I have problems compiling a model when a specific mod file is used in a parallel environment.
The modfile is 'lcafixed.mod' from ModelDB accession number 2730 http://senselab.med.yale.edu/modeldb/Sh ... afixed.mod and compiles on my local parallel environment (Ubuntu 10.04, Neuron 7.2) without problems.
The parallel environment is a Cray XE6 system: http://www.pdc.kth.se/resources/computers/lindgren
The error I get when compiling the model using lcafixed.mod is:
Code: Select all
cc -DHAVE_CONFIG_H -I. -I.. -I/cfs/nobackup/b/bkaplan/neuron-7.2/nrn-mpi/include/nrn -I/cfs/nobackup/b/bkaplan/neuron-7.2/nrn-mpi/x86_64/lib -g -c lcafixed.c
PGC-W-0221-Redefinition of symbol sinf (lcafixed.c: 83)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 58)
PGC-S-0043-Redefinition of symbol, sinf (lcafixed.c: 84)
PGC-S-0039-Use of undeclared variable sinf_lcafixed (lcafixed.c: 106)
PGC-S-0074-Non-constant expression in initializer (lcafixed.c: 106)
PGC-W-0093-Type cast required for this conversion of constant (lcafixed.c: 112)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 155)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 162)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 189)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 190)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 191)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 194)
PGC-S-0102-Illegal operand types for - operator (lcafixed.c: 202)
PGC-S-0104-Non-numeric operand for multiplicative operator (lcafixed.c: 216)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 262)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 263)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 273)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 281)
PGC-W-0136-Function rates has non-prototype declaration in scope (lcafixed.c: 281)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 286)
PGC-W-0136-Function _n_rates has non-prototype declaration in scope (lcafixed.c: 286)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 294)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 300)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 306)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 320)
PGC-W-0136-Function _ode_spec has non-prototype declaration in scope (lcafixed.c: 336)
PGC-W-0136-Function _ode_matsol has non-prototype declaration in scope (lcafixed.c: 357)
PGC-S-0094-Illegal type conversion required (lcafixed.c: 383)
PGC-W-0136-Function nrn_init has non-prototype declaration in scope (lcafixed.c: 391)
PGC-W-0136-Function nrn_cur has non-prototype declaration in scope (lcafixed.c: 420)
PGC-W-0136-Function nrn_jacob has non-prototype declaration in scope (lcafixed.c: 456)
PGC-W-0136-Function nrn_state has non-prototype declaration in scope (lcafixed.c: 476)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 509)
PGC-W-0156-Type not specified, 'int' assumed (lcafixed.c: 511)
PGC-W-0155-Long value is passed to a nonprototyped function - argument #1 (lcafixed.c: 516)
PGC-W-0155-Long value is passed to a nonprototyped function - argument #1 (lcafixed.c: 517)
PGC-W-0155-Long value is passed to a nonprototyped function - argument #1 (lcafixed.c: 518)
PGC-W-0155-Long value is passed to a nonprototyped function - argument #1 (lcafixed.c: 519)
PGC/x86-64 Linux 12.5-0: compilation completed with severe errors
make: *** [lcafixed.o] Error 2
I'm not an expert in writing / debugging modfiles, thus I would be really really happy if somebody could help me with this issue.
