Trouble about the spiking time will increase and get so bigger with the simulation epoch increasing.
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
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_simulati... 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@riken.jp sunzhe839@gmail.com Tel : 048-462-1111 (ext. 7828) http://www2.riken.jp/brict/Sun/index.html ---------------------------------------------------------
2020/12/19 12:59、enguang zhou 1240288839@qq.com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@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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
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 gridhttps://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.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
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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
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@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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Charl Linssen -
enguang zhou -
Jochen Martin Eppler -
SunZhe