C++太多寫入/讀取大小4

Question

我正在用C++編寫一個程序，它涉及解析很多文本文件。當我用valgrind運行我的程序時，我遇到了很多錯誤。

我使用的是Ubuntu 11，編譯器是g ++; 程序的目標是接收一個可選的參考文件，一個要處理的主文件，包含超過1000萬行的參數，以及要生成的14個文件的根名。

我將從第一個主要問題開始：遵循程序的奇怪行爲（有時它有效，有時不行，根據文件和作爲參數傳遞的字符串等），我決定檢查它與valgrind。它會產生大量的內存操作錯誤。從變量argv開始。

#include <iostream> 
    #include <stdio.h> 
    #include <stdlib.h> 
    #include <sstream> 
    #include "coverSamMulti.h" 
    #include "string.h" 

    using namespace std; 

    int main(int argc, char **argv) { 
bool mutYN; 
char * filerefgen; // The reference genome files 
char * filemap; // the mapping file 
char * fileroot; // the root name of all the generated files 

// two or three arguments? 
if (argc == 3) 
    { 
     mutYN= false; 
     filemap = new char[strlen(argv[1])+1]; 
     fileroot = new char[strlen(argv[2])+1]; 
     strcpy(filemap,argv[1]); 
     strcpy(fileroot,argv[2]); 
    } 
    else if (argc == 4) 
    { 
     mutYN= true; 
     filerefgen = new char[strlen(argv[1])+1]; 
     filemap = new char[strlen(argv[2])+1]; 
     fileroot = new char[strlen(argv[3])+1]; 
     strcpy(filerefgen,argv[1]); 
     strcpy(filemap,argv[2]); 
     strcpy(fileroot,argv[3]); 
    } 
    else { 
     cout << " \n Less or or too much parameter passed \n"; 
     return 0; 
    } 


    //call of the main function 

    GenF_Inf genfinf = ScanReadsMap(filemap); 

    // We will store for each positions and in 14 files respectively the coverage, the coverage of A, G, C and T, 
    // the number mismatches,the number of first position alignment, the number of first position alignment on the reverse strand, 
    // and the consensus genome of the sample, the segments size, the insertfs, the firsts, the ins and the del, 



       char * filecov = (char *)malloc(sizeof(char)*(strlen(fileroot)+10)); 
       char * filecov_A = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); 
       char * filecov_G = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); 
       char * filecov_C = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); 
       char * filecov_T = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); 
       char * filemis= (char *)malloc(sizeof(char)*(strlen(fileroot)+10)); 
       char * filefirst= (char *)malloc(sizeof(char)*(strlen(fileroot)+10)); 
       char * filefirstr = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); 
       char * filecons = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); 
       char * fileseg = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); 
       char * fileinsert = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); // the different insertsize 
       char * filefirsts = (char *)malloc(sizeof(char)*(strlen(fileroot)+12)); // the first position on single mapped reads 
       char * fileins = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); // the different insertsize 
       char * filedel = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); // the first position on single mapped reads 

       //building files' name; 

       strcpy(filecov,fileroot); 
       strcpy(filecov_A,fileroot); 
       strcpy(filecov_C,fileroot); 
       strcpy(filecov_G,fileroot); 
       strcpy(filecov_T,fileroot); 
       strcpy(filemis,fileroot); 
       strcpy(filefirst,fileroot); 
       strcpy(filefirstr,fileroot); 
       strcpy(filecons,fileroot); 
       strcpy(fileseg,fileroot); 
       strcpy(fileinsert,fileroot); 
       strcpy(filefirsts,fileroot); 
       strcpy(fileins,fileroot); 
       strcpy(filedel,fileroot); 

       strcat(filecov, "_cov.txt"); 
       strcat(filecov_A, "_cov_A.txt"); 
       strcat(filecov_C, "_cov_C.txt"); 
       strcat(filecov_G, "_cov_G.txt"); 
       strcat(filecov_T, "_cov_T.txt"); 
       strcat(filemis, "_mis.txt"); 
       strcat(filefirst, "_first.txt"); 
       strcat(filefirstr, "_firstr.txt"); 
       strcat(filecons, "_cons.txt"); 
       strcat(fileseg, "_seg.txt"); 
       strcat(fileinsert, "_insert.txt"); 
       strcat(filefirsts, "_firsts.txt"); 
       strcat(fileins, "_ins.txt"); 
       strcat(filedel, "_del.txt"); 

       ofstream covf(filecov); 
       ofstream covf_A(filecov_A); 
       ofstream covf_C(filecov_C); 
       ofstream covf_G(filecov_G); 
       ofstream covf_T(filecov_T); 
       ofstream misf(filemis); 
       ofstream firstf(filefirst); 
       ofstream firstrevf(filefirstr); 
       ofstream consf(filecons); 
       ofstream segf(fileseg); 
       ofstream insertf(fileinsert); 
       ofstream firstsf(filefirsts); 
       ofstream insf(fileins); 
       ofstream delf(filedel); 