If the lcafixed.c file is of any help, here it is:
Code: Select all
/* Created by Language version: 6.2.0 */
/* NOT VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib.h"
#undef PI
#include "md1redef.h"
#include "section.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#undef exp
#define exp hoc_Exp
extern double hoc_Exp();
#define _threadargscomma_ /**/
#define _threadargs_ /**/
/*SUPPRESS 761*/
/*SUPPRESS 762*/
/*SUPPRESS 763*/
/*SUPPRESS 765*/
extern double *getarg();
static double *_p; static Datum *_ppvar;
#define t nrn_threads->_t
#define dt nrn_threads->_dt
#define gcabar _p[0]
#define ica _p[1]
#define r _p[2]
#define s _p[3]
#define Dr _p[4]
#define Ds _p[5]
#define _g _p[6]
#define _ion_ica *_ppvar[0]._pval
#define _ion_dicadv *_ppvar[1]._pval
#if MAC
#if !defined(v)
#define v _mlhv
#endif
#if !defined(h)
#define h _mlhh
#endif
#endif
static int hoc_nrnpointerindex = -1;
/* external NEURON variables */
/* declaration of user functions */
static int _hoc_alp();
static int _hoc_bet();
static int _hoc_rates();
static int _mechtype;
extern int nrn_get_mechtype();
static _hoc_setdata() {
Prop *_prop, *hoc_getdata_range();
_prop = hoc_getdata_range(_mechtype);
_p = _prop->param; _ppvar = _prop->dparam;
ret(1.);
}
/* connect user functions to hoc names */
static IntFunc hoc_intfunc[] = {
"setdata_lcafixed", _hoc_setdata,
"alp_lcafixed", _hoc_alp,
"bet_lcafixed", _hoc_bet,
"rates_lcafixed", _hoc_rates,
0, 0
};
#define alp alp_lcafixed
#define bet bet_lcafixed
extern double alp();
extern double bet();
/* declare global and static user variables */
#define rtau rtau_lcafixed
double rtau = 0;
#define rinf rinf_lcafixed
double rinf = 0;
#define stau stau_lcafixed
double stau = 0;
#define sinf sinf_lcafixed
double sinf = 0;
#define usetable usetable_lcafixed
double usetable = 1;
/* some parameters have upper and lower limits */
static HocParmLimits _hoc_parm_limits[] = {
"gcabar_lcafixed", 0, 1e+09,
"usetable_lcafixed", 0, 1,
0,0,0
};
static HocParmUnits _hoc_parm_units[] = {
"stau_lcafixed", "ms",
"rtau_lcafixed", "ms",
"gcabar_lcafixed", "mho/cm2",
"ica_lcafixed", "mA/cm2",
0,0
};
static double delta_t = 1;
static double r0 = 0;
static double s0 = 0;
static double v = 0;
/* connect global user variables to hoc */
static DoubScal hoc_scdoub[] = {
"sinf_lcafixed", &sinf_lcafixed,
"rinf_lcafixed", &rinf_lcafixed,
"stau_lcafixed", &stau_lcafixed,
"rtau_lcafixed", &rtau_lcafixed,
"usetable_lcafixed", &usetable_lcafixed,
0,0
};
static DoubVec hoc_vdoub[] = {
0,0,0
};
static double _sav_indep;
static void nrn_alloc(), nrn_init(), nrn_state();
static void nrn_cur(), nrn_jacob();
static int _ode_count(), _ode_map(), _ode_spec(), _ode_matsol();
#define _cvode_ieq _ppvar[2]._i
/* connect range variables in _p that hoc is supposed to know about */
static char *_mechanism[] = {
"6.2.0",
"lcafixed",
"gcabar_lcafixed",
0,
"ica_lcafixed",
0,
"r_lcafixed",
"s_lcafixed",
0,
0};
static Symbol* _ca_sym;
static void nrn_alloc(_prop)
Prop *_prop;
{
Prop *prop_ion, *need_memb();
double *_p; Datum *_ppvar;
_p = nrn_prop_data_alloc(_mechtype, 7, _prop);
/*initialize range parameters*/
gcabar = 0.12;
_prop->param = _p;
_prop->param_size = 7;
_ppvar = nrn_prop_datum_alloc(_mechtype, 3, _prop);
_prop->dparam = _ppvar;
/*connect ionic variables to this model*/
prop_ion = need_memb(_ca_sym);
_ppvar[0]._pval = &prop_ion->param[3]; /* ica */
_ppvar[1]._pval = &prop_ion->param[4]; /* _ion_dicadv */
}
static _initlists();
/* some states have an absolute tolerance */
static Symbol** _atollist;
static HocStateTolerance _hoc_state_tol[] = {
0,0
};
static void _update_ion_pointer(Datum*);
_lcafixed_reg() {
int _vectorized = 0;
