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♻️ Refactoring: pulled definition of the GPU atom and neighbor representation from force.cu and put it into main

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This commit is contained in:
Martin Bauernfeind
2022-06-23 18:54:56 +02:00
parent b024adaf5b
commit 62cfc22856
2 changed files with 41 additions and 38 deletions
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41
src/force.cu
View File

@@ -124,9 +124,7 @@ __global__ void kernel_final_integrate(MD_FLOAT dtforce, int Nlocal, Atom a) {
extern "C" {
static Atom c_atom;
int *c_neighs;
int *c_neigh_numneigh;
int get_num_threads() {
@@ -178,38 +176,13 @@ void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom) {
checkCUDAError( "InitialIntegrate: position memcpy", cudaMemcpy(atom->x, c_atom.x, sizeof(MD_FLOAT) * atom->Nlocal * 3, cudaMemcpyDeviceToHost) );
}
void initCudaAtom(Atom *atom, Neighbor *neighbor) {
const int Nlocal = atom->Nlocal;
checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal * 3) );
checkCUDAError( "c_atom.vx malloc", cudaMalloc((void**)&(c_atom.vx), sizeof(MD_FLOAT) * Nlocal * 3) );
checkCUDAError( "c_atom.vx memcpy", cudaMemcpy(c_atom.vx, atom->vx, sizeof(MD_FLOAT) * Nlocal * 3, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.type malloc", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) );
checkCUDAError( "c_atom.epsilon malloc", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_atom.sigma6 malloc", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_atom.cutforcesq malloc", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_neighs malloc", cudaMalloc((void**)&c_neighs, sizeof(int) * Nlocal * neighbor->maxneighs) );
checkCUDAError( "c_neigh_numneigh malloc", cudaMalloc((void**)&c_neigh_numneigh, sizeof(int) * Nlocal) );
checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.cutforcesq memcpy", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
}
double computeForce(
bool reneighbourHappenend,
Parameter *param,
Atom *atom,
Neighbor *neighbor
Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor
)
{
int Nlocal = atom->Nlocal;
@@ -249,8 +222,8 @@ double computeForce(
checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
if(reneighbourHappenend) {
checkCUDAError( "c_neigh_numneigh memcpy", cudaMemcpy(c_neigh_numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) );
checkCUDAError( "c_neighs memcpy", cudaMemcpy(c_neighs, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
checkCUDAError( "c_neighbor->numneigh memcpy", cudaMemcpy(c_neighbor->numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) );
checkCUDAError( "c_neighbor->neighbors memcpy", cudaMemcpy(c_neighbor->neighbors, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
}
const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
@@ -259,7 +232,7 @@ double computeForce(
double S = getTimeStamp();
LIKWID_MARKER_START("force");
calc_force <<< num_blocks, num_threads_per_block >>> (c_atom, cutforcesq, sigma6, epsilon, Nlocal, neighbor->maxneighs, c_neighs, c_neigh_numneigh);
calc_force <<< num_blocks, num_threads_per_block >>> (c_atom, cutforcesq, sigma6, epsilon, Nlocal, neighbor->maxneighs, c_neighbor->neighbors, c_neighbor->numneigh);
checkCUDAError( "PeekAtLastError ComputeForce", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync ComputeForce", cudaDeviceSynchronize() );

38
src/main.c
View File

@@ -45,8 +45,6 @@
#define HLINE "----------------------------------------------------------------------------\n"
extern void initCudaAtom(Atom *atom, Neighbor *neighbor);
extern void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom);
extern void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom);
@@ -78,11 +76,41 @@ void init(Parameter *param)
param->proc_freq = 2.4;
}
void initCudaAtom(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor) {
const int Nlocal = atom->Nlocal;
checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal * 3) );
checkCUDAError( "c_atom.vx malloc", cudaMalloc((void**)&(c_atom.vx), sizeof(MD_FLOAT) * Nlocal * 3) );
checkCUDAError( "c_atom.vx memcpy", cudaMemcpy(c_atom.vx, atom->vx, sizeof(MD_FLOAT) * Nlocal * 3, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.type malloc", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) );
checkCUDAError( "c_atom.epsilon malloc", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_atom.sigma6 malloc", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_atom.cutforcesq malloc", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkCUDAError( "c_neighbor->neighbors malloc", cudaMalloc((void**)&c_neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs) );
checkCUDAError( "c_neighbor->numneigh malloc", cudaMalloc((void**)&c_neighbor->numneigh, sizeof(int) * Nlocal) );
checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.cutforcesq memcpy", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
}
double setup(
Parameter *param,
Eam *eam,
Atom *atom,
Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor,
Stats *stats)
{
if(param->force_field == FF_EAM) { initEam(eam, param); }
@@ -106,7 +134,7 @@ double setup(
buildNeighbor(atom, neighbor);
E = getTimeStamp();
initCudaAtom(atom, neighbor);
initCudaAtom(atom, neighbor, c_atom, c_neighbor);
return E-S;
}
@@ -186,6 +214,8 @@ int main(int argc, char** argv)
Neighbor neighbor;
Stats stats;
Parameter param;
Atom c_atom;
Neighbor c_neighbor;
LIKWID_MARKER_INIT;
#pragma omp parallel
@@ -256,7 +286,7 @@ int main(int argc, char** argv)
}
}
setup(&param, &eam, &atom, &neighbor, &stats);
setup(&param, &eam, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
computeThermo(0, &param, &atom);
if(param.force_field == FF_EAM) {
computeForceEam(&eam, &param, &atom, &neighbor, &stats, 1, 0);