       // generating the files 

cout << "\n ====================================== \n "; 
cout << "\n Generating the files \n "; 
cout << "\n ====================================== \n "; 



for(int j=0;j < NSEG; j++) 
    { segf << genfinf.start[j]; 
      for (int i =0; i <genfinf.lenght[j]; i++) 
      { if ((j!=NSEG-1) && (i!= genfinf.lenght[NSEG-1]-1)){ 
       firstf << genfinf.mapfinf[j].firstposcov[i] << ","; 
       misf << genfinf.mapfinf[j].nbmismatch[i]<< ","; 
       covf << genfinf.mapfinf[j].poscov[i] << ","; 
       covf_A << genfinf.mapfinf[j].poscov_A[i]<< ","; 
       covf_C << genfinf.mapfinf[j].poscov_C[i]<< ","; 
       covf_G << genfinf.mapfinf[j].poscov_G[i]<< ","; 
       covf_T << genfinf.mapfinf[j].poscov_T[i]<< ","; 
       firstrevf<< genfinf.mapfinf[j].first_rev[i]<< ","; 
       insf << genfinf.mapfinf[j].ins[i]<< ","; 
       delf << genfinf.mapfinf[j].del[i]<< ","; 
       firstsf << genfinf.mapfinf[j].firstposcovsingle[i]<< ","; 
      }} 
    } 


for(int j=0;j < 999; j++) insertf << genfinf.insert[j]<< ","; 

int j = NSEG-1;int i = genfinf.lenght[NSEG-1]-1; 

firstf << genfinf.mapfinf[j].firstposcov[i] ; 
misf << genfinf.mapfinf[j].nbmismatch[i]; 
covf << genfinf.mapfinf[j].poscov[i] ; 
covf_A << genfinf.mapfinf[j].poscov_A[i]; 
covf_C << genfinf.mapfinf[j].poscov_C[i]; 
covf_G << genfinf.mapfinf[j].poscov_G[i]; 
covf_T << genfinf.mapfinf[j].poscov_T[i]; 
firstrevf<< genfinf.mapfinf[j].first_rev[i]; 
insf << genfinf.mapfinf[j].ins[i]; 
delf << genfinf.mapfinf[j].del[i]; 
firstsf << genfinf.mapfinf[j].firstposcovsingle[i]; 

j =999; 
insertf << genfinf.insert[j]; 



//building the consensus genome 

cout << "\n ====================================== \n "; 
cout << "\n building the consensus \n "; 
cout << "\n ====================================== \n "; 



int A,G,C,T; 

for(int j=0;j < NSEG; j++) 
     { consf<<">segment_"<<j+1<<"\n"; 
      int k = 0; // for newline after 60 bp; 
       for (i =0; i <genfinf.lenght[j]; i++) 
       { 
        A=genfinf.mapfinf[j].poscov_A[i]; C=genfinf.mapfinf[j].poscov_C[i]; 
        G=genfinf.mapfinf[j].poscov_G[i]; T=genfinf.mapfinf[j].poscov_T[i]; 
        if ((A>=G)&&(A>=C)&&(A>=T)) {if (A!=0)consf<<"A"; else   consf<<"N";} 
        else if ((C>=A)&&(C>=G)&&(C>=T)) consf<<"C"; 
        else if ((G>=A)&&(G>=C)&&(G>=T)) consf<<"G"; 
        else if (((T>=A)&&(T>=G)&&(T>=C)))consf<<"T"; 
        k++; 
        if (k ==59){consf<<"\n";k=0;} 
       } 
       consf<<"\n"; 
     } 


    // closing all files 

covf.close(); 
covf_A.close(); 
covf_C.close(); 
covf_G.close(); 
covf_T.close(); 
misf.close(); 
firstf.close(); 
firstrevf.close(); 
consf.close(); 
segf.close(); 
insertf.close(); 
firstsf.close(); 
insf.close(); 
delf.close(); 



