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Commit 6caf992a authored by peastman's avatar peastman
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Merge pull request #229 from peastman/master 

Further optimizations to CPU platform
parents d600e589 99f3a8a2
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Showing with 77 additions and 69 deletions
openmmapi/include/openmm/internal/vectorize.h
View file @ 6caf992a
...@@ -273,5 +273,11 @@ static inline fvec4 operator/(float v1, fvec4 v2) { ...@@ -273,5 +273,11 @@ static inline fvec4 operator/(float v1, fvec4 v2) {
return fvec4(v1)/v2; return fvec4(v1)/v2;
} }
// Operations for blending fvec4s based on an ivec4.
static inline fvec4 blend(fvec4 v1, fvec4 v2, ivec4 mask) {
return fvec4(_mm_blendv_ps(v1.val, v2.val, _mm_castsi128_ps(mask.val)));
}
#endif /*OPENMM_VECTORIZE_H_*/ #endif /*OPENMM_VECTORIZE_H_*/
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 6caf992a
...@@ -477,7 +477,6 @@ void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double* ...@@ -477,7 +477,6 @@ void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double*
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex); const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex); const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
bool include[4];
for (int i = 0; i < (int) neighbors.size(); i++) { for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor. // Load the next neighbor.
...@@ -486,75 +485,77 @@ void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double* ...@@ -486,75 +485,77 @@ void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double*
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
bool any = false;
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
for (int j = 0; j < 4; j++) { ivec4 include;
include[j] = (((exclusions[i]>>j)&1) == 0 && (!cutoff || r2[j] < cutoffDistance*cutoffDistance)); char excl = exclusions[i];
any |= include[j]; if (excl == 0)
} include = -1;
if (!any) else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute. continue; // No interactions to compute.
// Compute the interactions. // Compute the interactions.
fvec4 r = sqrt(r2); fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r; fvec4 inverseR = fvec4(1.0f)/r;
fvec4 switchValue(1.0f), switchDeriv(0.0f); fvec4 energy, dEdR;
if (useSwitch) { float atomEpsilon = atomParameters[atom].second;
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance)); if (atomEpsilon != 0.0f) {
switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f)); fvec4 sig = blockAtomSigma+atomParameters[atom].first;
switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance); fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance));
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance);
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
} }
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomParameters[atom].second*sig6;
fvec4 dEdR = switchValue*epsSig6*(12.0f*sig6 - 6.0f);
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3]; fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
if (cutoff) if (cutoff)
dEdR += chargeProd*(inverseR-2.0f*krf*r2); dEdR += chargeProd*(inverseR-2.0f*krf*r2);
else else
dEdR += chargeProd*inverseR; dEdR += chargeProd*inverseR;
dEdR *= inverseR*inverseR; dEdR *= inverseR*inverseR;
fvec4 energy;
if (useSwitch) {
energy = epsSig6*(sig6-1.0f);
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
// Accumulate energies. // Accumulate energies.
if (totalEnergy) { if (totalEnergy) {
if (!useSwitch)
energy = epsSig6*(sig6-1.0f);
if (cutoff) if (cutoff)
energy += chargeProd*(inverseR+krf*r2-crf); energy += chargeProd*(inverseR+krf*r2-crf);
else else
energy += chargeProd*inverseR; energy += chargeProd*inverseR;
for (int j = 0; j < 4; j++) energy = blend(0.0f, energy, include);
if (include[j]) *totalEnergy += dot4(energy, 1.0f);
*totalEnergy += energy[j];
} }
// Accumulate forces. // Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f}; fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f};
transpose(result[0], result[1], result[2], result[3]); transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atom); fvec4 atomForce(forces+4*atom);
for (int j = 0; j < 4; j++) { for (int j = 0; j < 4; j++) {
if (include[j]) { blockAtomForce[j] += result[j];
blockAtomForce[j] += result[j]; atomForce -= result[j];
atomForce -= result[j];
}
} }
atomForce.store(forces+4*atom); atomForce.store(forces+4*atom);
} }
// Record the forces on the block atoms. // Record the forces on the block atoms.
for (int j = 0; j < 4; j++) for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+blockAtomForce[j]).store(forces+4*blockAtom[j]); (fvec4(forces+4*blockAtom[j])+blockAtomForce[j]).store(forces+4*blockAtom[j]);
} }
...@@ -588,7 +589,6 @@ void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, do ...@@ -588,7 +589,6 @@ void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, do
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex); const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex); const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
bool include[4];
for (int i = 0; i < (int) neighbors.size(); i++) { for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor. // Load the next neighbor.
...@@ -597,63 +597,65 @@ void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, do ...@@ -597,63 +597,65 @@ void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, do
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
bool any = false;
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
for (int j = 0; j < 4; j++) { ivec4 include;
include[j] = (((exclusions[i]>>j)&1) == 0 && r2[j] < cutoffDistance*cutoffDistance); char excl = exclusions[i];
any |= include[j]; if (excl == 0)
} include = -1;
if (!any) else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute. continue; // No interactions to compute.
// Compute the interactions. // Compute the interactions.
fvec4 r = sqrt(r2); fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r; fvec4 inverseR = fvec4(1.0f)/r;
fvec4 switchValue(1.0f), switchDeriv(0.0f); fvec4 energy, dEdR;
if (useSwitch) { float atomEpsilon = atomParameters[atom].second;
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance)); if (atomEpsilon != 0.0f) {
switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f)); fvec4 sig = blockAtomSigma+atomParameters[atom].first;
switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance); fvec4 sig2 = inverseR*sig;
} sig2 *= sig2;
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3]; fvec4 sig6 = sig2*sig2*sig2;
fvec4 dEdR = chargeProd*inverseR*ewaldScaleFunction(r); fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
fvec4 sig = blockAtomSigma+atomParameters[atom].first; dEdR = epsSig6*(12.0f*sig6 - 6.0f);
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomParameters[atom].second*sig6;
dEdR += switchValue*epsSig6*(12.0f*sig6 - 6.0f);
dEdR *= inverseR*inverseR;
fvec4 energy;
if (useSwitch) {
energy = epsSig6*(sig6-1.0f); energy = epsSig6*(sig6-1.0f);
dEdR -= energy*switchDeriv*inverseR; if (useSwitch) {
energy *= switchValue; fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance));
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance);
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
} }
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
dEdR += chargeProd*inverseR*ewaldScaleFunction(r);
dEdR *= inverseR*inverseR;
// Accumulate energies. // Accumulate energies.
if (totalEnergy) { if (totalEnergy) {
if (!useSwitch)
energy = epsSig6*(sig6-1.0f);
energy += chargeProd*inverseR*erfcApprox(alphaEwald*r); energy += chargeProd*inverseR*erfcApprox(alphaEwald*r);
for (int j = 0; j < 4; j++) energy = blend(0.0f, energy, include);
if (include[j]) *totalEnergy += dot4(energy, 1.0f);
*totalEnergy += energy[j];
} }
// Accumulate forces. // Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f}; fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f};
transpose(result[0], result[1], result[2], result[3]); transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atom); fvec4 atomForce(forces+4*atom);
for (int j = 0; j < 4; j++) { for (int j = 0; j < 4; j++) {
if (include[j]) { blockAtomForce[j] += result[j];
blockAtomForce[j] += result[j]; atomForce -= result[j];
atomForce -= result[j];
}
} }
atomForce.store(forces+4*atom); atomForce.store(forces+4*atom);
} }
......
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