c++ seg fault issue

Question

I am working on a C++ program that uses some external C libraries. As far as I can tell though that is not the cause of the problem, and the issue is with my C++ code. The program runs fine with no errors or anything on my test datasets, but after going through nearly the entire full dataset, I get a segfault. Running GDB gives me this segfault:

(gdb) run -speciesMain=allMis1 -speciesOther=anoCar2 -speciesMain=allMis1 -speciesOther=anoCar2 /hive/data/genomes/allMis1/bed/lastz.anoCar2/mafRBestNet/*.maf.gz
Starting program: /cluster/home/jstjohn/bin/mafPairwiseSyntenyDecay -speciesMain=allMis1 -speciesOther=anoCar2 -speciesMain=allMis1 -speciesOther=anoCar2 /hive/data/genome
s/allMis1/bed/lastz.anoCar2/mafRBestNet/*.maf.gz
Detaching after fork from child process 3718.

Program received signal SIGSEGV, Segmentation fault.
0x0000003009cb7672 in __gnu_cxx::__exchange_and_add(int volatile*, int) () from /usr/lib64/libstdc++.so.6
(gdb) up
#1  0x0000003009c9db59 in std::basic_string, std::allocator >::~basic_string() () from /usr/lib64/libstdc++.so.6
(gdb) up
#2  0x00000000004051e7 in PairAlnInfo::~PairAlnInfo (this=0x7fffffffcd70, __in_chrg=) at mafPairwiseSyntenyDecay.cpp:37
(gdb) up
#3  0x0000000000404eb0 in main (argc=2, argv=0x7fffffffcf78) at mafPairwiseSyntenyDecay.cpp:260

It looks like something is going on with a double free of my PairAlnInfo class. The weird thing is that I don't define a destructor, and I am not allocating anything with new. I have tried this both with g++44 and g++4.1.2 on the linux machine and have had the same results.

To make things even weirder, on my linux box (with more available RAM and everything, not that RAM is an issue with this program, but it is a beefy system) the seg fault happens as described above before the program reaches the loop to print output. On my much smaller macbook air using either g++ or clang++, the program still segfaults, but it doesn't do that until after the results are printed, right before the final return(0) out of the main function. Here is what the GDB trace looks like on my mac running on the same file after compiling with Mac's default g++4.2:

(more results)...
98000   27527   162181  0.83027
99000   27457   161467  0.829953
100000  27411   160794  0.829527

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x00004a2c00106077
0x00007fff9365a6e5 in std::string::_Rep::_M_dispose ()
(gdb) up
#1  0x00007fff9365a740 in std::basic_string, std::allocator >::~basic_string ()
(gdb) up
#2  0x0000000100003938 in main (argc=1261, argv=0x851d5fbff533) at mafPairwiseSyntenyDecay.cpp:301
(gdb)

Just in case you didn't notice the time of my posting, it's about 2:30AM now... I have been hacking away at this problem for about 10 hours now. Thanks so much for taking the time to look at this and help me out! The code and some instructions for replicating my situation follow.

If you are interested in downloading and installing the whole thing with dependencies then download my KentLib repository, make in the base directory, and then go to examples/mafPairwiseSyntenyDecay and run make there. An example (rather large) that causes the bug I am discussing is the gziped file available here: 100Mb file that the program crashes on. Then execute the program with these arguments -speciesMain=allMis1 -speciesOther=anoCar2 anoCar2.allMis1.rbest.maf.gz.

/**
 * mafPairwiseSyntenyDecay
 *  Author: John St. John
 *  Date: 4/26/2012
 *  
 *  calculates the mean synteny decay in different range bins
 *
 *
 */

//Kent source C imports
extern "C" {

#include "common.h"
#include "options.h"
#include "maf.h"

}

#include <map>
#include <string>
#include <set>
#include <vector>
#include <sstream>
#include <iostream>

//#define NDEBUG
#include <assert.h>

using namespace std;


/*
Global variables
 */

class PairAlnInfo {
public:
  string oname;
  int sstart;
  int send;
  int ostart;
  int oend;
  char strand;
  PairAlnInfo(string _oname,
      int _sstart, int _send,
      int _ostart, int _oend,
      char _strand):
        oname(_oname),
        sstart(_sstart),
        send(_send),
        ostart(_ostart),
        oend(_oend),
        strand(_strand){}
  PairAlnInfo():
    oname("DUMMY"),
    sstart(-1),
    send(-1),
    ostart(-1),
    oend(-1),
    strand(-1){}

};

vector<string> &split(const string &s, char delim, vector<string> &elems) {
  stringstream ss(s);
  string item;
  while(getline(ss, item, delim)) {
    elems.push_back(item);
  }
  return(elems);
}


vector<string> split(const string &s, char delim) {
  vector<string> elems;
  return(split(s, delim, elems));
}

