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

Runs fine (but slow), results seem to be slightly off from original

Browse Source
This commit is contained in:
Maximilian Gaul 2021-11-11 20:47:06 +01:00
parent 1f5c9c4b23
commit 4105c844c6
1 changed files with 16 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
src/force.cu
View File

@ -119,33 +119,28 @@ double computeForce(
c_atom.Nmax = atom->Nmax; c_atom.Nmax = atom->Nmax;
c_atom.ntypes = atom->ntypes; c_atom.ntypes = atom->ntypes;
size_t available, total;
cudaMemGetInfo(&available, &total);
printf("Available memory: %ldGB\r\n", available / 1024 / 1024 / 1024);
cudaDeviceSetLimit(cudaLimitMallocHeapSize, available);
// 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!!!
checkError( "Malloc1", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) ); checkError( "Malloc1", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
checkError( "Memcpy1", cudaMemcpy((void*)(c_atom.x), atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) ); checkError( "Memcpy1", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
checkError( "Malloc4", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) ); checkError( "Malloc2", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) );
checkError( "Memcpy4", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) ); checkError( "Memcpy2", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
checkError( "Malloc5", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) ); checkError( "Malloc3", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkError( "Memcpy5", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) ); checkError( "Memcpy3", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkError( "Malloc6", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) ); checkError( "Malloc4", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkError( "Memcpy6", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) ); checkError( "Memcpy4", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
checkError( "Malloc7", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) ); checkError( "Malloc5", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
checkError( "Memcpy7", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) ); checkError( "Memcpy5", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
double S = getTimeStamp(); double S = getTimeStamp();
LIKWID_MARKER_START("force"); LIKWID_MARKER_START("force");
// #pragma omp parallel for #pragma omp parallel for
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs]; neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i]; int numneighs = neighbor->numneigh[i];
@ -161,24 +156,25 @@ double computeForce(
checkError( "c_neighs malloc", cudaMalloc((void**)&c_neighs, sizeof(int) * numneighs) ); checkError( "c_neighs malloc", cudaMalloc((void**)&c_neighs, sizeof(int) * numneighs) );
checkError( "c_neighs memcpy", cudaMemcpy(c_neighs, neighs, sizeof(int) * numneighs, cudaMemcpyHostToDevice) ); checkError( "c_neighs memcpy", cudaMemcpy(c_neighs, neighs, sizeof(int) * numneighs, cudaMemcpyHostToDevice) );
const int num_blocks = 64;
const int num_threads_per_block = ceil((float)numneighs / (float)num_blocks);
// printf("numneighs: %d => num-blocks: %d, num_threads_per_block => %d\r\n", numneighs, num_blocks, num_threads_per_block);
MD_FLOAT *c_fix, *c_fiy, *c_fiz; MD_FLOAT *c_fix, *c_fiy, *c_fiz;
checkError( "c_fix malloc", cudaMalloc((void**)&c_fix, sizeof(MD_FLOAT) * numneighs) ); checkError( "c_fix malloc", cudaMalloc((void**)&c_fix, sizeof(MD_FLOAT) * numneighs) );
checkError( "c_fiy malloc", cudaMalloc((void**)&c_fiy, sizeof(MD_FLOAT) * numneighs) ); checkError( "c_fiy malloc", cudaMalloc((void**)&c_fiy, sizeof(MD_FLOAT) * numneighs) );
checkError( "c_fiz malloc", cudaMalloc((void**)&c_fiz, sizeof(MD_FLOAT) * numneighs) ); checkError( "c_fiz malloc", cudaMalloc((void**)&c_fiz, sizeof(MD_FLOAT) * numneighs) );
const int num_blocks = 64;
const int num_threads_per_block = ceil((float)numneighs / (float)num_blocks);
// printf("numneighs: %d => num-blocks: %d, num_threads_per_block => %d\r\n", numneighs, num_blocks, num_threads_per_block);
// launch cuda kernel // launch cuda kernel
calc_force <<< num_blocks, num_threads_per_block >>> (c_atom, xtmp, ytmp, ztmp, c_fix, c_fiy, c_fiz, cutforcesq, sigma6, epsilon, i, numneighs, c_neighs); calc_force <<< num_blocks, num_threads_per_block >>> (c_atom, xtmp, ytmp, ztmp, c_fix, c_fiy, c_fiz, cutforcesq, sigma6, epsilon, i, numneighs, c_neighs);
checkError( "PeekAtLastError", cudaPeekAtLastError() ); checkError( "PeekAtLastError", cudaPeekAtLastError() );
checkError( "DeviceSync", cudaDeviceSynchronize() ); checkError( "DeviceSync", cudaDeviceSynchronize() );
// sum result
MD_FLOAT *d_fix = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs); MD_FLOAT *d_fix = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
MD_FLOAT *d_fiy = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs); MD_FLOAT *d_fiy = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
MD_FLOAT *d_fiz = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs); MD_FLOAT *d_fiz = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
// sum result
checkError( "d_fix copy to host", cudaMemcpy(d_fix, c_fix, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) ); checkError( "d_fix copy to host", cudaMemcpy(d_fix, c_fix, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) );
checkError( "d_fiy copy to host", cudaMemcpy(d_fiy, c_fiy, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) ); checkError( "d_fiy copy to host", cudaMemcpy(d_fiy, c_fiy, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) );
checkError( "d_fiz copy to host", cudaMemcpy(d_fiz, c_fiz, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) ); checkError( "d_fiz copy to host", cudaMemcpy(d_fiz, c_fiz, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost) );