Thank you for your answer! I tried the 'nest.ResetKernel()' before, but it will
delete all the connections and the synapses weight data is gone which I want to keep that
during my all simulations.
Thank you again.
Best Wishes
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
13 Jan
13 Jan
4:05 p.m.
Dear Dr. Jochen Martin Eppler,
Thank you for your suggestion.But I got an error as below,
conn1 ((1, 2, 1.0), (1, 3, 1.0), (1, 4, 1.0))
Jan 13 22:52:44 ConnectionManager [Warning]:
New connections created, connection descriptors previously obtained using
'GetConnections' are now invalid.
conn2 ((5, 1, 1800.0),) conn3 ((6, 1, 1.0),) conn4 ((1, 7, 1.0),)
Jan 13 22:52:44 NodeManager::prepare_nodes [Info]:
Preparing 7 nodes for simulation.
Jan 13 22:52:44 SimulationManager::start_updating_ [Info]:
Number of local nodes: 7
Simulation time (ms): 10
Number of OpenMP threads: 1
Number of MPI processes: 1
Jan 13 22:52:44 SimulationManager::run [Info]:
Simulation finished.
time [5.]
Jan 13 22:52:44 SimulationManager::set_status [Warning]:
Simulation time reset to t=0.0. Resetting the simulation time is not fully
supported in NEST at present. Some spikes may be lost, and stimulating
devices may behave unexpectedly. PLEASE REVIEW YOUR SIMULATION OUTPUT
CAREFULLY!
Jan 13 22:52:44 NodeManager::prepare_nodes [Info]:
Preparing 7 nodes for simulation.
Jan 13 22:52:44 SimulationManager::start_updating_ [Info]:
Number of local nodes: 7
Simulation time (ms): 10
Number of OpenMP threads: 1
Number of MPI processes: 1
python3: /home/zhoueg/Downloads/nest-simulator-2.20.0/nestkernel/archiving_node.cpp:431:
virtual void nest::Archiving_Node::update_synaptic_elements(double): Assertion `t >=
Ca_t_' failed.
[zhoueg-Inspiron-3670:16175] *** Process received signal ***
[zhoueg-Inspiron-3670:16175] Signal: Aborted (6)
[zhoueg-Inspiron-3670:16175] Signal code: (-6)
[zhoueg-Inspiron-3670:16175] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(+0x3f040)[0x7f6c148e0040]
[zhoueg-Inspiron-3670:16175] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f6c148dffb7]
[zhoueg-Inspiron-3670:16175] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f6c148e1921]
[zhoueg-Inspiron-3670:16175] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(+0x3048a)[0x7f6c148d148a]
[zhoueg-Inspiron-3670:16175] [ 4]
/lib/x86_64-linux-gnu/libc.so.6(+0x30502)[0x7f6c148d1502]
[zhoueg-Inspiron-3670:16175] [ 5]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0x76f55)[0x7f6bef264f55]
[zhoueg-Inspiron-3670:16175] [ 6]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest14Archiving_Node13set_spiketimeERKNS_4TimeEd+0x67)[0x7f6bef2666a7]
[zhoueg-Inspiron-3670:16175] [ 7]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libmodels.so(_ZN4nest13iaf_psc_alpha6updateERKNS_4TimeEll+0x3ee)[0x7f6befaf84ae]
[zhoueg-Inspiron-3670:16175] [ 8]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xe7fd2)[0x7f6bef2d5fd2]
[zhoueg-Inspiron-3670:16175] [ 9]
/usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x42)[0x7f6bed7ea1f2]
[zhoueg-Inspiron-3670:16175] [10]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f6bef2d2e01]
[zhoueg-Inspiron-3670:16175] [11]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f6bef2d37b5]
[zhoueg-Inspiron-3670:16175] [12]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f6bef2d8543]