#define DEF_MIN_LEN (200)
#define DEF_MIN_SCORE (200)

typedef map<int,PairAlnInfo> PairAlnInfoByPos;
typedef map<string, PairAlnInfoByPos > ChromToPairAlnInfoByPos;
ChromToPairAlnInfoByPos pairAlnInfoByPosByChrom;


void usage()
/* Explain usage and exit. */
{
  errAbort(
      (char*)"mafPairwiseSyntenyDecay -- Calculates pairwise syntenic decay from maf alignment containing at least the two specified species.\n"
      "usage:\n"
      "\tmafPairwiseSyntenyDecay [options] [*required options] file1.maf[.gz] ... \n"
      "Options:\n"
      "\t-help\tPrints this message.\n"
      "\t-minScore=NUM\tMinimum MAF alignment score to consider (default 200)\n"
      "\t-minAlnLen=NUM\tMinimum MAF alignment block length to consider (default 200)\n"
      "\t-speciesMain=NAME\t*Name of the main species (exactly as it appears before the '.') in the maf file (REQUIRED)\n"
      "\t-speciesOther=NAME\t*Name of the other species (exactly as it appears before the '.') in the maf file (REQUIRED)\n"
  );
}//end usage()


static struct optionSpec options[] = {
    /* Structure holding command line options */
    {(char*)"help",OPTION_STRING},
    {(char*)"minScore",OPTION_INT},
    {(char*)"minAlnLen",OPTION_INT},
    {(char*)"speciesMain",OPTION_STRING},
    {(char*)"speciesOther",OPTION_STRING},
    {NULL, 0}
}; //end options()

/**
 * Main function, takes filenames for paired qseq reads
 * and outputs three files.
 */
int iterateOverAlignmentBlocksAndStorePairInfo(char *fileName, const int minScore, const int minAlnLen, const string speciesMain, const string speciesOther){
  struct mafFile * mFile = mafOpen(fileName);
  struct mafAli * mAli;

  //loop over alignment blocks
  while((mAli = mafNext(mFile)) != NULL){
    struct mafComp *first = mAli->components;
    int seqlen = mAli->textSize;
    //First find and store set of duplicates in this block
    set<string> seen;
    set<string> dups;
    if(mAli->score < minScore || seqlen < minAlnLen){
      //free here and pre-maturely end
      mafAliFree(&mAli);
      continue;
    }

    for(struct mafComp *item = first; item != NULL; item = item->next){
      string tmp(item->src);
      string tname = split(tmp,'.')[0];
      if(seen.count(tname)){
        //seen this item
        dups.insert(tname);
      }else{
        seen.insert(tname);
      }
    }
    for(struct mafComp *item1 = first; item1->next != NULL; item1 = item1->next){
      //stop one before the end
      string tmp1(item1->src);
      vector<string> nameSplit1(split(tmp1,'.'));
      string name1(nameSplit1[0]);
      if(dups.count(name1) || (name1 != speciesMain && name1 != speciesOther)){
        continue;
      }

      for(struct mafComp *item2 = item1->next; item2 != NULL; item2 = item2->next){
        string tmp2(item2->src);
        vector<string> nameSplit2(split(tmp2,'.'));
        string name2 = nameSplit2[0];
        if(dups.count(name2) || (name2 != speciesMain && name2 != speciesOther)){
          continue;
        }

        string chr1(nameSplit1[1]);
        string chr2(nameSplit2[1]);
        char strand;
        if(item1->strand == item2->strand)
          strand = '+';
        else
          strand = '-';

        int start1,end1,start2,end2;

        if(item1->strand == '+'){
          start1 = item1->start;
          end1 = start1 + item1->size;
        }else{
          end1 = item1->start;
          start1 = end1 - item1->size;
        }

        if(item2->strand == '+'){
          start2 = item2->start;
          end2 = start2+ item2->size;
        }else{
          end2 = item2->start;
          start2 = end2 - item2->size;
        }

        if(name1 == speciesMain){
          PairAlnInfo aln(chr2,start1,end1,start2,end2,strand);
          pairAlnInfoByPosByChrom[chr1][start1] = aln;
        }else{
          PairAlnInfo aln(chr1,start2,end2,start1,end1,strand);
          pairAlnInfoByPosByChrom[chr2][start2] = aln;
        }

      } //end loop over item2
    } //end loop over item1
    mafAliFree(&mAli);
  }//end loop over alignment blocks

  mafFileFree(&mFile);
  return(0);
}


int main(int argc, char *argv[])
/* Process command line. */
{
  optionInit(&argc, argv, options);
  if(optionExists((char*)"help") || argc <= 1){
    usage();
  }
  int minAlnScore = optionInt((char*)"minScore",DEF_MIN_SCORE);
  int minAlnLen = optionInt((char*)"minAlnLen",DEF_MIN_LEN);

  string speciesMain(optionVal((char*)"speciesMain",NULL));
  string speciesOther(optionVal((char*)"speciesOther",NULL));

  if(speciesMain.empty() || speciesOther.empty())
    usage();

