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Create separate structs DeviceAtom and DeviceNeighbor with device pointers

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-12 17:28:06 +02:00
parent 065b596074
commit 939197a785
13 changed files with 172 additions and 153 deletions
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42
lammps/main.c
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@@ -54,10 +54,10 @@ extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
#ifdef CUDA_TARGET
#include <cuda_atom.h>
extern double computeForceLJFullNeigh_cuda(Parameter*, Atom*, Neighbor*, Atom*, Neighbor*);
extern double computeForceLJFullNeigh_cuda(Parameter*, Atom*, Neighbor*);
#endif
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, Stats *stats) {
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
param->lattice = pow((4.0 / param->rho), (1.0 / 3.0));
@@ -81,23 +81,23 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Atom *c
if(param->input_file == NULL) { adjustThermo(param, atom); }
setupPbc(atom, param);
#ifdef CUDA_TARGET
initCuda(atom, neighbor, c_atom, c_neighbor);
initCuda(atom, neighbor);
#endif
updatePbc(atom, c_atom, param, true);
buildNeighbor(atom, neighbor, c_atom, c_neighbor);
updatePbc(atom, param, true);
buildNeighbor(atom, neighbor);
E = getTimeStamp();
return E-S;
}
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor) {
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
double S, E;
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, c_atom, param);
updateAtomsPbc(atom, param);
setupPbc(atom, param);
updatePbc(atom, c_atom, param, true);
updatePbc(atom, param, true);
//sortAtom(atom);
buildNeighbor(atom, neighbor, c_atom, c_neighbor);
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
return E-S;
@@ -111,7 +111,7 @@ void printAtomState(Atom *atom) {
// }
}
double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, Stats *stats) {
double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) {
return computeForceEam(eam, param, atom, neighbor, stats);
} else if(param->force_field == FF_DEM) {
@@ -128,7 +128,7 @@ double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor,
}
#ifdef CUDA_TARGET
return computeForceLJFullNeigh(param, atom, neighbor, c_atom, c_neighbor);
return computeForceLJFullNeigh(param, atom, neighbor);
#else
return computeForceLJFullNeigh(param, atom, neighbor, stats);
#endif
@@ -137,8 +137,8 @@ double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor,
int main(int argc, char** argv) {
double timer[NUMTIMER];
Eam eam;
Atom atom, c_atom;
Neighbor neighbor, c_neighbor;
Atom atom;
Neighbor neighbor;
Stats stats;
Parameter param;
@@ -226,7 +226,7 @@ int main(int argc, char** argv) {
}
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
setup(&param, &eam, &atom, &neighbor, &stats);
printParameter(&param);
printf("step\ttemp\t\tpressure\n");
@@ -235,7 +235,7 @@ int main(int argc, char** argv) {
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
timer[FORCE] = computeForce(&eam, &param, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
timer[FORCE] = computeForce(&eam, &param, &atom, &neighbor, &stats);
timer[NEIGH] = 0.0;
timer[TOTAL] = getTimeStamp();
@@ -245,23 +245,23 @@ int main(int argc, char** argv) {
for(int n = 0; n < param.ntimes; n++) {
bool reneigh = (n + 1) % param.reneigh_every == 0;
initialIntegrate(reneigh, &param, &atom, &c_atom);
initialIntegrate(reneigh, &param, &atom);
if((n + 1) % param.reneigh_every) {
updatePbc(&atom, &c_atom, &param, false);
updatePbc(&atom, &param, false);
} else {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor, &c_atom, &c_neighbor);
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
}
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
timer[FORCE] += computeForce(&eam, &param, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
finalIntegrate(reneigh, &param, &atom, &c_atom);
timer[FORCE] += computeForce(&eam, &param, &atom, &neighbor, &stats);
finalIntegrate(reneigh, &param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
#ifdef CUDA_TARGET
memcpyFromGPU(atom.x, c_atom.x, atom.Nmax * sizeof(MD_FLOAT) * 3);
memcpyFromGPU(atom.x, atom.d_atom.x, atom.Nmax * sizeof(MD_FLOAT) * 3);
#endif
computeThermo(n + 1, &param, &atom);
}