Difficulties running 84589
Posted: Fri Jun 04, 2010 2:42 am
Extracellular Action Potential Simulations (EAPS)
NEURON ModelDB Accession: 84589
http://senselab.med.yale.edu/ModelDB/sh ... odel=84589
===============================================================
Have everything needed.
Loaded in the software, done all the misc trimmings needed for windows (XP)
NOTE: do not use the recommended start-up command:
c:\nrn59\bin\neuron.exe -dll mod\nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
I modified it to....
c:\nrn71\bin\neuron.exe -dll mod/nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
================================================================
When you run it it fails badly, killing neuron and leaves files open/hung and does a stack dump file nrniv.exe.stackdump
Neuron window contents are below.
It seems to be main.hoc which falls over due to some LOCAL declarations and somehow it gets tied in knots over brace matching....
The originators GOLD, HOLT etc are all out of the picture... but I will approach them if I have to.
meanwhile.... If there's anyone out there who's used it I'd be very grateful for a little guidance. Surely I can't be the first person to use it!
regards,
Colin Hales (see below)
==========================================
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html
loading membrane mechanisms from mod/nrnmech.dll
Additional mechanisms from files
cadif.mod cal.mod can.mod car.mod cat.mod hdend.mod hsoma.mod kadist.mod kahp.mod kaprox.mod kc.mod kd.mod kk.mod km.mod naf.mod nax.mod
LOADING GEOMETRY FOR d151
-> Setting file roots...
SETTING WINDOWS FILE PATHS!
-> Updating trial number...
.\cells\d151_trial_num.txt
trial number 3
-> Making output directory...
COMMAND = mkdir output/d151_0003
RESULT = 0
COMMAND = mkdir output/d151_0003/nrn
RESULT = 0
-> Opening param & geometry files...
-> Loading param files...
LOADING CELL SPECIFIC MEMBRANE CONDUCTANCE DENSITIES...
param_dir = hoc/params
params file = hoc/params//d151_params.hoc
LOADING Cell Sepcific Params D151(A)!
LOADING STANDARD MEMBRANE PARAMS FOR CELL TYPE:ca1pyr
LOADING STANDARD PARAMS for CA1 pyramidal cells...
-> Loading code files...
open cell util: hoc/src/cell_util.hoc
open current util: hoc/src/current_util.hoc
nrniv: line_curr already declared local
in current_util.hoc near line 461
proc print_currents() {local i, line_num, arcloc, next_arcloc, line_arc_ratio, line_start_ratio, line_end_ratio,line_curr, seg_start_ratio, seg_end_ratio, line_curr
^
xopen("current_util.hoc" )
execute1("{xopen("current_util.hoc")}" )
load_file("hoc/src/current_util.hoc" )
load_code_files( )
open template for mechanism description: hoc/src/mechdesc.hoc
open membrane init file: hoc/src/membrane_init.hoc
nrniv: gbkd already declared local
in membrane_init.hoc near line 1006
proc jitter_gbars() {local x, percent, old, gbnaf, gbnax, gbkk, gbkd, gbkd, gbkm, gbkap, gbkad
^
xopen("membrane_init.hoc" )
execute1("{xopen("membrane_init.hoc")}" )
load_file("hoc/src/membrane_init.hoc" )
load_code_files( )
nrniv: syntax error
in membrane_init.hoc near line 1116
}
^
NEURON ModelDB Accession: 84589
http://senselab.med.yale.edu/ModelDB/sh ... odel=84589
===============================================================
Have everything needed.
Loaded in the software, done all the misc trimmings needed for windows (XP)
NOTE: do not use the recommended start-up command:
c:\nrn59\bin\neuron.exe -dll mod\nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
I modified it to....
c:\nrn71\bin\neuron.exe -dll mod/nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
================================================================
When you run it it fails badly, killing neuron and leaves files open/hung and does a stack dump file nrniv.exe.stackdump
Neuron window contents are below.
It seems to be main.hoc which falls over due to some LOCAL declarations and somehow it gets tied in knots over brace matching....
The originators GOLD, HOLT etc are all out of the picture... but I will approach them if I have to.
meanwhile.... If there's anyone out there who's used it I'd be very grateful for a little guidance. Surely I can't be the first person to use it!
regards,
Colin Hales (see below)
==========================================
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html
loading membrane mechanisms from mod/nrnmech.dll
Additional mechanisms from files
cadif.mod cal.mod can.mod car.mod cat.mod hdend.mod hsoma.mod kadist.mod kahp.mod kaprox.mod kc.mod kd.mod kk.mod km.mod naf.mod nax.mod
LOADING GEOMETRY FOR d151
-> Setting file roots...
SETTING WINDOWS FILE PATHS!
-> Updating trial number...
.\cells\d151_trial_num.txt
trial number 3
-> Making output directory...
COMMAND = mkdir output/d151_0003
RESULT = 0
COMMAND = mkdir output/d151_0003/nrn
RESULT = 0
-> Opening param & geometry files...
-> Loading param files...
LOADING CELL SPECIFIC MEMBRANE CONDUCTANCE DENSITIES...
param_dir = hoc/params
params file = hoc/params//d151_params.hoc
LOADING Cell Sepcific Params D151(A)!
LOADING STANDARD MEMBRANE PARAMS FOR CELL TYPE:ca1pyr
LOADING STANDARD PARAMS for CA1 pyramidal cells...
-> Loading code files...
open cell util: hoc/src/cell_util.hoc
open current util: hoc/src/current_util.hoc
nrniv: line_curr already declared local
in current_util.hoc near line 461
proc print_currents() {local i, line_num, arcloc, next_arcloc, line_arc_ratio, line_start_ratio, line_end_ratio,line_curr, seg_start_ratio, seg_end_ratio, line_curr
^
xopen("current_util.hoc" )
execute1("{xopen("current_util.hoc")}" )
load_file("hoc/src/current_util.hoc" )
load_code_files( )
open template for mechanism description: hoc/src/mechdesc.hoc
open membrane init file: hoc/src/membrane_init.hoc
nrniv: gbkd already declared local
in membrane_init.hoc near line 1006
proc jitter_gbars() {local x, percent, old, gbnaf, gbnax, gbkk, gbkd, gbkd, gbkm, gbkap, gbkad
^
xopen("membrane_init.hoc" )
execute1("{xopen("membrane_init.hoc")}" )
load_file("hoc/src/membrane_init.hoc" )
load_code_files( )
nrniv: syntax error
in membrane_init.hoc near line 1116
}
^