[zhoueg-Inspiron-3670:16175] [13]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f6bef2d87cc]
[zhoueg-Inspiron-3670:16175] [14]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f6bef2bd992]
[zhoueg-Inspiron-3670:16175] [15]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f6bef290003]
[zhoueg-Inspiron-3670:16175] [16]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f6beece7053]
[zhoueg-Inspiron-3670:16175] [17]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f6beece4d32]
[zhoueg-Inspiron-3670:16175] [18]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f6beece52ae]
[zhoueg-Inspiron-3670:16175] [19]
/usr/lib/python3.6/lib/python3.6/site-packages/nest/pynestkernel.so(+0x279b8)[0x7f6bf09919b8]
[zhoueg-Inspiron-3670:16175] [20] python3[0x50a1cc]
[zhoueg-Inspiron-3670:16175] [21] python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zhoueg-Inspiron-3670:16175] [22] python3[0x5095c8]
[zhoueg-Inspiron-3670:16175] [23] python3[0x50a2fd]
[zhoueg-Inspiron-3670:16175] [24] python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zhoueg-Inspiron-3670:16175] [25] python3[0x507be4]
[zhoueg-Inspiron-3670:16175] [26] python3[0x588d41]
[zhoueg-Inspiron-3670:16175] [27] python3(PyObject_Call+0x3e)[0x59fd0e]
[zhoueg-Inspiron-3670:16175] [28] python3(_PyEval_EvalFrameDefault+0x17e6)[0x50d256]
[zhoueg-Inspiron-3670:16175] [29] python3[0x507be4]
[zhoueg-Inspiron-3670:16175] *** End of error message ***
Aborted (core dumped)
Here is the way I try to run the simulate method multiple time but setting the beginning
time of every simulation to 0.0.
nest.Simulate(10.)
nest.SetKernelStatus({'time': 0.0})
nest.Simulate(10.)
Best Wishes,
Enguang
4:24 p.m.
Hi Enguang,
Could I ask you to try to call clear_history() on each of your neuron instances? This
should be in addition to calling nest.SetKernelStatus({'time': 0.0}).
Cheers,
Charl
On Wed, Jan 13, 2021, at 16:05, enguang zhou wrote:
> Dear Dr. Jochen Martin Eppler,
> Thank you for your suggestion.But I got an error as below,
> conn1 ((1, 2, 1.0), (1, 3, 1.0), (1, 4, 1.0))
>
> Jan 13 22:52:44 ConnectionManager [Warning]:
> New connections created, connection descriptors previously obtained using
> 'GetConnections' are now invalid.
> conn2 ((5, 1, 1800.0),) conn3 ((6, 1, 1.0),) conn4 ((1, 7, 1.0),)
>
> Jan 13 22:52:44 NodeManager::prepare_nodes [Info]:
> Preparing 7 nodes for simulation.
>
> Jan 13 22:52:44 SimulationManager::start_updating_ [Info]:
> Number of local nodes: 7
> Simulation time (ms): 10
> Number of OpenMP threads: 1
> Number of MPI processes: 1
>
> Jan 13 22:52:44 SimulationManager::run [Info]:
> Simulation finished.
> time [5.]
>
> Jan 13 22:52:44 SimulationManager::set_status [Warning]:
> Simulation time reset to t=0.0. Resetting the simulation time is not fully
> supported in NEST at present. Some spikes may be lost, and stimulating
> devices may behave unexpectedly. PLEASE REVIEW YOUR SIMULATION OUTPUT
> CAREFULLY!
>
> Jan 13 22:52:44 NodeManager::prepare_nodes [Info]:
> Preparing 7 nodes for simulation.
>
> Jan 13 22:52:44 SimulationManager::start_updating_ [Info]:
> Number of local nodes: 7
> Simulation time (ms): 10
> Number of OpenMP threads: 1
> Number of MPI processes: 1
> python3:
> /home/zhoueg/Downloads/nest-simulator-2.20.0/nestkernel/archiving_node.cpp:431:
virtual void nest::Archiving_Node::update_synaptic_elements(double): Assertion `t >=
Ca_t_' failed.
