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Commit 5b8cade7 authored by Peter Eastman's avatar Peter Eastman
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Completed CUDA implementation of new constraint algorithm

parent 47a6fb1e
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Showing with 70 additions and 80 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 5b8cade7
......@@ -355,10 +355,26 @@ void CudaCalcGBSAOBCForceKernel::executeForces(OpenMMContextImpl& context) {
}
static void initializeIntegration(const System& system, CudaPlatform::PlatformData& data, const Integrator& integrator) {
// Initialize any terms that haven't already been handled by a Force.
_gpuContext* gpu = data.gpu;
if (!data.hasBonds)
gpuSetBondParameters(gpu, vector<int>(), vector<int>(), vector<float>(), vector<float>());
if (!data.hasAngles)
gpuSetBondAngleParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>());
if (!data.hasPeriodicTorsions)
gpuSetDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<int>());
if (!data.hasRB)
gpuSetRbDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(),
vector<float>(), vector<float>(), vector<float>(), vector<float>());
if (!data.hasNonbonded) {
gpuSetCoulombParameters(gpu, 138.935485f, vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<char>(), vector<vector<int> >(), NO_CUTOFF);
gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<float>());
}
// Set masses.
_gpuContext* gpu = data.gpu;
int numParticles = system.getNumParticles();
vector<float> mass(numParticles);
for (int i = 0; i < numParticles; i++)
......@@ -385,22 +401,6 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa
}
gpuSetConstraintParameters(gpu, particle1, particle2, distance, invMass1, invMass2, (float)integrator.getConstraintTolerance(), 4);
// Initialize any terms that haven't already been handled by a Force.
if (!data.hasBonds)
gpuSetBondParameters(gpu, vector<int>(), vector<int>(), vector<float>(), vector<float>());
if (!data.hasAngles)
gpuSetBondAngleParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>());
if (!data.hasPeriodicTorsions)
gpuSetDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<int>());
if (!data.hasRB)
gpuSetRbDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(),
vector<float>(), vector<float>(), vector<float>(), vector<float>());
if (!data.hasNonbonded) {
gpuSetCoulombParameters(gpu, 138.935485f, vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<char>(), vector<vector<int> >(), NO_CUTOFF);
gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<float>());
}
// Finish initialization.
gpuBuildThreadBlockWorkList(gpu);
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 5b8cade7
......@@ -85,6 +85,18 @@ struct Constraint
float distance2;
};
struct ConstraintOrderer : public binary_function<int, int, bool> {
const vector<int>& atom1;
const vector<int>& atom2;
ConstraintOrderer(const vector<int>& atom1, const vector<int>& atom2) : atom1(atom1), atom2(atom2) {
}
bool operator()(int x, int y) {
if (atom1[x] != atom1[y])
return atom1[x] < atom1[y];
return atom2[x] < atom2[y];
}
};
struct Molecule {
vector<int> atoms;
vector<int> bonds;
......@@ -932,10 +944,6 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
for (unsigned i = 0; i < atomConstraints.size(); i++)
maxAtomConstraints = max(maxAtomConstraints, (int) atomConstraints[i].size());
// Compute the constraint coupling matrix
vector<vector<int> > atomAngles(gpu->natoms);
......@@ -950,34 +958,36 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
continue;
}
double scale;
int atomj0 = atom1[j];
int atomj1 = atom2[j];
int atomk0 = atom1[k];
int atomk1 = atom2[k];
int cj = lincsConstraints[j];
int ck = lincsConstraints[k];
int atomj0 = atom1[cj];
int atomj1 = atom2[cj];
int atomk0 = atom1[ck];
int atomk1 = atom2[ck];
int atoma, atomb, atomc;
if (atomj0 == atomk0) {
atoma = atomj1;
atomb = atomj0;
atomc = atomk1;
scale = invMass1[j]/(invMass1[j]+invMass2[j]);
scale = invMass1[cj]/(invMass1[cj]+invMass2[cj]);
}
else if (atomj1 == atomk1) {
atoma = atomj0;
atomb = atomj1;
atomc = atomk0;
scale = invMass2[j]/(invMass1[j]+invMass2[j]);
scale = invMass2[cj]/(invMass1[cj]+invMass2[cj]);
}
else if (atomj0 == atomk1) {
atoma = atomj1;
atomb = atomj0;
atomc = atomk0;
scale = invMass1[j]/(invMass1[j]+invMass2[j]);
scale = invMass1[cj]/(invMass1[cj]+invMass2[cj]);
}
else if (atomj1 == atomk0) {
atoma = atomj0;
atomb = atomj1;
atomc = atomk1;
scale = invMass2[j]/(invMass1[j]+invMass2[j]);
scale = invMass2[cj]/(invMass1[cj]+invMass2[cj]);
}
else
continue; // These constraints are not connected.
