Only malloc once at the beginning plus measurement csv
This commit is contained in:
Maximilian Gaul
parent
134e3f4b78
commit
0ea0587442
55
src/force.cu
55
src/force.cu
@ -98,7 +98,11 @@ __global__ void calc_force(
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extern "C" {
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bool initialized = false;
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Atom c_atom;
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double computeForce(
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bool reneighbourHappenend,
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Parameter *param,
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Atom *atom,
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Neighbor *neighbor
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@ -125,12 +129,11 @@ double computeForce(
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const char *num_threads_env = getenv("NUM_THREADS");
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int num_threads = 0;
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if(num_threads_env == nullptr)
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num_threads = 2;
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num_threads = 32;
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else {
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num_threads = atoi(num_threads_env);
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}
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Atom c_atom;
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c_atom.Natoms = atom->Natoms;
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c_atom.Nlocal = atom->Nlocal;
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c_atom.Nghost = atom->Nghost;
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@ -140,67 +143,55 @@ double computeForce(
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/*
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int nDevices;
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cudaGetDeviceCount(&nDevices);
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size_t free, total;
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for(int i = 0; i < nDevices; ++i) {
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cudaMemGetInfo( &free, &total );
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cudaDeviceProp prop;
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cudaGetDeviceProperties(&prop, i);
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printf("DEVICE %d/%d NAME: %s\r\n", i + 1, nDevices, prop.name);
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printf("DEVICE %d/%d NAME: %s\r\n with %ld MB/%ld MB memory used", i + 1, nDevices, prop.name, free / 1024 / 1024, total / 1024 / 1024);
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}
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*/
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// Choose GPU where you want to execute code on
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// It is possible to execute the same kernel on multiple GPUs but you have to copy the data multiple times
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// Executing `cudaSetDevice(N)` before cudaMalloc / cudaMemcpy / calc_force <<< >>> will set the GPU accordingly
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*/
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// HINT: Run with cuda-memcheck ./MDBench-NVCC in case of error
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// HINT: Only works for data layout = AOS!!!
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checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
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if(!initialized) {
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checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
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checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.fy malloc", cudaMalloc((void**)&(c_atom.fy), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.fz malloc", cudaMalloc((void**)&(c_atom.fz), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.type malloc", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) );
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checkCUDAError( "c_atom.epsilon malloc", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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checkCUDAError( "c_atom.sigma6 malloc", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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checkCUDAError( "c_atom.cutforcesq malloc", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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initialized = true;
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}
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checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.fx memcpy", cudaMemcpy(c_atom.fx, fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.fy malloc", cudaMalloc((void**)&(c_atom.fy), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.fy memcpy", cudaMemcpy(c_atom.fy, fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.fz malloc", cudaMalloc((void**)&(c_atom.fz), sizeof(MD_FLOAT) * Nlocal) );
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checkCUDAError( "c_atom.fz memcpy", cudaMemcpy(c_atom.fz, fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.type malloc", cudaMalloc((void**)&(c_atom.type), sizeof(int) * atom->Nmax) );
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checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.epsilon malloc", cudaMalloc((void**)&(c_atom.epsilon), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.sigma6 malloc", cudaMalloc((void**)&(c_atom.sigma6), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
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checkCUDAError( "c_atom.cutforcesq malloc", cudaMalloc((void**)&(c_atom.cutforcesq), sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes) );
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checkCUDAError( "c_atom.cutforcesq memcpy", cudaMemcpy(c_atom.cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
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// double start_memory_bandwidth = getTimeStamp();
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int *c_neighs;
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checkCUDAError( "c_neighs malloc", cudaMalloc((void**)&c_neighs, sizeof(int) * Nlocal * neighbor->maxneighs) );
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checkCUDAError( "c_neighs memcpy", cudaMemcpy(c_neighs, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
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/*
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double end_memory_bandwidth = getTimeStamp();
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double memory_bandwith_time = (end_memory_bandwidth - start_memory_bandwidth);
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const unsigned long bytes = sizeof(int) * Nlocal * neighbor->maxneighs;
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const double gb_per_second = ((double)bytes / memory_bandwith_time) / 1024.0 / 1024.0 / 1024.0;
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printf("Data transfer of %lu bytes took %fs => %f GB/s\r\n", bytes, memory_bandwith_time, gb_per_second);
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*/
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int *c_neigh_numneigh;
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checkCUDAError( "c_neigh_numneigh malloc", cudaMalloc((void**)&c_neigh_numneigh, sizeof(int) * Nlocal) );
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checkCUDAError( "c_neigh_numneigh memcpy", cudaMemcpy(c_neigh_numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) );
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const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
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const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
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// printf("Distribution size: %d\r\n%d Blocks with each %d threads\r\n", Nlocal, num_blocks, num_threads_per_block);
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double S = getTimeStamp();
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LIKWID_MARKER_START("force");
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@ -215,12 +206,14 @@ double computeForce(
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cudaMemcpy(atom->fy, c_atom.fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
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cudaMemcpy(atom->fz, c_atom.fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
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/*
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cudaFree(c_atom.x);
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cudaFree(c_atom.fx); cudaFree(c_atom.fy); cudaFree(c_atom.fz);
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cudaFree(c_atom.type);
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cudaFree(c_atom.epsilon);
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cudaFree(c_atom.sigma6);
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cudaFree(c_atom.cutforcesq);
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*/
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cudaFree(c_neighs); cudaFree(c_neigh_numneigh);
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15
src/main.c
15
src/main.c
@ -23,6 +23,7 @@
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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include <stdbool.h>
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#include <unistd.h>
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#include <limits.h>
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#include <math.h>
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@ -44,7 +45,7 @@
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#define HLINE "----------------------------------------------------------------------------\n"
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extern double computeForce(Parameter*, Atom*, Neighbor*);
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extern double computeForce(bool, Parameter*, Atom*, Neighbor*);
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extern double computeForceTracing(Parameter*, Atom*, Neighbor*, Stats*, int, int);
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extern double computeForceEam(Eam* eam, Parameter*, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep);
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@ -262,7 +263,7 @@ int main(int argc, char** argv)
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#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
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computeForceTracing(¶m, &atom, &neighbor, &stats, 1, 0);
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#else
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computeForce(¶m, &atom, &neighbor);
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computeForce(true, ¶m, &atom, &neighbor);
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#endif
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}
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@ -277,10 +278,12 @@ int main(int argc, char** argv)
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for(int n = 0; n < param.ntimes; n++) {
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initialIntegrate(¶m, &atom);
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if((n + 1) % param.every) {
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updatePbc(&atom, ¶m);
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} else {
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const bool doReneighbour = (n + 1) % param.every == 0;
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if(doReneighbour) {
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timer[NEIGH] += reneighbour(¶m, &atom, &neighbor);
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} else {
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updatePbc(&atom, ¶m);
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}
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if(param.force_field == FF_EAM) {
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@ -289,7 +292,7 @@ int main(int argc, char** argv)
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#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
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timer[FORCE] += computeForceTracing(¶m, &atom, &neighbor, &stats, 0, n + 1);
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#else
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timer[FORCE] += computeForce(¶m, &atom, &neighbor);
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timer[FORCE] += computeForce(doReneighbour, ¶m, &atom, &neighbor);
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#endif
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}
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finalIntegrate(¶m, &atom);
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