// finding mutations 


if (mutYN) 
{ 

     cout << "\n ====================================== \n "; 
     cout << "\n computing mutations \n "; 
     cout << "\n ====================================== \n "; 


     // Preparing the mutations file. 
     char * filemut = (char *)malloc(sizeof(char)*(strlen(fileroot)+9)); 
     strcpy(filemut,fileroot); 
     strcat(filemut, "_mut.txt"); 
     ofstream mutf(filemut); 

     char chrg, chcg;// Char from the reference genome, Char from the consensus genome 
     string strheader; // the first line of the reference genome file 

     ifstream refgen(filerefgen); 
     ifstream consf(filecons); 
      if (!refgen) 
         { 
           puts("Cannot open open the file") ; 
           refgen.close() ; 
           exit(0); 
         } 
      else 
        { 
       getline(refgen, strheader); 
       // read in the file without catching any non alpha caracter like space, tab, etc... 
       do {chrg = refgen.get();} while (!isalpha(chrg) && (chrg !=EOF)); 
       do {chcg=consf.get(); } while (!isalpha(chcg)&& (chcg !=EOF)); 
       int i =0; 

         while ((chrg !=EOF)&&(chcg !=EOF)) 
         { if (chrg != chcg) 
         { 
          mutf<< "Position "<< i << " : \n"; 
          mutf << "\t"<<chrg<<" by "<<chcg<<"\n"; 
         } 
         do {chrg = refgen.get();} while (!isalpha(chrg) && (chrg !=EOF)); 
         do {chcg=consf.get(); } while (!isalpha(chcg)&& (chcg !=EOF)); 
         i++; 
         } 
        } 

      cout << "\n Mutations computed \n "; 
      mutf.close(); 

    } 

    cout << "\n ====================================== \n "; 
    cout << "\n all files generated successfuly \n "; 
    cout << "\n ====================================== \n "; 


     return 0; 