......@@ -987,8 +997,8 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
bool foundConstraint = false;
for (int other = 0; other < numLincs; other++) {
if ((atom1[other] == atoma && atom2[other] == atomc) || (atom1[other] == atomc && atom2[other] == atoma)) {
double d1 = distance[j];
double d2 = distance[k];
double d1 = distance[cj];
double d2 = distance[ck];
double d3 = distance[other];
matrix[j].push_back(pair<int, double>(k, scale*(d1*d1+d2*d2-d3*d3)/(2.0*d1*d2)));
foundConstraint = true;
......@@ -1040,8 +1050,8 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
result = QUERN_multiply_with_q_transpose(numLincs, qRowStart, qColIndex, qValue, &rhs[0]);
result = QUERN_solve_with_r(numLincs, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numLincs; j++) {
double value = rhs[j]*distance[i]/distance[j];
if (abs(value) > 0.02)
double value = rhs[j]*distance[lincsConstraints[i]]/distance[lincsConstraints[j]];
if (abs(value) > 0.1)
matrix[j].push_back(pair<int, double>(i, value));
}
}
......@@ -1053,10 +1063,18 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
maxRowElements = max(maxRowElements, (int) matrix[i].size());
maxRowElements++;
// Sort the constraints.
vector<int> constraintOrder(numLincs);
for (int i = 0; i < numLincs; ++i)
constraintOrder[i] = i;
sort(constraintOrder.begin(), constraintOrder.end(), ConstraintOrderer(atom1, atom2));
vector<int> inverseOrder(numLincs);
for (int i = 0; i < numLincs; ++i)
inverseOrder[constraintOrder[i]] = i;
for (int i = 0; i < matrix.size(); ++i)
for (int j = 0; j < matrix[i].size(); ++j)
matrix[i][j].first = inverseOrder[matrix[i][j].first];
// Fill in the CUDA streams.
......@@ -1110,20 +1128,21 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
gpu->sim.pConstraintMatrixValue = psConstraintMatrixValue->_pDevData;
gpu->sim.lincsConstraints = numLincs;
for (int i = 0; i < numLincs; i++) {
int c = lincsConstraints[i];
int index = constraintOrder[i];
int c = lincsConstraints[index];
(*psLincsAtoms)[i].x = atom1[c];
(*psLincsAtoms)[i].y = atom2[c];
(*psLincsDistance)[i].w = distance[c];
(*psLincsS)[i] = 1.0f/sqrt(invMass1[c]+invMass2[c]);
(*psShakeReducedMass)[i] = 0.5f/(invMass1[c]+invMass2[c]);
(*psLincsNumConnections)[i] = linkedConstraints[i].size();
for (unsigned int j = 0; j < linkedConstraints[i].size(); j++)
(*psLincsConnections)[i+j*numLincs] = linkedConstraints[i][j];
for (unsigned int j = 0; j < matrix[i].size(); j++) {
(*psConstraintMatrixColumn)[i+j*numLincs] = matrix[i][j].first;
(*psConstraintMatrixValue)[i+j*numLincs] = matrix[i][j].second;
(*psLincsNumConnections)[i] = linkedConstraints[index].size();
for (unsigned int j = 0; j < linkedConstraints[index].size(); j++)
(*psLincsConnections)[i+j*numLincs] = linkedConstraints[index][j];
for (unsigned int j = 0; j < matrix[index].size(); j++) {
(*psConstraintMatrixColumn)[i+j*numLincs] = matrix[index][j].first;
(*psConstraintMatrixValue)[i+j*numLincs] = matrix[index][j].second;
}
(*psConstraintMatrixColumn)[i+matrix[i].size()*numLincs] = numLincs;
(*psConstraintMatrixColumn)[i+matrix[index].size()*numLincs] = numLincs;
}
for (unsigned int i = 0; i < psSyncCounter->_length; i++)
(*psSyncCounter)[i] = -1;
......@@ -1131,7 +1150,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
(*psLincsNumAtomConstraints)[i] = atomConstraints[i].size();
for (unsigned int j = 0; j < atomConstraints[i].size(); j++) {
bool forward = (atom1[lincsConstraints[atomConstraints[i][j]]] == i);
(*psLincsAtomConstraints)[i+j*gpu->natoms] = (forward ? atomConstraints[i][j]+1 : -atomConstraints[i][j]-1);
(*psLincsAtomConstraints)[i+j*gpu->natoms] = (forward ? inverseOrder[atomConstraints[i][j]]+1 : -inverseOrder[atomConstraints[i][j]]-1);
}
}
psLincsAtoms->Upload();
......
