C++ Making sure 2D vector is compact in memory - c++

Question

I'm writing a C++ program to perform calculations on a huge graph and therefore has to be as fast as possible. I have a 100MB textfile of unweighted edges and am reading them into a 2D vector of integers (first index = nodeID, then a sorted list of nodeIDs of nodes which have edges to that node). Also, during the program, the edges are looked up exactly in the order in which they're stored in the list. So my expectation was that, apart from a few bigger gaps, it'd always be nicely preloaded to the cache. However, according to my profiler, iterating through the edges of a player is an issue. Therefore I suspect, that the 2D vector isn't placed in memory compactly.
How can I ensure that my 2D vector is as compact as possible and the subvectors in the order in which they should be?
(I thought for example about making a "2D array" from the 2D vector, first an array of pointers, then the lists.)
BTW: In case it wasn't clear: The nodes can have different numbers of edges, so a normal 2D array is no option. There are a couple ones with lots of edges, but most have very few.
EDIT:
I've solved the problem and my program is now more than twice as fast:
There was a first solution and then a slight improvement:
I put the lists of neighbour ids into a 1D integer array and had another array to know where a certain id's neighbour lists start
I got a noticeable speedup by replacing the pointer array (a pointer needs 64 bit) with a 32 bit integer array containing indices instead

Answer 1

What data structure are you using for the 2d vector? If you use std::vector then the memory will be contiguous.
Next, if pointers are stored then only the address will take advantage of the vectors spacial locality. Are you accessing the object pointed to when iterating the edges and if so this could be a bottleneck. To get around this perhaps you can setup your objects so they are also in contiguous memory and take advantage of spacial locality.
Finally the way in which you access the members of a vector affects the caching. Make sure you are accessing in an order advantageous to the container used (eg change column index first when iterating).
Here's some helpful links:
Cache Blocking Techniques
SO on cache friendly code

Answer 2

I have written a few of these type structures by having a 2D view onto a 1D vector and there are lots of different ways to do it. I have never made one that allows the internal arrays to vary in length before so this may contain bugs but should illustrate the general approach:
#include <cassert>
#include <iostream>
#include <vector>
template<typename T>
class array_of_arrays
{
public:
array_of_arrays() {}
template<typename Iter>
void push_back(Iter beg, Iter end)
{
m_idx.push_back(m_vec.size());
m_vec.insert(std::end(m_vec), beg, end);
}
T* operator[](std::size_t row) { assert(row < rows()); return &m_vec[m_idx[row]]; }
T const* operator[](std::size_t row) const { assert(row < rows()); return &m_vec[m_idx[row]]; }
std::size_t rows() const { return m_idx.size(); }
std::size_t cols(std::size_t row) const
{
assert(row <= m_idx.size());
auto b = m_idx[row];
auto e = row + 1 >= m_idx.size() ? m_vec.size() : m_idx[row + 1];
return std::size_t(e - b);
}
private:
std::vector<T> m_vec;
std::vector<std::size_t> m_idx;
};
int main()
{
array_of_arrays<int> aoa;
auto data = {2, 4, 3, 5, 7, 2, 8, 1, 3, 6, 1};
aoa.push_back(std::begin(data), std::begin(data) + 3);
aoa.push_back(std::begin(data) + 3, std::begin(data) + 8);
for(auto row = 0UL; row < aoa.rows(); ++row)
{
for(auto col = 0UL; col < aoa.cols(row); ++col)
{
std::cout << aoa[row][col] << ' ';
}
std::cout << '\n';
}
}
Output:
2 4 3
5 7 2 8 1