_initlists();
ion_reg("ca", -10000.);
_ca_sym = hoc_lookup("ca_ion");
register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 0);
_mechtype = nrn_get_mechtype(_mechanism[1]);
_nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
hoc_register_dparam_size(_mechtype, 3);
hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
ivoc_help("help ?1 lcafixed /cfs/klemming/nobackup/b/bkaplan/test/x86_64/lcafixed.mod\n");
hoc_register_limits(_mechtype, _hoc_parm_limits);
hoc_register_units(_mechtype, _hoc_parm_units);
}
static double eca = 70;
static double *_t_sinf;
static double *_t_rinf;
static double *_t_stau;
static double *_t_rtau;
static int _reset;
static char *modelname = "LCa calcium channel with fixed reversal potential";
static int error;
static int _ninits = 0;
static int _match_recurse=1;
static _modl_cleanup(){ _match_recurse=1;}
static _f_rates();
static rates();
static int _ode_spec1(), _ode_matsol1();
static _n_rates();
static int _slist1[2], _dlist1[2];
static int states();
/*CVODE*/
static int _ode_spec1 () {_reset=0;
{
rates ( _threadargscomma_ v ) ;
Ds = ( sinf - s ) / stau ;
Dr = ( rinf - r ) / rtau ;
}
return _reset;
}
static int _ode_matsol1 () {
rates ( _threadargscomma_ v ) ;
Ds = Ds / (1. - dt*( ( ( ( - 1.0 ) ) ) / stau )) ;
Dr = Dr / (1. - dt*( ( ( ( - 1.0 ) ) ) / rtau )) ;
}
/*END CVODE*/
static int states () {_reset=0;
{
rates ( _threadargscomma_ v ) ;
s = s + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / stau)))*(- ( ( ( sinf ) ) / stau ) / ( ( ( ( - 1.0) ) ) / stau ) - s) ;
r = r + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / rtau)))*(- ( ( ( rinf ) ) / rtau ) / ( ( ( ( - 1.0) ) ) / rtau ) - r) ;
}
return 0;
}
double alp ( _lv , _li )
double _lv , _li ;
{
double _lalp;
if ( _li == 0.0 ) {
_lalp = 7.5 / ( 1.0 + exp ( ( - _lv * 1.0 + 13.0 ) / 7.0 ) ) ;
}
else if ( _li == 1.0 ) {
_lalp = 0.0068 / ( 1.0 + exp ( ( _lv * 1.0 + 30.0 ) / 12.0 ) ) ;
}
return _lalp;
}
static int _hoc_alp() {
double _r;
_r = alp ( *getarg(1) , *getarg(2) ) ;
ret(_r);
}
double bet ( _lv , _li )
double _lv , _li ;
{
double _lbet;
if ( _li == 0.0 ) {
_lbet = 1.65 / ( 1.0 + exp ( ( _lv * 1.0 - 14.0 ) / 4.0 ) ) ;
}
else if ( _li == 1.0 ) {
_lbet = 0.06 / ( 1.0 + exp ( - _lv * 1.0 / 11.0 ) ) ;
}
return _lbet;
}
static int _hoc_bet() {
double _r;
_r = bet ( *getarg(1) , *getarg(2) ) ;
ret(_r);
}
static double _mfac_rates, _tmin_rates;
static _check_rates();
static _check_rates() {
static int _maktable=1; int _i, _j, _ix = 0;
double _xi, _tmax;
if (!usetable) {return;}
if (_maktable) { double _x, _dx; _maktable=0;
_tmin_rates = - 100.0 ;
_tmax = 100.0 ;
_dx = (_tmax - _tmin_rates)/200.; _mfac_rates = 1./_dx;
for (_i=0, _x=_tmin_rates; _i < 201; _x += _dx, _i++) {
_f_rates(_x);
_t_sinf[_i] = sinf;
_t_rinf[_i] = rinf;
_t_stau[_i] = stau;
_t_rtau[_i] = rtau;
}
}
}
static rates(double _lv){ _check_rates();
_n_rates(_lv);
return;
}
static _n_rates(double _lv){ int _i, _j;
double _xi, _theta;
if (!usetable) {
_f_rates(_lv); return;
}
_xi = _mfac_rates * (_lv - _tmin_rates);
_i = (int) _xi;
if (_xi <= 0.) {
sinf = _t_sinf[0];
rinf = _t_rinf[0];
stau = _t_stau[0];
rtau = _t_rtau[0];
return; }
if (_i >= 200) {
sinf = _t_sinf[200];
rinf = _t_rinf[200];
stau = _t_stau[200];
rtau = _t_rtau[200];
return; }
_theta = _xi - (double)_i;
sinf = _t_sinf[_i] + _theta*(_t_sinf[_i+1] - _t_sinf[_i]);
rinf = _t_rinf[_i] + _theta*(_t_rinf[_i+1] - _t_rinf[_i]);
stau = _t_stau[_i] + _theta*(_t_stau[_i+1] - _t_stau[_i]);
rtau = _t_rtau[_i] + _theta*(_t_rtau[_i+1] - _t_rtau[_i]);
}
static int _f_rates ( _lv )
double _lv ;
{
double _la , _lb ;
_la = alp ( _threadargscomma_ _lv , 0.0 ) ;
