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 Comput Neurosci 21:119-29 [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
parbush
data
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
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
vecst.mod
batch_.hoc
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
modstat
netcon.inc
test1.sh
xtmp
                            
: $Id: misc.mod,v 1.1.1.1 2005/12/15 15:16:39 hines Exp $
COMMENT
Misc. routines:
sassign() // assign a string from system
dassign()// assign a double
nokill() // chatch SIGHUP
prtime() // gives date/time
fspitchar(c,file) // sends single char to a file
spitchar(c)       // sends single char to stdout: eg c=1 => ^A
file_exist(file) // returns 1 if filename exists
hocgetc(file) // get single char from a file

  Note that with a SUFFIX equal to "nothing" these functions do not
have a suffix in hoc.  Thus to call sassign() in hoc use simply type
"sassign()" <- without the quotes.

    file_exist(filename)
        - returns 1 if filename exists

    sassign()  (string assign, written by Bill Lytton)
        - This routine is used to set a string in Hoc to something that has
          been returned by a system call.  sassign("name","shell_call ...")
          will produce a file called "sassign" in the cwd that will contain
          a hoc call that sets string 'name' to the result of shell_call 
          which should be a string.
        
    dassign()  (double assign, written and used by Bill Lytton)
        - This routine is used to set a variable in Hoc to something that has
          been returned by a system call.  sassign("name","shell_call ...")
          will produce a file called "dassign" in the cwd that will contain
          a hoc call that sets variable 'name' to the result of shell_call 
          which should be a number.

ENDCOMMENT
                           
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

NEURON {
    SUFFIX nothing
}

VERBATIM
#include <unistd.h>     /* F_OK     */
#include <errno.h>      /* errno    */
#include <signal.h>
#include <sys/types.h>         /* MUST REMEMBER THIS */
#include <time.h>
#include <stdio.h>
#include <limits.h>
ENDVERBATIM

:* FUNCTION file_exist()
FUNCTION file_exist() {
VERBATIM
    /* Returns TRUE if file exists, if file not exist the need to reset
       errno else will get a nrnoc error.  Seems to be a problem even
       if I don't include <errno.h> */

    char *gargstr(), *filename;

    filename = gargstr(1);

    if (*filename && !access(filename, F_OK)) {
        _lfile_exist = 1;

    } else {
        /* Errno set to 2 when file not found */
        errno = 0;

        _lfile_exist = 0;
    }
ENDVERBATIM
}

:* PROCEDURE sassign()
PROCEDURE sassign() {
VERBATIM
    FILE *pipein;
    char string[BUFSIZ], **strname, *syscall;
    char** hoc_pgargstr();

    strname = hoc_pgargstr(1);
    syscall = gargstr(2);

    if( !(pipein = popen(syscall, "r"))) {
        fprintf(stderr,"System call failed\n");
        return; 
    }
    
    if (fgets(string,BUFSIZ,pipein) == NULL) {
        fprintf(stderr,"System call did not return a string\n");
        pclose(pipein); return;
    }

    /*  assign_hoc_str(strname, string, 0); */
    hoc_assign_str(strname, string);

    pclose(pipein);
    errno = 0;
ENDVERBATIM
}

:* PROCEDURE dassign() 
PROCEDURE dassign() {
VERBATIM
    FILE *pipein, *outfile;
    char *strname, *syscall;
    double num;

    strname = gargstr(1);
    syscall = gargstr(2);

    if ( !(outfile = fopen("dassign","w"))) {
        fprintf(stderr,"Can't open output file dassign\n");
        return; 
    }

    if( !(pipein = popen(syscall, "r"))) {
        fprintf(stderr,"System call failed\n");
        fclose(outfile); return; 
    }
    
    if (fscanf(pipein,"%lf",&num) != 1) {
        fprintf(stderr,"System call did not return a number\n");
        fclose(outfile); pclose(pipein); return; 
    }

    fprintf(outfile,"%s=%g\n",strname,num);
    fprintf(outfile,"system(\"rm dassign\")\n");

    fclose(outfile); pclose(pipein);
    errno = 0;
ENDVERBATIM
}

:* PROCEDURE nokill() 
: nohup
PROCEDURE nokill() {
VERBATIM
  signal(SIGHUP, SIG_IGN);
ENDVERBATIM
}

:* FUNCTION prtime()
FUNCTION prtime () {
VERBATIM
  double prt;
  static double PRTIME;
  prt = (clock()-PRTIME)/CLOCKS_PER_SEC;
  // UINT_MAX for 32 bit machine -- see 'man clock'
  if (prt<0) prt += UINT_MAX/CLOCKS_PER_SEC; 
  PRTIME=clock();
  _lprtime = prt;
ENDVERBATIM
}

:* FUNCTION now ()
FUNCTION now () {
VERBATIM
  _lnow = time((time_t*)0);
  _lnow -= (12784) * 24*60*60; // time from the Epoch to 01/01/05
ENDVERBATIM
}

:* PROCEDURE sleepfor ()
PROCEDURE sleepfor (sec) {
VERBATIM
  struct timespec ts;
  ts.tv_sec = (time_t)_lsec;
  ts.tv_nsec = (long)0;
  nanosleep(&ts,(struct timespec*)0);
ENDVERBATIM
}

:* PROCEDURE fspitchar
PROCEDURE fspitchar(c) {
VERBATIM
{	
  FILE* f, *hoc_obj_file_arg();
  f = hoc_obj_file_arg(2);
  fprintf(f, "%c", (int)_lc);
}
ENDVERBATIM
}

:* PROCEDURE spitchar
PROCEDURE spitchar(c) {
VERBATIM
{	
  printf("%c", (int)_lc);
}
ENDVERBATIM
}

:* FUNCTION hocgetc
FUNCTION hocgetc() {
VERBATIM
{	
  FILE* f, *hoc_obj_file_arg();
  f = hoc_obj_file_arg(1);
  _lhocgetc = (double)getc(f);
}
ENDVERBATIM
}

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