cpp stringstream read input file algorithm to find LCS - c++

Question

Hi here's my first questions here, I would write as clear as possible, if I am too newbie here, please bear it with me. Thanks
Backgroud: I was asked to solve longest common substring(lcs) problem with given input files in c++.
Its purpose is to optimize the algorithm, so it has limited run-time and RAM requirement.(case insensitive)
My Approach: I used to stringstream to parse the every input line and stored them into a vector. use something like suffix tree to chop the string, sort it and put into a vector array (vector that store vectors) and compare every 2 lines (v1,v2) to find common substirng.(I used nested foop loop to compare each word inside every vector), and then put common substrings back to array and remove v1 and v2.
suffix tree eg. banana -> anana -> nana -> ana -> na -> a..[I stored all 5 elements into the vector]
result: it works for most of the files (normal textfiles)
problem: I got 2 special test case that took me forever to find lcs.
1. has 10000 line input, and each line has ave 3000 chars (include space). It took me 50 mins to find lcs. the requirement is not exceed 5 mins.
2. has 100 line input, and each line has ave 60k chars. It never finish running
what I tried:build a common word dictionary for first 2 sentence
read first two lines and stored into vectors
used suffix tree again to find common elements(substring) and named as dictionary
for rest of input lines,
if (words read is within dictionary)
fine do what I did before, read next one
else if (word is not in dictionary)
ignore this word, read next one
help needed: I still cannot read the first two lines if each line contains 60k char, so building the dict itself would exceed the run time limitations. I am not sure if the hashed table would work way better than vectors. I knew a bit about HT but never write anything with it, so if you can explain HT with patience, I would appreciate that.
Update:
As suggested, I put some code here (first one for parse and store into vector， second involve how I compare 2 string and find common element)
vector< vector<string> > parsed_array;
vector<string> choped_element;
// Num1::read from file in a while loop
while (getline (myfile,line))
{
cout << "< InputlineLoopCounter: "<<InputlineLoopCounter<<endl;:q
choped_element.clear();
choped_element.push_back(line); //whole string as first element, eg'Hello World"
stringstream ss(line);
string copystr (line);
while (ss >> temp)
{
copystr.erase(0,copystr.find_first_of(" \t")+1); // here turns into "World"
choped_element.push_back(copystr);
}
choped_element.pop_back();//since I stored whole string as frist element, last one is not necessary
sort(choped_element.begin(),choped_element.end());
parsed_array.push_back(choped_element);//stored into vector array
InputlineLoopCounter ++;
}
//Num::2 compare part in 2 diff string and assembly into new string
//v1 and v2 and 2 vectors full of chopped strings and v3 should be common element
// eg. v1[0]="hello world"; v1[1]="world"
// eg. v2[0]="I dislike hello world"; v2[1]="dislike hello word"; v2[2]="hello word"; v2[4]="word"
// eg. v3 as result would be v3[0]="hello word";v3[1]="word"
for (size_t i = 0; i < v1len; i++)
{
for (size_t j = 0; j< v2len; j++)
{
stringstream ss1(v1[i]);
string fword1;
ss1>>fword1;
stringstream ss2(v2[j]);
string fword2;
ss2>>fword2;
if(fword1 == fword2) //v1[i] and v2[j] are space seperated words
{
string nword1;
string nword2;
string lcommon;
int comlen = 1;
string combine;
combine.append(fword1);
combine.append(space);
while (ss1>>nword1 && ss2>>nword2)
{
if (nword1 == nword2)
{
combine.append(nword1);
combine.append(space);
comlen ++;
}
else
break;
}
combine.erase(combine.find_last_of(" "));
cout<< "common word: "<<combine<<endl;
v3.push_back(combine);
}
}
}