_lb = bet ( _threadargscomma_ _lv , 0.0 ) ;
stau = 1.0 / ( _la + _lb ) ;
sinf = _la / ( _la + _lb ) ;
_la = alp ( _threadargscomma_ _lv , 1.0 ) ;
_lb = bet ( _threadargscomma_ _lv , 1.0 ) ;
rtau = 1.0 / ( _la + _lb ) ;
rinf = _la / ( _la + _lb ) ;
return 0; }
static int _hoc_rates() {
double _r;
_r = 1.;
rates ( *getarg(1) ) ;
ret(_r);
}
static int _ode_count(_type) int _type;{ return 2;}
static int _ode_spec(_NrnThread* _nt, _Memb_list* _ml, int _type) {
Datum* _thread;
Node* _nd; double _v; int _iml, _cntml;
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
_nd = _ml->_nodelist[_iml];
v = NODEV(_nd);
_ode_spec1 ();
}}
static int _ode_map(_ieq, _pv, _pvdot, _pp, _ppd, _atol, _type) int _ieq, _type; double** _pv, **_pvdot, *_pp, *_atol; Datum* _ppd; {
int _i; _p = _pp; _ppvar = _ppd;
_cvode_ieq = _ieq;
for (_i=0; _i < 2; ++_i) {
_pv[_i] = _pp + _slist1[_i]; _pvdot[_i] = _pp + _dlist1[_i];
_cvode_abstol(_atollist, _atol, _i);
}
}
static int _ode_matsol(_NrnThread* _nt, _Memb_list* _ml, int _type) {
Datum* _thread;
Node* _nd; double _v; int _iml, _cntml;
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
_nd = _ml->_nodelist[_iml];
v = NODEV(_nd);
_ode_matsol1 ();
}}
extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
static void _update_ion_pointer(Datum* _ppvar) {
nrn_update_ion_pointer(_ca_sym, _ppvar, 0, 3);
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 4);
}
static void initmodel() {
int _i; double _save;_ninits++;
_save = t;
t = 0.0;
{
r = r0;
s = s0;
{
rates ( _threadargscomma_ v ) ;
s = sinf ;
r = rinf ;
}
_sav_indep = t; t = _save;
}
}
static void nrn_init(_NrnThread* _nt, _Memb_list* _ml, int _type){
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
if (use_cachevec) {
_v = VEC_V(_ni[_iml]);
}else
#endif
{
_nd = _ml->_nodelist[_iml];
_v = NODEV(_nd);
}
v = _v;
initmodel();
}}
static double _nrn_current(double _v){double _current=0.;v=_v;{ {
ica = gcabar * s * r * ( v - eca ) ;
}
_current += ica;
} return _current;
}
static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type){
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
if (use_cachevec) {
_v = VEC_V(_ni[_iml]);
}else
#endif
{
_nd = _ml->_nodelist[_iml];
_v = NODEV(_nd);
}
_g = _nrn_current(_v + .001);
{ double _dica;
_dica = ica;
_rhs = _nrn_current(_v);
_ion_dicadv += (_dica - ica)/.001 ;
}
_g = (_g - _rhs)/.001;
_ion_ica += ica ;
#if CACHEVEC
if (use_cachevec) {
VEC_RHS(_ni[_iml]) -= _rhs;
}else
#endif
{
NODERHS(_nd) -= _rhs;
}
}}
static void nrn_jacob(_NrnThread* _nt, _Memb_list* _ml, int _type){
Node *_nd; int* _ni; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml];
#if CACHEVEC
if (use_cachevec) {
VEC_D(_ni[_iml]) += _g;
}else
#endif
{
_nd = _ml->_nodelist[_iml];
NODED(_nd) += _g;
}
}}
static void nrn_state(_NrnThread* _nt, _Memb_list* _ml, int _type){
double _break, _save;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
_nd = _ml->_nodelist[_iml];
#if CACHEVEC
if (use_cachevec) {
_v = VEC_V(_ni[_iml]);
}else
#endif
{
_nd = _ml->_nodelist[_iml];
_v = NODEV(_nd);
}
_break = t + .5*dt; _save = t;
v=_v;
{
{ {
for (; t < _break; t += dt) {
error = states();
if(error){fprintf(stderr,"at line 52 in file lcafixed.mod:\n SOLVE states METHOD cnexp\n"); nrn_complain(_p); abort_run(error);}
}}
t = _save;
} }}
}
static terminal(){}
static _initlists() {
int _i; static int _first = 1;
if (!_first) return;
_slist1[0] = &(s) - _p; _dlist1[0] = &(Ds) - _p;
_slist1[1] = &(r) - _p; _dlist1[1] = &(Dr) - _p;
_t_sinf = makevector(201*sizeof(double));
_t_rinf = makevector(201*sizeof(double));
_t_stau = makevector(201*sizeof(double));
_t_rtau = makevector(201*sizeof(double));
_first = 0;
}
Best regards,
Bernhard Kaplan.