> [zhoueg-Inspiron-3670:16175] *** Process received signal ***
> [zhoueg-Inspiron-3670:16175] Signal: Aborted (6)
> [zhoueg-Inspiron-3670:16175] Signal code: (-6)
> [zhoueg-Inspiron-3670:16175] [ 0]
> /lib/x86_64-linux-gnu/libc.so.6(+0x3f040)[0x7f6c148e0040]
> [zhoueg-Inspiron-3670:16175] [ 1]
> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f6c148dffb7]
> [zhoueg-Inspiron-3670:16175] [ 2]
> /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f6c148e1921]
> [zhoueg-Inspiron-3670:16175] [ 3]
> /lib/x86_64-linux-gnu/libc.so.6(+0x3048a)[0x7f6c148d148a]
> [zhoueg-Inspiron-3670:16175] [ 4]
> /lib/x86_64-linux-gnu/libc.so.6(+0x30502)[0x7f6c148d1502]
> [zhoueg-Inspiron-3670:16175] [ 5]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0x76f55)[0x7f6bef264f55]
> [zhoueg-Inspiron-3670:16175] [ 6]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest14Archiving_Node13set_spiketimeERKNS_4TimeEd+0x67)[0x7f6bef2666a7]
> [zhoueg-Inspiron-3670:16175] [ 7]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libmodels.so(_ZN4nest13iaf_psc_alpha6updateERKNS_4TimeEll+0x3ee)[0x7f6befaf84ae]
> [zhoueg-Inspiron-3670:16175] [ 8]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xe7fd2)[0x7f6bef2d5fd2]
> [zhoueg-Inspiron-3670:16175] [ 9]
> /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x42)[0x7f6bed7ea1f2]
> [zhoueg-Inspiron-3670:16175] [10]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f6bef2d2e01]
> [zhoueg-Inspiron-3670:16175] [11]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f6bef2d37b5]
> [zhoueg-Inspiron-3670:16175] [12]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f6bef2d8543]
> [zhoueg-Inspiron-3670:16175] [13]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f6bef2d87cc]
> [zhoueg-Inspiron-3670:16175] [14]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f6bef2bd992]
> [zhoueg-Inspiron-3670:16175] [15]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f6bef290003]
> [zhoueg-Inspiron-3670:16175] [16]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f6beece7053]
> [zhoueg-Inspiron-3670:16175] [17]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f6beece4d32]
> [zhoueg-Inspiron-3670:16175] [18]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f6beece52ae]
> [zhoueg-Inspiron-3670:16175] [19]
>
/usr/lib/python3.6/lib/python3.6/site-packages/nest/pynestkernel.so(+0x279b8)[0x7f6bf09919b8]
> [zhoueg-Inspiron-3670:16175] [20] python3[0x50a1cc]
> [zhoueg-Inspiron-3670:16175] [21]
> python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
> [zhoueg-Inspiron-3670:16175] [22] python3[0x5095c8]
> [zhoueg-Inspiron-3670:16175] [23] python3[0x50a2fd]
> [zhoueg-Inspiron-3670:16175] [24]
> python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
> [zhoueg-Inspiron-3670:16175] [25] python3[0x507be4]
> [zhoueg-Inspiron-3670:16175] [26] python3[0x588d41]
> [zhoueg-Inspiron-3670:16175] [27] python3(PyObject_Call+0x3e)[0x59fd0e]
> [zhoueg-Inspiron-3670:16175] [28]
> python3(_PyEval_EvalFrameDefault+0x17e6)[0x50d256]
> [zhoueg-Inspiron-3670:16175] [29] python3[0x507be4]
> [zhoueg-Inspiron-3670:16175] *** End of error message ***
> Aborted (core dumped)
>
> Here is the way I try to run the simulate method multiple time but
> setting the beginning time of every simulation to 0.0.
> nest.Simulate(10.)
> nest.SetKernelStatus({'time': 0.0})
> nest.Simulate(10.)
> Best Wishes,
> Enguang
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
>
1196
days inactive
1221
days old
5 comments
4 participants
participants (4)
-
Charl Linssen -
enguang zhou -
Jochen Martin Eppler -
SunZhe