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Removed debug prints, only zero atom forces and not copy them, added measurements

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This commit is contained in:
Maximilian Gaul 2021-12-28 16:32:54 +01:00
parent 8009b54113
commit bf1ae3d013
3 changed files with 13 additions and 73 deletions
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56
src/force.cu
View File

@ -111,26 +111,14 @@ double computeForce(
) )
{ {
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES #ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6; MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon; MD_FLOAT epsilon = param->epsilon;
#endif #endif
printf("-1\r\n");
cudaProfilerStart(); cudaProfilerStart();
printf("0\r\n");
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
const char *num_threads_env = getenv("NUM_THREADS"); const char *num_threads_env = getenv("NUM_THREADS");
int num_threads = 0; int num_threads = 0;
if(num_threads_env == nullptr) if(num_threads_env == nullptr)
@ -145,8 +133,6 @@ double computeForce(
c_atom.Nmax = atom->Nmax; c_atom.Nmax = atom->Nmax;
c_atom.ntypes = atom->ntypes; c_atom.ntypes = atom->ntypes;
printf("0.1\r\n");
/* /*
int nDevices; int nDevices;
cudaGetDeviceCount(&nDevices); cudaGetDeviceCount(&nDevices);
@ -167,8 +153,6 @@ double computeForce(
// HINT: Run with cuda-memcheck ./MDBench-NVCC in case of error // HINT: Run with cuda-memcheck ./MDBench-NVCC in case of error
// HINT: Only works for data layout = AOS!!! // HINT: Only works for data layout = AOS!!!
printf("1\r\n");
if(!initialized) { if(!initialized) {
checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) ); checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal) ); checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal) );
@ -183,27 +167,18 @@ double computeForce(
checkCUDAError( "c_neigh_numneigh malloc", cudaMalloc((void**)&c_neigh_numneigh, sizeof(int) * Nlocal) ); checkCUDAError( "c_neigh_numneigh malloc", cudaMalloc((void**)&c_neigh_numneigh, sizeof(int) * Nlocal) );
} }
printf("2\r\n"); checkCUDAError( "c_atom.fx memset", cudaMemset(c_atom.fx, 0, sizeof(MD_FLOAT) * Nlocal) );
checkCUDAError( "c_atom.fy memset", cudaMemset(c_atom.fy, 0, sizeof(MD_FLOAT) * Nlocal) );
checkCUDAError( "c_atom.fz memset", cudaMemset(c_atom.fz, 0, sizeof(MD_FLOAT) * Nlocal) );
if(reneighbourHappenend || !initialized) { 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) ); checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.fx memcpy", cudaMemcpy(c_atom.fx, fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) ); checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.fy memcpy", cudaMemcpy(c_atom.fy, fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) ); checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.fz memcpy", cudaMemcpy(c_atom.fz, fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) ); checkCUDAError( "c_atom.cutforcesq memcpy", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, 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) );
checkCUDAError( "c_neigh_numneigh memcpy", cudaMemcpy(c_neigh_numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) ); 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_neighs memcpy", cudaMemcpy(c_neighs, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
}
printf("3\r\n");
printf("4\r\n");
printf("5\r\n");
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
const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block); const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
@ -216,16 +191,11 @@ double computeForce(
checkCUDAError( "PeekAtLastError", cudaPeekAtLastError() ); checkCUDAError( "PeekAtLastError", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync", cudaDeviceSynchronize() ); checkCUDAError( "DeviceSync", cudaDeviceSynchronize() );
printf("6\r\n");
// copy results in c_atom.fx/fy/fz to atom->fx/fy/fz // copy results in c_atom.fx/fy/fz to atom->fx/fy/fz
if(reneighbourHappenend) {
cudaMemcpy(atom->fx, c_atom.fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
cudaMemcpy(atom->fy, c_atom.fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
cudaMemcpy(atom->fz, c_atom.fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
}
printf("7\r\n"); cudaMemcpy(atom->fx, c_atom.fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
cudaMemcpy(atom->fy, c_atom.fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
cudaMemcpy(atom->fz, c_atom.fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
/* /*
cudaFree(c_atom.x); cudaFree(c_atom.x);

