I recently got interested in programming molecular mechanics force fields on CPUs and GPUs. One of the hurdles you have to get through, is the non bonded interactions, which you have to iterate over all pairs of atoms. It thus scales as N^2 with the number of atoms, whereas the bonded terms scale only linearly. A good example is the OPLS force field (read more on Wikipedia). Here the non-bonded interactions are given by a Lennard-Jones potential term an an electrostatic term:

For more information about molecular modeling and force fields, I can recommend reading the Molecular Modeling Basics book, which has excellent pages on the subject. You can also just ask in the comment sections, if you have anything. Finally, the code can be found for download at the bottom of this post.

Now let's get started! I've put the coordinates of all atoms in the double coordinates[] 2D array. In the example I'm using the coordinates of the protein structure of Cutinase 1CEX, which has 2867 atoms. I used pdb2pqr for protonation. I'm going to assume (for simplicity), that all interactions use the same parameters. The naive way to implement the non-bonded OPLS interaction could be (in C/C++):

// Lennard-Jones parameters double A = 10.0; double C = 10.0; // Electrostatic parameter double E = -10.0; double non_bonded_interaction(const double a[3], const double b[3]) { // Fastest way of getting distance double distance = sqrt((a[0] - b[0]) * (a[0] - b[0]) + (a[1] - b[1]) * (a[1] - b[1]) + (a[2] - b[2]) * (a[2] - b[2])); return A*pow(distance, -12.0) + C*pow(distance, -6.0) + E/distance; } int main() { // Set energy to 0 double energy = 0.0; // Loop over all atoms for (unsigned int i = 0; i < n_atoms; i++) { // Only up to i-1, to avoid double counting // interactions, and self-interactions for (unsigned int j = 0; j < i; j++) { energy += non_bonded_interaction(coordinates[i], coordinates[j]); } } std::cout << "E = " << energy << std::endl return 0; }

Timing this gives 0.0300 µs per iteration with the Intel icpc compiler, and 0.189 µs with the g++ compiler, both with -O3 optimization.

As I will demonstrate, this is because pow() is horribly implemented in g++. Lets further optimize the non_bonded_interaction() function:

double non_bonded_interaction(const double a[3], const double b[3]) { double distance = sqrt((a[0] - b[0]) * (a[0] - b[0]) + (a[1] - b[1]) * (a[1] - b[1]) + (a[2] - b[2]) * (a[2] - b[2])); double distance6 = distance * distance * distance * distance * distance * distance; double distance12 = distance6 * distance6; return A/distance12 + C/distance6 + E/distance; }

Now we get: 0.0295 µs with icpc and 0.0313 µs with g++. Clearly pow() shouldn't be used with GNU compilers!

Next on our list of optimizations is getting rid of divisions. Divisions are performed iteratively by the CPU, while multiplications are done bit-parallel by specialized circuits hard-coded into the CPU silicon. We have three divisions, but we can write everything in terms of only one, using reciprocal distances:

double non_bonded_interaction(const double a[3], const double b[3]) { double distance = sqrt((a[0] - b[0]) * (a[0] - b[0]) + (a[1] - b[1]) * (a[1] - b[1]) + (a[2] - b[2]) * (a[2] - b[2])); double inv_distance = 1.0/distance; double inv_distance6 = inv_distance * inv_distance * inv_distance * inv_distance * inv_distance * inv_distance; double inv_distance12 = inv_distance6 * inv_distance6; return A * inv_distance12 + C * inv_distance6 + E * inv_distance; }

This gives us 0.0173 µs with icpc and 0.0189 µs with g++. Still ... there is one division left and also a square-root which is problematic. These are what takes up by far the most time in the calculation. But there is a hacky trick we can use. I'm going to show you how to use an approach by Newton to estimate inverse square roots .. take a look at this Wikipedia page for more info. The method became famous after it was found in the Quake III open source engine. Here it is in double type, so slightly different than the float type example on wikipedia. I'm using two final iterations to achieve sufficient accuracy.

inline double fast_inv_sqrt(double number) { long long i; double x2, y; const double threehalfs = 1.5; x2 = number * 0.5; y = number; i = * ( long long * ) &y; i = 0x5fe6ec85e7de30da - ( i >> 1 ); y = * ( double * ) &i; y = y * ( threehalfs - ( x2 * y * y ) ); y = y * ( threehalfs - ( x2 * y * y ) ); return y; }

Using this, we can avoid ever dividing and taking square roots, and reduce our code to:

double non_bonded_interaction(const double a[3], const double b[3]) { double dx = (a[0] - b[0]); double dy = (a[1] - b[1]); double dz = (a[2] - b[2]); double distance_sqr = dx*dx + dy*dy + dz*dz; double inv_distance = fast_inv_sqrt(distance_sqr); double inv2_distance = inv_distance * inv_distance; double inv6_distance = inv2_distance * inv2_distance * inv2_distance; double inv12_distance = inv6_distance * inv6_distance; return A * inv_distance12 + C * inv_distance6 + E * inv_distance; }

Now, timings are down to 0.0118 µs for icpc and 0.0155 µs for g++ per iteration. It's hard to optimize the code further from here, using code that isn't very hacky, but we still got a x2.5 times speed-up with the Intel compiler and x12.2! times speed-up with the GNU C++ compiler. Still, we can always try and parallelize the code using OpenMP. This is the easiest way to parallelize code there ever was. We only need to add ONE compiler flag, which tells it to parallelize the next loop. Take a look:

// Loop over all atoms for (unsigned int i = 0; i < n_atoms; i++) { // Tell compiler, to run next in loop in parallel #pragma omp parallel for reduction(+:energy) //Only up to i-1, to avoid double counting interactions, and self-interactions for (unsigned int j = 0; j < i; j++) { energy += non_bonded_interaction(coordinates[i], coordinates[j]); } }

To compile we also must remember to link to OpenMP:

icpc -O3 cpuff.cpp -o cpuff -openmp (for Intel)

g++ -O3 cpuff.cpp -o cpuff -fopenmp (for GNU)

On four cores instead of one, this gives us: 0.0042 µs for icpc and 0.0042 for g++ as well. That's a x2.8 and x3.6 speed up for Intel and GNU, respectively! Not too shabby, by no means! Compared to the unparallelized code, this is a x7.1 speed-up for Intel and a whooping x45.0 speed-up for the initial lazy GNU compiled code.

I hope this post will inspire you to play around with these easy-to-do optimizations yourself. You can download code examples here:

cpuff.cpp (the implementation)

cpuff.cpp (the implementation)

DISCLAIMER: The above was carried out on an Intel Core i5-760 running 64-bit Ubuntu Server 10.04.3, icpc (ICC) 12.0.0 20101006 and g++ (Ubuntu 4.4.3-4ubuntu5) 4.4.3. Timings are averages over 10 consecutive runs. I compiled everything with -O3 optimization.

You don't need a sqrt(), because the powers of r are even you can just use (r^2)^6 where r^2=x^2+y^2+z^2, hence the square root is completely avoided!

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