AMPA, NMDA, GAMBAa NOT COMPÄ°LE CVODE ERROR

[okanerkaymaz]

hi, all friends
i download mr. Alain Destexhe's publication's demo file BAKCP.zip but i can't compile with NEURON 5.9 and i have errors
folowing error code in NEURON 5.9

Code: Select all

gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c mod_func.c
nocmodl AMPA
Translating AMPA.mod into AMPA.c
Notice: This mechanism cannot be used with CVODE
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c AMPA.c
rm AMPA.c
nocmodl GABAa
Translating GABAa.mod into GABAa.c
Notice: This mechanism cannot be used with CVODE
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c GABAa.c
rm GABAa.c
nocmodl ICaL_gutnick_nernst
Translating ICaL_gutnick_nernst.mod into ICaL_gutnick_nernst.c
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c ICaL_gutnick_nernst.c
rm ICaL_gutnick_nernst.c
nocmodl IKCa
Translating IKCa.mod into IKCa.c
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default 5e-05 of PARAMETER cai will be ignored and set by NEURON.
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c IKCa.c
rm IKCa.c
nocmodl IKM_zach
Translating IKM_zach.mod into IKM_zach.c
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default -90 of PARAMETER ek will be ignored and set by NEURON.
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c IKM_zach.c
rm IKM_zach.c
nocmodl IKd_traub
Translating IKd_traub.mod into IKd_traub.c
Notice: This mechanism cannot be used with CVODE
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default -90 of PARAMETER ek will be ignored and set by NEURON.
VECTORIZED
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c IKd_traub.c
rm IKd_traub.c
nocmodl INa_traub
Translating INa_traub.mod into INa_traub.c
Notice: This mechanism cannot be used with CVODE
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default 50 of PARAMETER ena will be ignored and set by NEURON.
VECTORIZED
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c INa_traub.c
rm INa_traub.c
nocmodl NMDA
Translating NMDA.mod into NMDA.c
Notice: This mechanism cannot be used with CVODE
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c NMDA.c
rm NMDA.c
nocmodl cadecay
Translating cadecay.mod into cadecay.c
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c cadecay.c
rm cadecay.c
nocmodl trig
Translating trig.mod into trig.c
Notice: This mechanism cannot be used with CVODE
VECTORIZED
gcc -mno-cygwin -I/cygdrive/c/nrn59/src/scopmath -I/cygdrive/c/nrn59/src/nrnoc -I/cygdrive/c/nrn59/src/oc -I/cygdrive/c/nrn59/lib -I/cygdrive/c/nrn59/mingw -c trig.c
rm trig.c
ld -d -S -x -r -o nrnmech.dll mod_func.o AMPA.o GABAa.o ICaL_gutnick_nernst.o IKCa.o IKM_zach.o IKd_traub.o INa_traub.o NMDA.o cadecay.o trig.o -L/cygdrive/c/nrn59/lib -lscpmt

nrnmech.dll was built successfully.
Press Return key to exit

how this errors can solve ?

best regard

[ted]

You ask tough questions.

hi, all friends
i download mr. Alain Destexhe's publication's demo file BAKCP.zip but i can't compile with NEURON 5.9 and i have errors

They're not really errors, they're just warnings. The compiled mechanisms
will work.

Here's what the messages mean.

Code: Select all

Notice: This mechanism cannot be used with CVODE

This means that the mechanism can only be used with fixed time step
integration. The usual reason is that the mechanism computes a gating
variable from the analytic solution of the first order differential equation
(DE) that describes gating of HH-style channel mechanisms. For example,
instead of numerically integrating
m' = (minf - m)/mtau
the NMODL code does something like this
m = minf + (m-minf)*exp(dt/mtau)
This is OK as long as dt remains constant during the simulation.

Code: Select all

Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.

This means exactly what it says. celsius does not "belong" to any
individual mechanism. Confusion would result if more than one mechanism
tried to assign different values to celsius. The value of celsius is specified
by code that lies outside of any mod file.

Code: Select all

Warning: Default 5e-05 of PARAMETER cai will be ignored and set by NEURON.

The values of cai is defined by the ca_ion mechanism, which NEURON
creates automatically when a section has a mechanism whose NMODL
source code contains a USEION ca statement. The same applies to other
ions. The best way to initialize ionic concentrations in any particular model
depends on the design and intended use of the model--see chapter 8 of
The NEURON Book.

Code: Select all

Warning: Default -90 of PARAMETER ek will be ignored and set by NEURON.

If the model has a potassium accumulation mechanism, NEURON will
automatically compute ek from the Nernst equation. Otherwise, you can
specify ek from hoc with a simple assignment statement. Similar
considerations apply to other ionic equilibrium potentials.

[epokh]

hi, all friends
i download mr. Alain Destexhe's publication's demo file BAKCP.zip but i can't compile with NEURON 5.9 and i have errors
folowing error code in NEURON 5.9

best regard

I'm searching for the same file, anybody has the link?

[csh]

hi, all friends
i download mr. Alain Destexhe's publication's demo file BAKCP.zip but i can't compile with NEURON 5.9 and i have errors
folowing error code in NEURON 5.9

best regard

I'm searching for the same file, anybody has the link?

Direct link to the file:
http://cns.iaf.cnrs-gif.fr/files/BACKP.ZIP

Link to download page:
http://cns.iaf.cnrs-gif.fr/alain_demos.html