moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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

Browse Source
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

41
src/force.cu
View File

@ -124,9 +124,7 @@ __global__ void kernel_final_integrate(MD_FLOAT dtforce, int Nlocal, Atom a) {
extern "C" { extern "C" {
static Atom c_atom;
int *c_neighs;
int *c_neigh_numneigh;
int get_num_threads() { 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) ); 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( double computeForce(
bool reneighbourHappenend, bool reneighbourHappenend,
Parameter *param, Parameter *param,
Atom *atom, Atom *atom,
Neighbor *neighbor Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor
) )
{ {
int Nlocal = atom->Nlocal; 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) ); checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
if(reneighbourHappenend) { if(reneighbourHappenend) {
checkCUDAError( "c_neigh_numneigh memcpy", cudaMemcpy(c_neigh_numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) ); checkCUDAError( "c_neighbor->numneigh memcpy", cudaMemcpy(c_neighbor->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->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 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(); double S = getTimeStamp();
LIKWID_MARKER_START("force"); 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( "PeekAtLastError ComputeForce", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync ComputeForce", cudaDeviceSynchronize() ); checkCUDAError( "DeviceSync ComputeForce", cudaDeviceSynchronize() );

38
src/main.c
View File

@ -45,8 +45,6 @@
#define HLINE "----------------------------------------------------------------------------\n" #define HLINE "----------------------------------------------------------------------------\n"
extern void initCudaAtom(Atom *atom, Neighbor *neighbor);
extern void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom); extern void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom);
extern void cuda_initial_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; 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( double setup(
Parameter *param, Parameter *param,
Eam *eam, Eam *eam,
Atom *atom, Atom *atom,
Neighbor *neighbor, Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor,
Stats *stats) Stats *stats)
{ {
if(param->force_field == FF_EAM) { initEam(eam, param); } if(param->force_field == FF_EAM) { initEam(eam, param); }
@ -106,7 +134,7 @@ double setup(
buildNeighbor(atom, neighbor); buildNeighbor(atom, neighbor);
E = getTimeStamp(); E = getTimeStamp();
initCudaAtom(atom, neighbor); initCudaAtom(atom, neighbor, c_atom, c_neighbor);
return E-S; return E-S;
} }
@ -186,6 +214,8 @@ int main(int argc, char** argv)
Neighbor neighbor; Neighbor neighbor;
Stats stats; Stats stats;
Parameter param; Parameter param;
Atom c_atom;
Neighbor c_neighbor;
LIKWID_MARKER_INIT; LIKWID_MARKER_INIT;
#pragma omp parallel #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); computeThermo(0, &param, &atom);
if(param.force_field == FF_EAM) { if(param.force_field == FF_EAM) {
computeForceEam(&eam, &param, &atom, &neighbor, &stats, 1, 0); computeForceEam(&eam, &param, &atom, &neighbor, &stats, 1, 0);