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Ported updateAtomsPbc to cuda and changed the code to use the cuda version from now on

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Martin Bauernfeind 2022-07-13 14:07:19 +02:00
parent f61f59ba3f
commit 5a6d1851ed
4 changed files with 43 additions and 2 deletions
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1
src/force.cu
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@ -153,7 +153,6 @@ void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom, At
if(doReneighbour) { if(doReneighbour) {
checkCUDAError( "InitialIntegrate: velocity memcpy", cudaMemcpy(atom->vx, c_atom->vx, sizeof(MD_FLOAT) * atom->Nlocal * 3, cudaMemcpyDeviceToHost) ); checkCUDAError( "InitialIntegrate: velocity memcpy", cudaMemcpy(atom->vx, c_atom->vx, sizeof(MD_FLOAT) * atom->Nlocal * 3, cudaMemcpyDeviceToHost) );
checkCUDAError( "InitialIntegrate: position memcpy", cudaMemcpy(atom->x, c_atom->x, sizeof(MD_FLOAT) * atom->Nlocal * 3, cudaMemcpyDeviceToHost) );
} }
} }

1
src/includes/pbc.h
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@ -29,5 +29,6 @@ extern void initPbc(Atom*);
extern void updatePbc(Atom*, Parameter*); extern void updatePbc(Atom*, Parameter*);
extern void updatePbc_cuda(Atom*, Parameter*, Atom*, bool, const int); extern void updatePbc_cuda(Atom*, Parameter*, Atom*, bool, const int);
extern void updateAtomsPbc(Atom*, Parameter*); extern void updateAtomsPbc(Atom*, Parameter*);
extern void updateAtomsPbc_cuda(Atom*, Parameter*, Atom*, const int);
extern void setupPbc(Atom*, Parameter*); extern void setupPbc(Atom*, Parameter*);
#endif #endif

2
src/main.c
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@ -164,7 +164,7 @@ double reneighbour(
S = getTimeStamp(); S = getTimeStamp();
LIKWID_MARKER_START("reneighbour"); LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param); updateAtomsPbc_cuda(atom, param, c_atom, num_threads_per_block);
setupPbc(atom, param); setupPbc(atom, param);
updatePbc_cuda(atom, param, c_atom, true, num_threads_per_block); updatePbc_cuda(atom, param, c_atom, true, num_threads_per_block);
//sortAtom(atom); //sortAtom(atom);

41
src/pbc.cu
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@ -33,6 +33,32 @@ extern "C" {
} }
__global__ void computeAtomsPbcUpdate(Atom a, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd){
const int i = blockIdx.x * blockDim.x + threadIdx.x;
Atom* atom = &a;
if( i >= atom->Nlocal ){
return;
}
if (atom_x(i) < 0.0) {
atom_x(i) += xprd;
} else if (atom_x(i) >= xprd) {
atom_x(i) -= xprd;
}
if (atom_y(i) < 0.0) {
atom_y(i) += yprd;
} else if (atom_y(i) >= yprd) {
atom_y(i) -= yprd;
}
if (atom_z(i) < 0.0) {
atom_z(i) += zprd;
} else if (atom_z(i) >= zprd) {
atom_z(i) -= zprd;
}
}
__global__ void computePbcUpdate(Atom a, int* PBCx, int* PBCy, int* PBCz, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd){ __global__ void computePbcUpdate(Atom a, int* PBCx, int* PBCy, int* PBCz, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd){
const int i = blockIdx.x * blockDim.x + threadIdx.x; const int i = blockIdx.x * blockDim.x + threadIdx.x;
const int Nghost = a.Nghost; const int Nghost = a.Nghost;
@ -163,6 +189,21 @@ void updateAtomsPbc(Atom *atom, Parameter *param) {
} }
} }
void updateAtomsPbc_cuda(Atom* atom, Parameter* param, Atom* c_atom, const int num_threads_per_block){
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
const int num_blocks = ceil((float)atom->Nlocal / (float)num_threads_per_block);
/*void computeAtomsPbcUpdate(Atom a, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd)*/
computeAtomsPbcUpdate<<<num_blocks, num_threads_per_block>>>(*c_atom, xprd, yprd, zprd);
checkCUDAError( "PeekAtLastError UpdateAtomsPbc", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync UpdateAtomsPbc", cudaDeviceSynchronize() );
checkCUDAError( "updateAtomsPbc position memcpy back", cudaMemcpy(atom->x, c_atom->x, sizeof(MD_FLOAT) * atom->Nlocal * 3, cudaMemcpyDeviceToHost) );
}
/* setup periodic boundary conditions by /* setup periodic boundary conditions by
* defining ghost atoms around domain * defining ghost atoms around domain
* only creates mapping and coordinate corrections * only creates mapping and coordinate corrections