segmentation fault when recording specific time points into h.Vector

General issues of interest both for network and
individual cell parallelization.

Moderator: hines

Post Reply
rlindroos
Posts: 17
Joined: Thu Jan 02, 2014 2:23 pm

segmentation fault when recording specific time points into h.Vector

Post by rlindroos »

Hi,
I get a segmentation error when running multiple version of the same simulations (with different parameters) in parallel on a super computer (Beskow; PDC; Royal Institutet of Technology; Stockholm).

I only get the error when I use the tvec argument of the Vector.record() method:
vdest.record(var_reference, tvec)
https://www.neuron.yale.edu/neuron/stat ... tor.record
And I do not get the error if I run the same simulation locally.

Error message:
special: ../../../../src/nrn-7.4/src/nrniv/../nrncvode/netcvode.cpp:5737: virtual void VecRecordDiscrete::deliver(double, NetCvode*): Assertion `osMath::equal(t_->elem(j), tt, 1e-8)' failed.
_pmiu_daemon(SIGCHLD): [NID 00110] [c0-0c1s11n2] [Mon Nov 12 16:25:05 2018] PE RANK 117 exit signal Aborted
Am I doing something wrong or is there a known error with this method? Do you have any ideas of what could be going on?
I'm using Neuron+Python v7.4.

The simulation runs if I do not use the tvec argument and instead pick certain time points after the simulation is finished. But it would be nice if I could get this to work since it would save some computing time and memory storage.



Example code

Code: Select all

tvec_local_vm   = [600,800] + range(1000, 1100, 10) + [1100, 1120, 1150, 1200, 1300]
tv_local       = h.Vector()
tv_local.from_python( tvec_local_vm )
local_vm        = {}
for section in stim:
    sec = spike_list['name_to_sec'][section]
    
    local_vm[section] = h.Vector()
    local_vm[section].record(sec(0.5)._ref_v, tv_local)
    
# finalize and run
h.finitialize(-70)
while h.t < tstop:
    h.fadvance() 

Thanks!
Robert
ted
Site Admin
Posts: 6286
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: segmentation fault when recording specific time points into h.Vector

Post by ted »

Suggest you update to the latest version of NEURON and see if that makes the problem go away. There have been many bug fixes and performance enhancements since 7.4.
Post Reply