Hello,
My name is Ick Hoon Jin and I am Ph. D. student in Texas A & M Univ..
When I run the C embedded in R in the Linux system, I confront the
following error after 6,000 iteration. By googling I found this error is
from the problem in C.
*** caught segfault ***
address (nil), cause 'memory not mapped'
My C code is following:
---------------------------------------------------------------------------
#include<stdio.h>
#include<stdlib.h>
#include<R.h>
#include<Rmath.h>
#include<malloc.h>
#define Min(X,Y) ((X) < (Y) ? (X) : (Y))
void SecondMH(int *n, int *X, int *length_X, double *theta_new, int
*n_para, double *out);
int MH_Result(double *theta_new, int n_para, int *M1, int *M2, int n);
double Count_Edges(int *X, int n);
double Cal_GWD(int *X, int n);
int Cal_Degree(int *M3, int n);
double Inner_Product( double *vector1, double *vector2, int length);
int rdtsc();
void SecondMH(int *n, int *X, int *length_X, double *theta_new, int
*n_para, double *out)
{
int i, j, a, k;
int *M1, *M2;
M1 = (int *)calloc(*length_X, sizeof(int));
M2 = (int *)calloc(*length_X, sizeof(int));
for(i = 1; i < *n; i++)
{
for(j = 0; j < i; j++)
{
for(k = 0; k < *length_X; k++ )
{
M1[k] = X[k];
M2[k] = X[k];
}
if(X[i * *n + j] == 1)
{
M1[i * *n + j] = 0;
a = MH_Result(theta_new, *n_para, M1, M2, *n);
if(a == 1)
{
X[i * *n + j] = 0;
}
}
else
{
M1[i * *n + j] = 1;
a = MH_Result(theta_new, *n_para, M1, M2, *n);
if(a == 1)
{
X[i * *n + j] = 1;
}
}
}
}
for(i = 1; i < *n; i++)
{
for(j = 0; j < i; j++)
{
X[j * *n + i] = 0;
}
}
for(i = 0; i < *length_X; i++)
{
out[i] = (double)X[i];
}
free(M1);
free(M2);
return;
}
int MH_Result(double *theta_new, int n_para, int *M1, int *M2, int n)
{
double *M1_STAT, *M2_STAT;
double pi_Num, pi_Denom, MH_Ratio, v;
M1_STAT = (double *)calloc( n_para, sizeof( double ) );
M2_STAT = (double *)calloc( n_para, sizeof( double ) );
M1_STAT[0] = Count_Edges(M1, n);
M2_STAT[0] = Count_Edges(M2, n);
M1_STAT[1] = Cal_GWD(M1, n);
M2_STAT[1] = Cal_GWD(M2, n);
pi_Num = Inner_Product(theta_new, M1_STAT, n_para);
pi_Denom = Inner_Product(theta_new, M2_STAT, n_para);
MH_Ratio = pi_Num - pi_Denom;
srand(rdtsc());
v = (double)rand() / ( (double)RAND_MAX + (double)1 );
if( log( v ) < Min( 0, MH_Ratio ) )
return 1;
else
return 0;
free(M1_STAT);
free(M2_STAT);
}
double Count_Edges(int *X, int n)
{
double temp;
int i, j;
temp = 0;
for(i = 1; i < n; i++)
{
for(j = 0; j < i; j++)
{
temp += X[i * n + j];
}
}
return temp;
}
double Cal_GWD(int *X, int n)
{
int *M3, *Degree, *D_Y;
int i, j;
double theta = 0.25;
double GWD = 0.00;
M3 = (int *)calloc(n, sizeof(int));
Degree = (int *)calloc(n, sizeof(int));
D_Y = (int *)calloc((n - 1), sizeof(int));
for(i = 0; i < n; i++)
{
for(j = 0; j < n; j++)
{
M3[j] = X[i * n + j];
}
Degree[i] = Cal_Degree(M3, n);
}
for(i = 0; i < n - 1; i++)
{
D_Y[i] = 0;
for(j = 0; j < n; j++)
{
if(Degree[j] = i + 1)
{
D_Y[i] += 1;
}
}
}
for(i = 0; i < n-1; i++)
{
GWD += ( 1 - pow( (1 - exp(theta*(-1))), (i + 1) ) ) *
(double)D_Y[i];
}
GWD = GWD * exp(theta);
free(M3);
free(Degree);
free(D_Y);
return GWD;
}
int Cal_Degree(int *M3, int n)
{
int i, result;
result = 0;
for(i = 0; i < n; i++)
{
result += M3[i];
}
return result;
}
double Inner_Product(double *vector1, double *vector2, int length)
{
int i;
double result;
result = 0;
for(i = 0; i < length; i++)
{
result += vector1[i] * vector2[i];
}
return result;
}
int rdtsc()
{
__asm__ __volatile__("rdtsc");
}
-------------------------------------------------------------------------
and my R-code to call C function is following;
#-------------------------------------------------------------------------------
# Function for Second Gibbs with Metropolis-Hasting Step
#-------------------------------------------------------------------------------
dyn.load("SecondMH.so")
second.MH<-function(Adj.Matrix,theta.new,nodes){
n<-as.integer(nodes)
Y<-as.matrix.network(X,matrix.type="adjacency",directed=FALSE)
Z<-as.integer(as.vector(Y))
length.Z<-as.integer(length(Z))
theta.star<-as.double(as.vector(theta.new))
n.para<-as.integer(length(theta.star))
result<-.C("SecondMH",n,Z,length.Z,theta.star,n.para,out=as.double(rep(0.0,length.Z)))
X.new<-matrix(result$out,n,n)
Adj.Matrix<-network(X.new, directed=FALSE)
return(Adj.Matrix)}
--------------------------------------------------------------------------
Until this time, I have used only R and I am really a beginner for C
programming. How can I solve the segfault error? Please answer it.
Thank you very much.
Sincerely,
Jin, Ick Hoon
Ph. D. Student, Department of Statistics
Texas A&M University, College Station, TX
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