Parallel network simulations with NEURON (Migliore et al 2006)

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Accession:64229
The NEURON simulation environment has been extended to support parallel network simulations. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
Reference:
1 . Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
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netmod
parscalebush
AMPA.mod *
arhRT03.mod *
cadecay.mod
cadRT03.mod
cah.mod
calRT03.mod
catRT03.mod *
GABAa.mod *
GABAb.mod *
intf.mod
k2RT03.mod *
kahpRT03.mod
kaRT03.mod *
kca.mod *
kcRT03.mod
kdr.mod
kdrp.mod
kdrRT03.mod *
kmRT03.mod *
misc.mod
myfit.mod
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
stats.mod
vecst.mod
batch.hoc
bg
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
geom.hoc
init.hoc
netcon.inc
network.hoc
nqsnet.hoc
nspike.dat
params.hoc
parnetwork.hoc
parnqsnet.hoc
perfrun.hoc
prebatch_.hoc
run.hoc
spkplt.hoc *
x_vs_nspike.hoc
                            
: $Id: myfit.mod,v 1.2 2006/02/14 13:11:29 hines Exp $
 
:* COMMENT
COMMENT
ENDCOMMENT

NEURON {
  SUFFIX nothing
  GLOBAL FIT_INSTALLED
}

PARAMETER {
  FIT_INSTALLED=0
}

ASSIGNED { RES }

VERBATIM
#include <stdlib.h>
#include <math.h>
/*#include <values.h> /* contains MAXLONG */
#include <limits.h> /* contains MAXLONG */
#include <sys/time.h> 
extern double* hoc_pgetarg();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern Object** hoc_objgetarg();
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double* vector_vec();
extern double hoc_epsilon;
extern void set_seed();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
extern int list_vector_px2();
int list_vector_px();
int list_vector_resize();

typedef struct BVEC {
 int size;
 int bufsize;
 short *x;
 Object* o;
} bvec;
ENDVERBATIM

: spkcmp(modlist,targlist,flag)
: compare spike times from left to right finding the closest for each one
: better algorithm would do all pairwise comparisons and take the smallest, next smallest, etc.
VERBATIM
static double spkcmp (void* vv) {
  int flag, i, j, k, nx, nm[10], nt[10], num, sum, minind;
  Object *ob, *ob1;
  double *vvm[10], *vvt[10], *x, err, diff, min;

  nx = vector_instance_px(vv, &x);
  ob  =   *hoc_objgetarg(1);
  ob1 =   *hoc_objgetarg(2);
  if (ifarg(3)) flag=(int)*getarg(3); else flag=0;

  num = ivoc_list_count(ob);
  i = ivoc_list_count(ob1);
  if (num>10) hoc_execerror("ERR: spkcmp can only handle 10 vectors", 0);
  if (num!=i) hoc_execerror("ERR: spkcmp different sized lists", 0);
  if (nx!=num*2) hoc_execerror("ERR: spkcmp vec should be 2*list length", 0);
  for (i=0;i<num;i++) { 
    nm[i] = list_vector_px(ob,  i,  &vvm[i]);
    nt[i] = list_vector_px(ob1, i,  &vvt[i]);
  }
  for (i=0;i<num;i++) {            /* spike vectors */
    if (nm[i]<=nt[i]) { /* fewer model spikes */
      for (j=0,err=0;j<nm[i];j++) {     /* model spike times */
        for (k=0,min=1e9;k<nt[i];k++) {           /* find min time diff with target spikes */
          diff=fabs(vvm[i][j]-vvt[i][k]);
          if (diff<min) { 
            min=diff;       /* closest spike to this model spike */
            minind=k;
          }
          /* printf("%d %d %d %g %g %g %g %g\n",i,j,k,vvm[i][j],vvt[i][k],diff,min,err); */
        }
        err+=min; 
        vvt[i][minind]=1e9; /* remove that spike */
      }
    } else {  /* go through target spike list */
      for (k=0,err=0;k<nt[i];k++) {         /*  */
        for (j=0,min=1e9;j<nm[i];j++) {     /* model spike times */
          diff=fabs(vvm[i][j]-vvt[i][k]);
          if (diff<min) { 
            min=diff;       /* closest spike to this model spike */
            minind=j;
          }
          /* printf("%d %d %d %g %g %g %g %g\n",i,j,k,vvm[i][j],vvt[i][k],diff,min,err); */
        }
        err+=min; 
        vvm[i][minind]=1e9; /* remove that spike */
      }
    }
    x[i]=err;
  }
  for (i=0;i<num;i++) x[i+num]=(double)abs(nm[i]-nt[i]);
  for (i=0,err=0;i<2*num;i++) err+=x[i];
  return err;
}
ENDVERBATIM

: bursty(modlist,mininvl) -- measure burstiness
VERBATIM
static double bursty (void* vv) {
  int i, j, k, nx, nm[10], nt[10], num, minind;
  Object *ob, *ob1;
  double *vvm[10], *vvt[10], *x, err, diff, mininvl, invl, last, sum, cnt;

  nx = vector_instance_px(vv, &x);
  ob  =   *hoc_objgetarg(1);
  if (ifarg(2)) mininvl=*getarg(2); else mininvl=3.;

  num = ivoc_list_count(ob);
  if (num>10) hoc_execerror("ERR: spkcmp can only handle 10 vectors", 0);
  if (nx!=2*num) hoc_execerror("ERR: spkcmp vec should be 2*list length", 0);
  for (i=0;i<num;i++) { 
    nm[i] = list_vector_px(ob,  i,  &vvm[i]);
  }
  for (i=0;i<num;i++) {            /* spike vectors */
    for (j=1,last=vvm[i][0],sum=0.,cnt=0.;j<nm[i];j++) {
      if ((invl=vvm[i][j]-last)<mininvl) { sum+=invl; cnt+=1; }
      last=vvm[i][j];
    }
    x[2*i]=cnt; x[2*i+1]=sum/cnt; /* #of spikes in bursts, ave invl */
  }
  return x[0];
}
ENDVERBATIM

:* PROCEDURE install_myfit()
PROCEDURE install_myfit () {
  FIT_INSTALLED=1
  VERBATIM
  install_vector_method("spkcmp", spkcmp);
  install_vector_method("bursty", bursty);
  ENDVERBATIM
}

:* idptr(&x) gives location of a pointer
PROCEDURE idptr () {
VERBATIM
  double *fr;
  fr = hoc_pgetarg(1);
  printf("%x\n",fr);
ENDVERBATIM
}

:* veclistcp(src,dest)
FUNCTION veclistcp () {
  VERBATIM {
  int code, i, j, ns, nd, num, n[2];
  Object *obs, *obd;
  double *vvs, *vvd;

  obs =   *hoc_objgetarg(1);
  obd =   *hoc_objgetarg(2);
  num = ivoc_list_count(obs);
  i =   ivoc_list_count(obd);
  if (num!=i) hoc_execerror("veclistcp ERR: different sized lists", 0);

  for (i=0;i<num;i++) { 
    ns = list_vector_px(obs,  i, &vvs);
    nd = list_vector_px(obd, i, &vvd);
    if (ns!=nd) { printf("veclistcp ERR %d %d %d\n",i,ns,nd);
      hoc_execerror("Vectors must all be same size: ", 0); }
    for (j=0;j<ns;j++) vvd[j]=vvs[j];
  }
  return num;
  }
  ENDVERBATIM
}

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