garbage collection - java.lang.OutOfMemoryError: GC overhead limit -

i have program reads large list of sequences file , calculation among of pairs in list. stores of these calculations hashset. when running program halfway through, gc overhead limit error.

i realize because garbage collector using 98% of computation time , unable recover 2% of heap. here code have:

arraylist<string> c = loadsequences("file.txt"); // loads 60 char dna sequences hashset<dnapair,double> lsa = new hashset<dnapair,double>();  for(int = 0; < c.size(); i++) {     for(int j = i+1; j < c.size(); j++) {         lsa.put(new dnapair(c.get(i),c.get(j)),localseqalignmentsimilarity(c.get(i),c.get(j)));     } } 

and here's code actual method:

public static double localseqalignmentsimilarity(string s1, string s2) {     s1 = " " + s1;     s2 = " " + s2;     int max = 0,h = 0,maxi = 0,maxj = 0;      int[][] score = new int[61][61];     int[][] pointers = new int[61][61];      for(int = 1; < s1.length(); i++) {         pointers[i][0] = 2;     }     for(int = 1; < s2.length(); i++) {         pointers[0][i] = 1;     }      boolean ingap = false;     for(int = 1; < s1.length(); i++) {         for(int j = 1; j < s2.length();  j++) {             h = -99;             if(score[i-1][j-1] + match(s1.charat(i),s2.charat(j)) > h) {                 h = score[i-1][j-1] + match(s1.charat(i),s2.charat(j));                 pointers[i][j] = 3;                 ingap = false;             }              if(!ingap) {                 if(score[i-1][j] + gappenalty > h) {                     h = score[i-1][j] + gappenalty;                     pointers[i][j] = 2;                     ingap = true;                 }                  if(score[i][j-1] + gappenalty > h) {                     h = score[i][j-1] + gappenalty;                     pointers[i][j] = 1;                     ingap = true;                 }             } else {                 if(score[i-1][j] + gapextension > h) {                     h = score[i-1][j] + gapextension;                     pointers[i][j] = 2;                     ingap = true;                 }                  if(score[i][j-1] + gapextension > h) {                     h = score[i][j-1] + gapextension;                     pointers[i][j] = 1;                     ingap = true;                 }             }              if(0 > h) h = 0;              score[i][j] = h;             if(h >= max) {                 max = h;                 maxi = i;                 maxj = j;             }         }     }      double matches = 0;     string o1 = "",  o2 = "";     while(!(maxi == 0 && maxj == 0)) {         if(pointers[maxi][maxj] == 3) {             o1 += s1.charat(maxi);             o2 += s2.charat(maxj);             maxi--;             maxj--;         } else if(pointers[maxi][maxj] == 2) {             o1 += s1.charat(maxi);             o2 += "_";             maxi--;         } else if(pointers[maxi][maxj] == 1) {             o1 += "_";             o2 += s2.charat(maxj);             maxj--;         }     }      stringbuilder = new stringbuilder(o1);     b = new stringbuilder(o2);     o1 = a.reverse().tostring();     o2 = b.reverse().tostring();     a.setlength(0);     b.setlength(0);      for(int = 0; < math.min(o1.length(), o2.length()); i++) {         if(o1.charat(i) == o2.charat(i)) matches++;     }     return matches/math.min(o1.length(), o2.length()); } 

i thought because of variables declare inside method (the 2 int arrays , stringbuilders etc.) creating more , more objects every time method run changed them static fields , cleared them everytime (ex. arrays.fill(score,0);) instead of creating new object.

however didn't @ , still got same error.

could hashset stores of calculations getting big , unable stored java? i'm not getting out of heap space error seems kind of strange.

i changed command line argument give more space jvm didn't seem help.

any insight on problem helpful. thanks!

this problem, if c.size() 73657 , sequences unique:

hashset<dnapair,double> lsa = new hashset<dnapair,double>();   for(int = 0; < c.size(); i++) {    for(int j = i+1; j < c.size(); j++) {       lsa.put(...);    }  } 

assuming these unique sequences, you're adding element lsa each pair. mention have 70k sequences, going have 70k * 70k = ~5 billion pairs, each of take @ minimum 4 bytes store, meaning you'd need 20+ gb allocated @ minimum feasible.