diff --git a/src/force.cu b/src/force.cu index d68567b..2ed6887 100644 --- a/src/force.cu +++ b/src/force.cu @@ -111,26 +111,14 @@ double computeForce( ) { int Nlocal = atom->Nlocal; - MD_FLOAT* fx = atom->fx; - MD_FLOAT* fy = atom->fy; - MD_FLOAT* fz = atom->fz; #ifndef EXPLICIT_TYPES MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT sigma6 = param->sigma6; MD_FLOAT epsilon = param->epsilon; #endif - printf("-1\r\n"); 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"); int num_threads = 0; if(num_threads_env == nullptr) @@ -145,8 +133,6 @@ double computeForce( c_atom.Nmax = atom->Nmax; c_atom.ntypes = atom->ntypes; - printf("0.1\r\n"); - /* int nDevices; cudaGetDeviceCount(&nDevices); @@ -167,8 +153,6 @@ double computeForce( // HINT: Run with cuda-memcheck ./MDBench-NVCC in case of error // HINT: Only works for data layout = AOS!!! - printf("1\r\n"); - if(!initialized) { 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) ); @@ -183,27 +167,18 @@ double computeForce( 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.fx memcpy", cudaMemcpy(c_atom.fx, fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) ); - checkCUDAError( "c_atom.fy memcpy", cudaMemcpy(c_atom.fy, fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) ); - checkCUDAError( "c_atom.fz memcpy", cudaMemcpy(c_atom.fz, fz, sizeof(MD_FLOAT) * Nlocal, 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_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.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_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"); + 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) ); 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); @@ -216,16 +191,11 @@ double computeForce( checkCUDAError( "PeekAtLastError", cudaPeekAtLastError() ); checkCUDAError( "DeviceSync", cudaDeviceSynchronize() ); - printf("6\r\n"); - // 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); diff --git a/src/main.c b/src/main.c index 1730dc3..cb8a4f3 100644 --- a/src/main.c +++ b/src/main.c @@ -111,20 +111,13 @@ double reneighbour( { double S, E; - printf("10.1\r\n"); - S = getTimeStamp(); LIKWID_MARKER_START("reneighbour"); - printf("10.2\r\n"); updateAtomsPbc(atom, param); - printf("10.3\r\n"); setupPbc(atom, param); - printf("10.4\r\n"); updatePbc(atom, param); - printf("10.5\r\n"); //sortAtom(atom); buildNeighbor(atom, neighbor); - printf("10.6\r\n"); LIKWID_MARKER_STOP("reneighbour"); E = getTimeStamp(); @@ -288,18 +281,12 @@ int main(int argc, char** argv) const bool doReneighbour = (n + 1) % 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) { timer[NEIGH] += reneighbour(¶m, &atom, &neighbor); } else { updatePbc(&atom, ¶m); } - printf("11\r\n"); - if(param.force_field == FF_EAM) { timer[FORCE] += computeForceEam(&eam, ¶m, &atom, &neighbor, &stats, 0, n + 1); } else { diff --git a/src/neighbor.c b/src/neighbor.c index 0abbb26..c9f9634 100644 --- a/src/neighbor.c +++ b/src/neighbor.c @@ -172,8 +172,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) { int nall = atom->Nlocal + atom->Nghost; - printf("nall: %d, nmax: %d\r\n", nall, nmax); - /* extend atom arrays if necessary */ if(nall > nmax) { nmax = nall; @@ -185,14 +183,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) // neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*)); } - printf("10.5.1\r\n"); - /* bin local & ghost atoms */ binatoms(atom); int resize = 1; - printf("10.5.2\r\n"); - /* loop over each atom, storing neighbors */ while(resize) { int new_maxneighs = neighbor->maxneighs; @@ -322,14 +316,9 @@ int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin) void binatoms(Atom *atom) { - printf("10.5.1.1\r\n"); int nall = atom->Nlocal + atom->Nghost; int resize = 1; - printf("10.5.1.2\r\n"); - - printf("nall: %d, atom->Nmax: %d\r\n", nall, atom->Nmax); - while(resize > 0) { resize = 0; @@ -337,8 +326,6 @@ void binatoms(Atom *atom) bincount[i] = 0; } - printf("10.5.1.3\r\n"); - for(int i = 0; i < nall; i++) { MD_FLOAT x = atom_x(i); MD_FLOAT y = atom_y(i); @@ -353,15 +340,11 @@ void binatoms(Atom *atom) } } - printf("10.5.1.4\r\n"); - if(resize) { free(bins); atoms_per_bin *= 2; bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int)); } - - printf("10.5.1.5\r\n"); } }