}

而且Valrind輸出的只是一小部分，第一行：

 ==28950== Memcheck, a memory error detector 
    ==28950== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. 
    ==28950== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info 
    ==28950== Command: ./echantillon Ftooshort.sam covsam/echan1 
    ==28950== Parent PID: 1928 
    ==28950== 
    ==28950== Warning: client switching stacks? SP change: 0xbeee91f8 --> 0xbeb8b910 
    ==28950==   to suppress, use: --max-stackframe=3528936 or greater 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049000: main (echantillon.cpp:11) 
    ==28950== Location 0xbeb8b92c is 0 bytes inside local var "argv" 
    ==28950== declared at echantillon.cpp:11, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x804900D: main (echantillon.cpp:11) 
    ==28950== Address 0xbeee91ec is on thread 1's stack 
    ==28950== 
    ==28950== Invalid write of size 1 
    ==28950== at 0x804901B: main (echantillon.cpp:20) 
    ==28950== Location 0xbeee7f8d is 0 bytes inside local var "mutYN" 
    ==28950== declared at echantillon.cpp:12, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x8049022: main (echantillon.cpp:21) 
    ==28950== Location 0xbeb8b92c is 0 bytes inside local var "argv" 
    ==28950== declared at echantillon.cpp:11, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x804902D: main (echantillon.cpp:21) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A225: strlen (mc_replace_strmem.c:390) 
    ==28950== by 0x8049034: main (echantillon.cpp:21) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "str" 
    ==28950== declared at mc_replace_strmem.c:390, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049038: main (echantillon.cpp:21) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x4029149: operator new[](unsigned int) (vg_replace_malloc.c:343) 
    ==28950== by 0x804903F: main (echantillon.cpp:21) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "n" 
    ==28950== declared at vg_replace_malloc.c:343, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049040: main (echantillon.cpp:21) 
    ==28950== Location 0xbeee7f18 is 0 bytes inside local var "filemap" 
    ==28950== declared at echantillon.cpp:14, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x8049046: main (echantillon.cpp:22) 
    ==28950== Location 0xbeb8b92c is 0 bytes inside local var "argv" 
    ==28950== declared at echantillon.cpp:11, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049051: main (echantillon.cpp:22) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A225: strlen (mc_replace_strmem.c:390) 
    ==28950== by 0x8049058: main (echantillon.cpp:22) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "str" 
    ==28950== declared at mc_replace_strmem.c:390, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x804905C: main (echantillon.cpp:22) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x4029149: operator new[](unsigned int) (vg_replace_malloc.c:343) 
    ==28950== by 0x8049063: main (echantillon.cpp:22) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "n" 
    ==28950== declared at vg_replace_malloc.c:343, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049064: main (echantillon.cpp:22) 
    ==28950== Location 0xbeee7f1c is 0 bytes inside local var "fileroot" 
    ==28950== declared at echantillon.cpp:15, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x804906A: main (echantillon.cpp:23) 
    ==28950== Location 0xbeb8b92c is 0 bytes inside local var "argv" 
    ==28950== declared at echantillon.cpp:11, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049075: main (echantillon.cpp:23) 
    ==28950== Address 0xbeb8b914 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x8049079: main (echantillon.cpp:23) 
    ==28950== Location 0xbeee7f18 is 0 bytes inside local var "filemap" 
    ==28950== declared at echantillon.cpp:14, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x804907F: main (echantillon.cpp:23) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A269: strcpy (mc_replace_strmem.c:429) 
    ==28950== by 0x8049086: main (echantillon.cpp:23) 
    ==28950== Location 0xbeb8b914 is 0 bytes inside local var "src" 
    ==28950== declared at mc_replace_strmem.c:429, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A26C: strcpy (mc_replace_strmem.c:429) 
    ==28950== by 0x8049086: main (echantillon.cpp:23) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "dst" 
    ==28950== declared at mc_replace_strmem.c:429, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x8049087: main (echantillon.cpp:24) 
    ==28950== Location 0xbeb8b92c is 0 bytes inside local var "argv" 
    ==28950== declared at echantillon.cpp:11, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049092: main (echantillon.cpp:24) 
    ==28950== Address 0xbeb8b914 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x8049096: main (echantillon.cpp:24) 
    ==28950== Location 0xbeee7f1c is 0 bytes inside local var "fileroot" 
    ==28950== declared at echantillon.cpp:15, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x804909C: main (echantillon.cpp:24) 
    ==28950== Address 0xbeb8b910 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A269: strcpy (mc_replace_strmem.c:429) 
    ==28950== by 0x80490A3: main (echantillon.cpp:24) 
    ==28950== Location 0xbeb8b914 is 0 bytes inside local var "src" 
    ==28950== declared at mc_replace_strmem.c:429, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x402A26C: strcpy (mc_replace_strmem.c:429) 
    ==28950== by 0x80490A3: main (echantillon.cpp:24) 
    ==28950== Location 0xbeb8b910 is 0 bytes inside local var "dst" 
    ==28950== declared at mc_replace_strmem.c:429, in frame #0 of thread 1 
    ==28950== 

    // And many others almost 30 per each mentioning char * or file I mean fileroot, filemap, filecons, filedes, and so on. 

    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x804D29C: std::operator|(std::_Ios_Openmode, std::_Ios_Openmode) (ios_base.h:122) 
    ==28950== by 0x8049867: main (echantillon.cpp:99) 
    ==28950== Location 0xbeb8b914 is 0 bytes inside local var "__b" 
    ==28950== declared at ios_base.h:121, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049868: main (echantillon.cpp:99) 
    ==28950== Address 0xbeb8b918 is on thread 1's stack 
    ==28950== 
    ==28950== Invalid read of size 4 
    ==28950== at 0x804986C: main (echantillon.cpp:99) 
    ==28950== Location 0xbeee7f3c is 0 bytes inside local var "filecov" 
    ==28950== declared at echantillon.cpp:52, in frame #0 of thread 1 
    ==28950== 
    ==28950== Invalid write of size 4 
    ==28950== at 0x8049872: main (echantillon.cpp:99) 
    ==28950== Address 0xbeb8b914 is on thread 1's stack 

所以，請任何人能幫助我理清這個問題？

Answer 1

從Valgrind的docs：

警告：客戶機切換棧？

Valgrind在堆棧指針中發現了這麼大的變化，它 猜測客戶端正在切換到不同的堆棧。此時， 會猜測新堆棧的基址，並相應地設置內存許可。如果Valgrind猜測錯誤，您可能會在此之後收到許多僞造錯誤消息 。此刻「大 更改」被定義爲在堆棧指針寄存器的值 中多於2000000的變化。

嘗試解決這個第一，看看後續的錯誤消失。日誌告訴你如何解決它。

如果不解決您的問題，請張貼再現它的最小編譯代碼 - 你上面的OP是巨大的，看起來大多是無關緊要的。