  //load the relevant alignment info from the maf(s)
  for(int i = 1; i<argc; i++){
    iterateOverAlignmentBlocksAndStorePairInfo(argv[i], minAlnScore, minAlnLen, speciesMain, speciesOther);
  }

  const int blockSize = 1000;
  const int blockCount = 100;

  int totalWindows[blockCount] = {0};
  int containBreak[blockCount] = {0};

  //we want the fraction of windows of each size that contain a break
  //


  for(ChromToPairAlnInfoByPos::iterator mainChromItter = pairAlnInfoByPosByChrom.begin();
      mainChromItter != pairAlnInfoByPosByChrom.end();
      mainChromItter++){
    //process the alignments shared by this chromosome
    //note that map stores them sorted by begin position
    vector<int> keys;
    for(PairAlnInfoByPos::iterator posIter = mainChromItter->second.begin();
        posIter != mainChromItter->second.end();
        posIter++){
      keys.push_back(posIter->first);
    }

    for(int i = 0; i < keys.size(); i++){
      //first check for trivial window (ie our block)
      PairAlnInfo pi1 = mainChromItter->second[keys[i]];
      assert(pi1.send > pi1.sstart);
      assert(pi1.sstart == keys[i]);
      int numBucketsThisWindow = (pi1.send - pi1.sstart) / blockSize;
      for(int k = 0; k < numBucketsThisWindow && k < blockCount; k++)
        totalWindows[k]++;


      for(int j = i+1; j < keys.size(); j++){

        PairAlnInfo pi2 = mainChromItter->second[keys[j]];

        assert(pi2.sstart == keys[j]);
        assert(pi2.send > pi2.sstart);
        assert(pi2.sstart > pi1.sstart);

        if(pi2.oname == pi1.oname){
          int moreToInc = (pi2.send - pi1.sstart) / blockSize;
          for(int k = numBucketsThisWindow; k < moreToInc && k < blockCount; k++)
            totalWindows[k]++;
          numBucketsThisWindow = moreToInc; //so we don't double count
        }else{

          int numDiscontigBuckets = (pi2.send - pi1.sstart) / blockSize;
          for(int k = numBucketsThisWindow; k < numDiscontigBuckets && k < blockSize; k++){
            containBreak[k]++;
            totalWindows[k]++;
          }
          numBucketsThisWindow = numDiscontigBuckets;
        }
        if((keys[j] - keys[i]) >= (blockSize * blockCount)){
          //i = j;
          break;
        }
      }
    }
  }



  cout << "#WindowSize\tNumContainBreak\tNumTotal\t1-(NumContainBreak/NumTotal)" << endl;
  for(int i = 0; i < blockCount; i++){
    cout << (i+1)*blockSize << '\t';
    cout << containBreak[i] << '\t';
    cout << totalWindows[i] << '\t';
    cout << (totalWindows[i] > 0? 1.0 - (double(containBreak[i])/double(totalWindows[i])): 0) << endl;
  }


  return(0);
} //end main()

Is sure looks like a heap overwrite somewhere in the program. Possibly from an out of range access, which is hard to find by just looking at the source. — Bo Persson
– Bo Persson, Commented Apr 28, 2012 at 9:53

Julian · Accepted Answer · 2012-04-28 09:30:33Z

5

Try running your program under valgrind. This will give you a report of possibly or actually lost memory, uninitialised, etc.

answered Apr 28, 2012 at 9:30

Julian

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3 Comments

John St. John Over a year ago

Thanks for the valgrind suggestion @Julian. I had to choose someone else as the person who answered because he actually found my bug! That said I tried using valgrind on my mac, and the diagnostic that would have really saved me if I am reading the documentation right (checking stack array access out of bounds issues) is unfortunately not supported on Darwin (--tool=exp-sgcheck). I did run this tool on my linux box just to see if it would help in the future, and it identified the error in the code. I will definitely be using valgrind in the future, thanks!

Julian Over a year ago

valgrind rocks doesn't it? Finding the bug from your code was a much harder task and deserves the credit.

thang Over a year ago

:) valgrind saved me a lot of time. i had a similar problem. uninitialized variable caused crashes in random places every time.

uesp · Accepted Answer · 2012-04-28 14:01:54Z

3

Your issues are probably due to due memory corruption occurring at some point in the program sometime prior to the actual errors you are seeing.

One potential issue in the code you posted is the loop:

 for(int k = numBucketsThisWindow; k<numDiscontigBuckets && k < blockSize; k++){

which uses blockSize instead of the correct blockCount which leads to a possible overflow of both the totalWindows[] and containBreak[] arrays. This would overwrite the speciesMain and speciesOther strings, alonth with anything else on the stack, which might very well result in the errors you are seeing.

answered Apr 28, 2012 at 14:01

uesp

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