13 Jan
2021
13 Jan
'21
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
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