Thread: Error while writing into a File; after certain file size

Hi all,

I am executing a C program that writes into a file. I get the following error after the file reaches certain size ( < 0.4 GB).

10 [main] anj3 4872 _cygtls::handle_exceptions: Error while dumping state (
probably corrupted stack)
Segmentation fault (core dumped)

It always happens when the size of the file is too big. Is it because of too big a file if so how can I let my program know the file needs to be Big enff.


If not what else could be wrong.

Note: I use a loop that executes at least 4000 times and each time it writes 1000000 or more chars into the file.

Same iteration but after some 2000 iteration it just halts with the error.
If I stop the loop right before the halting point ( by changing the condition) no error occurs and the program continues with the code after the loop.

IS there any file size limitation in C or the operating system
I am using cygwin and vista

I believe Problem with my program is due to excessive use of memory.


I have more than 2000 iteration. In each iteration I open at least 2 files. Windows vista does not close these files anticipating they will be used in future.

I close them after every iteration using fclose() method. Is there anything I can do to tell OS to remove the file from run time memory.

I tried using sleep() method after very 1000 iterations to kind of stop the memory usage. But it is does not seem to work well for my problem. I do not understand why this problem happens. The weird thing is I get the error message

[see the error in the first message]


at different time during differ run. Meaning something outside the program is causing it.


Please help. I just want to know what I am doing wrong

The following is the my code partially. The first while loop is the one that I want to execute way more than 2000 times. But I kind of get stuck at about 2350 or 2260 (I do not know why the difference)

Code:

       loop: while(!feof(rf))
	{
		fgets(line,380,rf);
		
	//	Reading a line from pdb list file printf(line);
			strncpy(filename,line,4);
			filename[4] ='\0';
			strncpy(profile,line,5);
			profile[5] = '\0';
			strcpy(pdbName,profile);
			strcat(profile,".profile");
			strncpy(chain,line+4,1);
			strcat(filename,".pdb");
			char st[100] = cullpdb;
			strcat(st,filename);			//	Getting the file name of the pdb entry
			char st4[100] = psiblast;
			strcat(st4,profile );
			st4[strlen(psiblast)+1+13]='\0';
			st[strlen(cullpdb)+1+8]='\0';
			//printf("Profile File Name = %s", st4);


    // These are two files I open in every iteration
			if((fpro = fopen(st4,"r"))==0)              
			{
				printf("Profile File Not found %s", st4);
				goto loop;
				
				}
					if((f = fopen(st,"r")) == 0)
			{ printf(" File %s is not in Directory", &st); 
				goto loop; 
			}
			else
			{
					strcpy(pdb_list[pdbn],pdbName);
					pdbn++;
				}
				
				
				
					fprintf(fp,"1  ");
					featureNum = 1;
		//Profile data converted into features for SVM
			while(!feof(fpro))
			{
				fgets(proLine,380,fpro);
				int k=0;
				char str3[100];
				
				for(i=0; i < strlen(proLine); i++)
				{
						
						if(proLine[i] != ' ')
						{
							str3[k] = proLine[i];
							k++;
						}
						else
						{
							str3[k]='\0';
							j = atoi(str3);
							if(j!=0)
							{
								fprintf(fp,"%d:%d ", featureNum,j);
							
								}
							featureNum++;
							k=0	;
						}					
					  		
				}
			
				
			}
			
	
		n=0;
		modelFlag = 0;
		
			while(!feof(f))
			{
				
						fgets(pline,380,f);
   	
						strncpy(st2,pline,5);
						st2[5] = '\0';
						if(strcmp(st2,"MODEL") ==0)
						{
								if(modelFlag ==0)
										modelFlag = 1;
								else
										goto Dist;
						}
						strncpy(st2,pline,4);
			
						st2[4] = '\0';
			
						if(strcmp(st2, "ATOM") == 0)
						{
							strncpy(st3,pline+13,2);
							st3[2] ='\0';
							strncpy(seq_chain,pline+21 ,1);
							seq_chain[1]='\0';
					if((strcmp(st3,"CA") ==0) && (strcmp(seq_chain,chain) ==0))
							{
													
								strncpy(xc,pline+26,12); 
								strncpy(yc,pline+38,8);
								strncpy(zc,pline+46,8);
								xc[12] ='\0'; yc[8]= '\0'; zc[8] = '\0';
													
							ca[n].x = atof(xc); ca[n].y = atof(yc); ca[n].z =atof(zc);
								n++; 
							}
						}
			
			}
			
			
		Dist: 	
			for(i=0;i<n;i++)					
	// Make number 4 to n for N*N distance matrix or it will be N*4 matrix
     {
        for(j=i+1;j<n;j++)
        {
           dist = sqrt((ca[i].x -ca[j].x)*(ca[i].x-ca[j].x) +  (ca[i].y -ca[j].y)*(ca[i].y-ca[j].y) +  (ca[i].z -ca[j].z)*(ca[i].z-ca[j].z));
           fprintf(fp,"%d:%.3lf ", featureNum,dist);
           featureNum++;
           
        }
       }
       fprintf(fp,"# %s %s", pdbName,seqn);
			printf(".");
			printf("\nDone with one vector %d pdb ID is %s Feature Number is %d",posn,pdbName,featureNum);
			if(maxF<featureNum)
				maxF = featureNum;
				avgF = avgF+ featureNum;
			posn++;
			if(posn>C1000*1000)
			{
				sleep(200);
				C1000++;
			}
			//scanf("%c",st2);
			fclose(f);                       // I am closing BOth files here
			fclose(fpro);
			fprintf(fp,"\n");
		}

I closed the fpro file. I still get the same problem after 2387 iterations




388 [main] a 5060 _cygtls::handle_exceptions: Error while dumping state (pro
bably corrupted stack)
Segmentation fault (core dumped)

GASP! Is that a "goto" I see???