platforms/cuda/src/kernels/kCShake.cu
View file @ 5b8cade7
......@@ -68,8 +68,6 @@ __device__ void kSyncAllThreads_kernel(short* syncCounter, short newCount)
__global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
{
extern __shared__ float temp[];
// Initialize counters used for monitoring convergence and doing global thread synchronization.
__shared__ unsigned int requiredIterations;
......@@ -136,43 +134,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
if (threadIdx.x == 0 && requiredIterations > iteration)
cSim.pRequiredIterations[0] = requiredIterations;
// Multiply by the inverse constraint matrix for each rigid cluster.
// if (cSim.rigidClusters > 0)
// {
// pos = threadIdx.x + blockIdx.x * blockDim.x;
// unsigned int block = pos/cSim.clusterShakeBlockSize;
// unsigned int indexInBlock = pos-block*cSim.clusterShakeBlockSize;
// while (block < cSim.rigidClusters)
// {
// unsigned int firstConstraint = cSim.pRigidClusterConstraintIndex[block];
// unsigned int blockSize = cSim.pRigidClusterConstraintIndex[block+1]-firstConstraint;
// if (indexInBlock < blockSize)
// {
// // Load the constraint forces and matrix.
//
// temp[threadIdx.x] = cSim.pLincsSolution[firstConstraint+indexInBlock];
// unsigned int firstMatrixIndex = cSim.pRigidClusterMatrixIndex[block];
//
// // Multiply by the matrix.
//
// float sum = 0.0f;
// for (unsigned int i = 0; i < blockSize; i++)
// sum += temp[threadIdx.x-indexInBlock+i]*cSim.pRigidClusterMatrix[firstMatrixIndex+i*blockSize+indexInBlock];
// cSim.pLincsSolution[firstConstraint+indexInBlock] = sum;
// }
// block += (blockDim.x*gridDim.x)/cSim.clusterShakeBlockSize;
// }
// kSyncAllThreads_kernel(&cSim.pSyncCounter[gridDim.x], iteration);
// }
// Multiply by the inverse constraint matrix.
pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
{
float sum = 0.0f;
for (unsigned int i = 0; ; i++)
{
int index = pos+i*cSim.lincsConstraints;
unsigned int column = cSim.pConstraintMatrixColumn[pos+i*cSim.lincsConstraints];
unsigned int index = pos+i*cSim.lincsConstraints;
unsigned int column = cSim.pConstraintMatrixColumn[index];
if (column >= cSim.lincsConstraints)
break;
sum += cSim.pLincsRhs1[column]*cSim.pConstraintMatrixValue[index];
......@@ -222,7 +193,7 @@ void kApplyFirstCShake(gpuContext gpu)
// printf("kApplyFirstCShake\n");
if (gpu->sim.lincsConstraints > 0)
{
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block, 4*gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosqP, true);
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosqP, true);
LAUNCHERROR("kApplyCShake");
}
}
......@@ -232,7 +203,7 @@ void kApplySecondCShake(gpuContext gpu)
// printf("kApplySecondCShake\n");
if (gpu->sim.lincsConstraints > 0)
{
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block, 4*gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosq, false);
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosq, false);
LAUNCHERROR("kApplyCShake");
}
}
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