VecStim() errors

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rllin

VecStim() errors

Post by rllin » Tue Jun 26, 2012 8:16 pm

I am trying to use Vecstim(). I have read the other recent thread on this.

I get a not very enlightening error report which I think is complaining about my use of VecStim() as sometimes the error is:

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net_send td-t = -5.20789e+214 SelfEvent target=VecStim[0] -5.20789341415904e+214 flag=1
after this gives:

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../path/i386/special: line 13: 28854 Abort trap: 6           "${NRNIV}" -dll "/path/i386/.libs/libnrnmech.so" "$@"
Most times the error reports:

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/Applications/NEURON-7.2/nrn/i386/bin/nrniv.app/Contents/MacOS/nrniv: Bus error See $NEURONHOME/lib/help/oc.help
 in ./loadfiles/B100.hoc near line 321
 run()
      ^
        finitialize(-65)
      init()
    stdinit()
  run()

I then try some troubleshooting based on the recent thread about VecStim().

I have vecevent.mod and compiled. I navigate to the folder with vecevent.mod and compiled i386.
I do nrngui and then attempt to load_file("vecevent.ses") This results in an error.


Any ideas? Thanks!

ted
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Re: VecStim() errors

Post by ted » Wed Jun 27, 2012 12:13 am

Make a toy network that consists of the following:
Presynaptic cell: a VecStim.
Postsynaptic cell: a single compartment model with surface area 100 um2, with pas mechanism.
Synaptic mechanism: an ExpSyn with default properties
NetCon that connects the VecStim to the ExpSyn: set weight to 0.001, leave other parameters with their default values.
Vector of event times that is used by the VecStim: keep this simple. Give it just two elements, with values 1 and 2.
Set tstop to 5 (no point in running long simulations).

Once you get that working, you'll know how to use VecStim in your own model.

rllin

Re: VecStim() errors

Post by rllin » Wed Jun 27, 2012 2:38 am

Well, I have other working models with VecStim(). I was just afraid I was missing something obvious.

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objref presyn, syn, nc, eventvec
tstop = 100


eventvec = new Vector()
eventvec.append(30)
eventvec.append(60)

create soma
insert pas

presyn = new VecStim()
presyn.play(eventvec)

syn = new Exp2Syn(0.5)
nc = new NetCon(presyn, syn)
nc.weight = 1
is my toy network and it works. I guess I'll just check my code further. Thanks.

regger
Posts: 21
Joined: Sun Apr 22, 2012 9:49 pm

Re: VecStim() errors

Post by regger » Sun Aug 12, 2012 2:58 pm

I don't know if you're still having the problem, but I'm just answering here because I saw another recent post with a segfault/bus error using VecStim (see http://www.neuron.yale.edu/phpbb/viewto ... f=8&t=2294).
This has come up before, but in the Python section of the forum, maybe that's why it was missed. It turns out, it's not a Python/hoc problem, but rather that the vecevent.mod file does not implement reference counting. Michael Hines has posted a nice explanation and solution here: http://www.neuron.yale.edu/phpbb/viewto ... f=2&t=2147.
I don't know if this applies exactly to your problem, but I hope it helps.

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