13
src/main.c
View File

@ -111,20 +111,13 @@ double reneighbour(
{ {
double S, E; double S, E;
printf("10.1\r\n");
S = getTimeStamp(); S = getTimeStamp();
LIKWID_MARKER_START("reneighbour"); LIKWID_MARKER_START("reneighbour");
printf("10.2\r\n");
updateAtomsPbc(atom, param); updateAtomsPbc(atom, param);
printf("10.3\r\n");
setupPbc(atom, param); setupPbc(atom, param);
printf("10.4\r\n");
updatePbc(atom, param); updatePbc(atom, param);
printf("10.5\r\n");
//sortAtom(atom); //sortAtom(atom);
buildNeighbor(atom, neighbor); buildNeighbor(atom, neighbor);
printf("10.6\r\n");
LIKWID_MARKER_STOP("reneighbour"); LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp(); E = getTimeStamp();
@ -288,18 +281,12 @@ int main(int argc, char** argv)
const bool doReneighbour = (n + 1) % param.every == 0; const bool doReneighbour = (n + 1) % param.every == 0;
const bool doesReneighbourNextRound = (n + 2) % param.every == 0; const bool doesReneighbourNextRound = (n + 2) % param.every == 0;
printf("Run %d does reneighbour: %d\r\n", n, doReneighbour);
printf("10\r\n");
if(doReneighbour) { if(doReneighbour) {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor); timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
} else { } else {
updatePbc(&atom, &param); updatePbc(&atom, &param);
} }
printf("11\r\n");
if(param.force_field == FF_EAM) { if(param.force_field == FF_EAM) {
timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats, 0, n + 1); timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats, 0, n + 1);
} else { } else {

17
src/neighbor.c
View File

@ -172,8 +172,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
{ {
int nall = atom->Nlocal + atom->Nghost; int nall = atom->Nlocal + atom->Nghost;
printf("nall: %d, nmax: %d\r\n", nall, nmax);
/* extend atom arrays if necessary */ /* extend atom arrays if necessary */
if(nall > nmax) { if(nall > nmax) {
nmax = nall; nmax = nall;
@ -185,14 +183,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
// neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*)); // neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
} }
printf("10.5.1\r\n");
/* bin local & ghost atoms */ /* bin local & ghost atoms */
binatoms(atom); binatoms(atom);
int resize = 1; int resize = 1;
printf("10.5.2\r\n");
/* loop over each atom, storing neighbors */ /* loop over each atom, storing neighbors */
while(resize) { while(resize) {
int new_maxneighs = neighbor->maxneighs; int new_maxneighs = neighbor->maxneighs;
@ -322,14 +316,9 @@ int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin)
void binatoms(Atom *atom) void binatoms(Atom *atom)
{ {
printf("10.5.1.1\r\n");
int nall = atom->Nlocal + atom->Nghost; int nall = atom->Nlocal + atom->Nghost;
int resize = 1; int resize = 1;
printf("10.5.1.2\r\n");
printf("nall: %d, atom->Nmax: %d\r\n", nall, atom->Nmax);
while(resize > 0) { while(resize > 0) {
resize = 0; resize = 0;
@ -337,8 +326,6 @@ void binatoms(Atom *atom)
bincount[i] = 0; bincount[i] = 0;
} }
printf("10.5.1.3\r\n");
for(int i = 0; i < nall; i++) { for(int i = 0; i < nall; i++) {
MD_FLOAT x = atom_x(i); MD_FLOAT x = atom_x(i);
MD_FLOAT y = atom_y(i); MD_FLOAT y = atom_y(i);
@ -353,15 +340,11 @@ void binatoms(Atom *atom)
} }
} }
printf("10.5.1.4\r\n");
if(resize) { if(resize) {
free(bins); free(bins);
atoms_per_bin *= 2; atoms_per_bin *= 2;
bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int)); bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
} }
printf("10.5.1.5\r\n");
} }
} }