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Commit e4653fb7 authored by peastman's avatar peastman
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Optimized finding duplicate interactions in interaction groups

parent 7639d0bd
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Showing with 30 additions and 40 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ e4653fb7
......@@ -54,6 +54,7 @@
#include "jama_eig.h"
#include <algorithm>
#include <cmath>
#include <iterator>
#include <set>
using namespace OpenMM;
......@@ -2429,7 +2430,8 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
vector<vector<int> > atomLists;
vector<pair<int, int> > tiles;
map<pair<int, int>, int> duplicateInteractions;
vector<int> tileGroup;
vector<vector<int> > duplicateAtomsForGroup;
for (int group = 0; group < force.getNumInteractionGroups(); group++) {
// Get the list of atoms in this group and sort them.
......@@ -2440,6 +2442,10 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
atoms2.insert(atoms2.begin(), set2.begin(), set2.end());
sort(atoms1.begin(), atoms1.end());
sort(atoms2.begin(), atoms2.end());
duplicateAtomsForGroup.push_back(vector<int>());
set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(),
inserter(duplicateAtomsForGroup[group], duplicateAtomsForGroup[group].begin()));
sort(duplicateAtomsForGroup[group].begin(), duplicateAtomsForGroup[group].end());
// Find how many tiles we will create for this group.
......@@ -2451,9 +2457,12 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
// Add the tiles.
int firstTile = tiles.size();
for (int i = 0; i < numBlocks1; i++)
for (int j = 0; j < numBlocks2; j++)
for (int j = 0; j < numBlocks2; j++) {
tiles.push_back(make_pair(atomLists.size()+i, atomLists.size()+numBlocks1+j));
tileGroup.push_back(group);
}
// Add the atom lists.
......@@ -2473,22 +2482,6 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
atoms.push_back(atoms2[j]);
atomLists.push_back(atoms);
}
// If this group contains duplicate interactions, record that we need to skip them once.
for (int a1 : atoms1) {
if (set2.find(a1) == set2.end())
continue;
for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
int a2 = atoms2[j];
if (set1.find(a2) != set1.end()) {
pair<int, int> key = make_pair(a2, a1);
if (duplicateInteractions.find(key) == duplicateInteractions.end())
duplicateInteractions[key] = 0;
duplicateInteractions[key]++;
}
}
}
}
// Build a lookup table for quickly identifying excluded interactions.
......@@ -2506,15 +2499,18 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
vector<vector<int> > exclusionFlags(tiles.size());
vector<pair<int, int> > tileOrder;
for (int tile = 0; tile < tiles.size(); tile++) {
bool swapped = false;
if (atomLists[tiles[tile].first].size() < atomLists[tiles[tile].second].size()) {
// For efficiency, we want the first axis to be the larger one.
int swap = tiles[tile].first;
tiles[tile].first = tiles[tile].second;
tiles[tile].second = swap;
swapped = true;
}
vector<int>& atoms1 = atomLists[tiles[tile].first];
vector<int>& atoms2 = atomLists[tiles[tile].second];
vector<int>& duplicateAtoms = duplicateAtomsForGroup[tileGroup[tile]];
vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
int numExcluded = 0;
for (int i = 0; i < (int) atoms1.size(); i++)
......@@ -2525,11 +2521,10 @@ void CudaCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbo
pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
if (a1 == a2 || exclusions.find(key) != exclusions.end())
isExcluded = true; // This is an excluded interaction.
else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
else if ((a1 > a2) == swapped && binary_search(duplicateAtoms.begin(), duplicateAtoms.end(), a1) && binary_search(duplicateAtoms.begin(), duplicateAtoms.end(), a2)) {
// Both atoms are in both sets, so skip duplicate interactions.
isExcluded = true;
duplicateInteractions[key]--;
}
if (isExcluded) {
flags[i] &= -1-(1<<j);
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ e4653fb7
......@@ -54,6 +54,7 @@
#include "jama_eig.h"
#include <algorithm>
#include <cmath>
#include <iterator>
#include <set>
using namespace OpenMM;
......@@ -2550,7 +2551,8 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
vector<vector<int> > atomLists;
vector<pair<int, int> > tiles;
map<pair<int, int>, int> duplicateInteractions;
vector<int> tileGroup;
vector<vector<int> > duplicateAtomsForGroup;
for (int group = 0; group < force.getNumInteractionGroups(); group++) {
// Get the list of atoms in this group and sort them.
......@@ -2561,6 +2563,10 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
atoms2.insert(atoms2.begin(), set2.begin(), set2.end());
sort(atoms1.begin(), atoms1.end());
sort(atoms2.begin(), atoms2.end());
duplicateAtomsForGroup.push_back(vector<int>());
set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(),
inserter(duplicateAtomsForGroup[group], duplicateAtomsForGroup[group].begin()));
sort(duplicateAtomsForGroup[group].begin(), duplicateAtomsForGroup[group].end());
// Find how many tiles we will create for this group.
......@@ -2572,9 +2578,12 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
// Add the tiles.
int firstTile = tiles.size();
for (int i = 0; i < numBlocks1; i++)
for (int j = 0; j < numBlocks2; j++)
for (int j = 0; j < numBlocks2; j++) {
tiles.push_back(make_pair(atomLists.size()+i, atomLists.size()+numBlocks1+j));
tileGroup.push_back(group);
}
// Add the atom lists.
......@@ -2594,22 +2603,6 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
atoms.push_back(atoms2[j]);
atomLists.push_back(atoms);
}
// If this group contains duplicate interactions, record that we need to skip them once.
for (int a1 : atoms1) {
if (set2.find(a1) == set2.end())
continue;
for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
int a2 = atoms2[j];
if (set1.find(a2) != set1.end()) {
pair<int, int> key = make_pair(a2, a1);
if (duplicateInteractions.find(key) == duplicateInteractions.end())
duplicateInteractions[key] = 0;
duplicateInteractions[key]++;
}
}
}
}
// Build a lookup table for quickly identifying excluded interactions.
......@@ -2627,15 +2620,18 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
vector<vector<int> > exclusionFlags(tiles.size());
vector<pair<int, int> > tileOrder;
for (int tile = 0; tile < tiles.size(); tile++) {
bool swapped = false;
if (atomLists[tiles[tile].first].size() < atomLists[tiles[tile].second].size()) {
// For efficiency, we want the first axis to be the larger one.
int swap = tiles[tile].first;
tiles[tile].first = tiles[tile].second;
tiles[tile].second = swap;
swapped = true;
}
vector<int>& atoms1 = atomLists[tiles[tile].first];
vector<int>& atoms2 = atomLists[tiles[tile].second];
vector<int>& duplicateAtoms = duplicateAtomsForGroup[tileGroup[tile]];
vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
int numExcluded = 0;
for (int i = 0; i < (int) atoms1.size(); i++)
......@@ -2646,11 +2642,10 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
if (a1 == a2 || exclusions.find(key) != exclusions.end())
isExcluded = true; // This is an excluded interaction.
else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
else if ((a1 > a2) == swapped && binary_search(duplicateAtoms.begin(), duplicateAtoms.end(), a1) && binary_search(duplicateAtoms.begin(), duplicateAtoms.end(), a2)) {
// Both atoms are in both sets, so skip duplicate interactions.
isExcluded = true;
duplicateInteractions[key]--;
}
if (isExcluded) {
flags[i] &= -1-(1<<j);
......
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