[Bug report] Coreneuron: Assertion `nc->target_ == pnt' failed

[jhielson]

Hi everyone,

I am getting the following error when I run my model:

python3 completeModel-100GC.py 

Start time:  2022-05-21 19:24:55.200888

Creating network of 149 cell populations on 1 hosts...
  Number of cells on node 0: 303 
  Done; cell creation time = 0.03 s.
Making connections...
  Number of connections on node 0: 2994 
  Number of synaptic contacts on node 0: 3032 
  Done; cell connection time = 0.34 s.
Adding stims...
  Number of stims on node 0: 182 
  Done; cell stims creation time = 0.01 s.
exp(789.212) out of range, returning exp(700)
exp(789.212) out of range, returning exp(700)
exp(789.212) out of range, returning exp(700)
exp(789.212) out of range, returning exp(700)
No more errno warnings during this execution

Running with interval func using CoreNEURON for 300000.0 ms...

 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020
 Version : 1.0 22e6e405 (2022-03-16 16:55:25 +0100)

 Additional mechanisms from files
 GP.mod Izhi2003b.mod STN2.mod Str.mod SynExp2NMDA.mod exp2syn.mod expsyn.mod fi_stdp.mod hh.mod izhi2007a.mod izhi2007bS.mod mySTDP.mod netstim.mod passive.mod pattern.mod spikeout.mod stdwa_songabbott.mod stim.mod svclmp.mod thalamus.mod

 Memory (MBs) :             After mk_mech : Max 158.8672, Min 158.8672, Avg 158.8672 
 Memory (MBs) :            After MPI_Init : Max 158.8672, Min 158.8672, Avg 158.8672 
 Memory (MBs) :          Before nrn_setup : Max 158.8672, Min 158.8672, Avg 158.8672 
best_balance=0.996454 ncell=282 ntype=1 nwarp=282
 Setup Done   : 0.00 seconds 
 Model size   : 679.12 kB
 Memory (MBs) :          After nrn_setup  : Max 158.8672, Min 158.8672, Avg 158.8672 
GENERAL PARAMETERS
--mpi=false
--mpi-lib=/home/neuro4pd/.local/lib/python3.10/site-packages/neuron/.data/lib/libcorenrnmpi_ompi.so
--gpu=true
--dt=0.1
--tstop=1

GPU
--nwarp=65536
--cell-permute=2
--cuda-interface=false

INPUT PARAMETERS
--voltage=1000
--seed=-1
--datpath=.
--filesdat=files.dat
--pattern=
--report-conf=
--restore=     

PARALLEL COMPUTATION PARAMETERS
--threading=false
--skip_mpi_finalize=true

SPIKE EXCHANGE
--ms_phases=2
--ms_subintervals=2
--multisend=false
--spk_compress=0
--binqueue=false

CONFIGURATION
--spikebuf=100000
--prcellgid=-1
--forwardskip=0
--celsius=6.3
--mindelay=10
--report-buffer-size=4

OUTPUT PARAMETERS
--dt_io=0.1
--outpath=.
--checkpoint=

 Start time (t) = 0

 Memory (MBs) :  After mk_spikevec_buffer : Max 158.8672, Min 158.8672, Avg 158.8672 
 Memory (MBs) :     After nrn_finitialize : Max 158.8672, Min 158.8672, Avg 158.8672 

psolve |=========================================================| t: 1.00   ETA: 0h00m00s

Solver Time : 0.00103211

 Simulation Statistics
 Number of cells: 282
 Number of compartments: 846
 Number of presyns: 481
 Number of input presyns: 0
 Number of synapses: 3052
 Number of point processes: 3413
 Number of transfer sources: 0
 Number of transfer targets: 0
 Number of spikes: 10
 Number of spikes with non negative gid-s: 10
python3: /root/nrn/src/nrniv/nrncore_write/callbacks/nrncore_callbacks.cpp:1033: void core2nrn_SelfEvent_event(int, double, int, int, double, size_t, int): Assertion `nc->target_ == pnt' failed.
Aborted (core dumped)

Can you please help me with this issue?

[jhielson]

Hi everyone,

I tried to use a different command and got the following error:

mpirun -n 6 ./x86_64/corenrn/ --mpi --gpu completeModel-100GC.py 
--------------------------------------------------------------------------
Open MPI tried to fork a new process via the "execve" system call but
failed.  Open MPI checks many things before attempting to launch a
child process, but nothing is perfect. This error may be indicative
of another problem on the target host, or even something as silly as
having specified a directory for your application. Your job will now
abort.

  Local host:        neuro4pd-Alienware-Area-51m
  Working dir:       /home/neuro4pd/cerebellum/src
  Application name:  ./x86_64/corenrn/
  Error:             Permission denied
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun was unable to start the specified application as it encountered an
error:

Error code: 1
Error name: (null)
Node: neuro4pd-Alienware-Area-51m

when attempting to start process rank 0.
--------------------------------------------------------------------------
6 total processes failed to start
[neuro4pd-Alienware-Area-51m:158407] 5 more processes have sent help message help-orte-odls-default.txt / execve error
[neuro4pd-Alienware-Area-51m:158407] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Using sudo is strongly not recommended. How can I fix this issue?

[salvadord]

closing as this is probably outdated since several newer coreNEURON versions have been released, but please reopen if still an issue