From mathieu.ribatet at epfl.ch  Fri Apr  3 08:35:30 2009
From: mathieu.ribatet at epfl.ch (Mathieu Ribatet)
Date: Fri, 03 Apr 2009 08:35:30 +0200
Subject: [Rd] Hello! I got error in C - R
In-Reply-To: <39726.165.91.115.6.1238723226.squirrel@www.stat.tamu.edu>
References: <39726.165.91.115.6.1238723226.squirrel@www.stat.tamu.edu>
Message-ID: <1238740530.3608.4.camel@ubuntu>

Dear Ick Hoon Jin,

Your problem is probably due to a misspecification in memory allocation
within your C code. To solve this you can:

      * check by yourself whenever there is C memory allocation - by the
        way I think it's best to use R memory allocation i.e. R_alloc
      * use valgrind (see Writing R extension for this) as you're under
        Linux and this will give you some guidance to find where the
        problem is.

Best,
Mathieu


Le vendredi 03 avril 2009 ? 03:47 +0200, kentjin at stat.tamu.edu a ?crit :
> 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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Hello! I got error in C - R
Mathieu Ribatet