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Replace hipMallocManaged with hipMalloc+hipMemcpy #326

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Replace hipMallocManaged with hipMalloc+hipMemcpy #326

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125 changes: 86 additions & 39 deletions src/nbnxm-hip/main.cu
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#include <chrono>
#include <iostream>
#include <hip/hip_runtime.h>
#include <cstring>
#include "vectypes.h"

typedef float2 Float2;
Expand Down Expand Up @@ -399,61 +400,83 @@ int main(int argc, char* argv[]) {
const dim3 blocks ( block_x, block_y, 1 );
const dim3 grids ( 1, 1, grid_z );

// Host buffers
Float4* h_xq = new Float4[NUM_ATOMS];
Float3* h_f = new Float3[NUM_ATOMS];
Float3* h_shiftVec = new Float3[45];
Float3* h_fShift = new Float3[45];
nbnxn_cj4_t* h_cj4 = new nbnxn_cj4_t[56881];
nbnxn_sci_t* h_sci = new nbnxn_sci_t[4806];
nbnxn_excl_t* h_excl = new nbnxn_excl_t[19205];
int* h_atomTypes = new int[NUM_ATOMS];
Float2* h_nbfp = new Float2[1024];

// Device buffers
Float4* a_xq;
hipMallocManaged(&a_xq, sizeof(Float4) * NUM_ATOMS);
hipMalloc(&a_xq, sizeof(Float4) * NUM_ATOMS);

Float3* a_f;
hipMallocManaged(&a_f, sizeof(Float3) * NUM_ATOMS);
hipMalloc(&a_f, sizeof(Float3) * NUM_ATOMS);

Float3* shiftVec;
hipMallocManaged(&shiftVec, sizeof(Float3) * 45);
hipMalloc(&shiftVec, sizeof(Float3) * 45);

Float3* fShift;
hipMallocManaged(&fShift, sizeof(Float3) * 45);
hipMalloc(&fShift, sizeof(Float3) * 45);

nbnxn_cj4_t* cj4;
hipMallocManaged(&cj4, sizeof(nbnxn_cj4_t) * 56881);
hipMalloc(&cj4, sizeof(nbnxn_cj4_t) * 56881);

nbnxn_sci_t* sci;
hipMallocManaged(&sci, sizeof(nbnxn_sci_t) * 4806);
hipMalloc(&sci, sizeof(nbnxn_sci_t) * 4806);

nbnxn_excl_t* excl;
hipMallocManaged(&excl, sizeof(nbnxn_excl_t) * 19205);
hipMalloc(&excl, sizeof(nbnxn_excl_t) * 19205);

int* atomTypes;
hipMallocManaged(&atomTypes, sizeof(int) * NUM_ATOMS);
hipMalloc(&atomTypes, sizeof(int) * NUM_ATOMS);

Float2* nbfp;
hipMallocManaged(&nbfp, sizeof(Float2) * 1024);
hipMalloc(&nbfp, sizeof(Float2) * 1024);

for (int i = 0; i < NUM_ATOMS; ++i) {
a_xq[i] = make_float4(1.0f, 0.5f, 0.25f, 0.125f);
h_xq[i] = make_float4(1.0f, 0.5f, 0.25f, 0.125f);
}
for (int i = 0; i < NUM_ATOMS; ++i) {
a_f[i] = Float3(1.0f, 0.5f, 0.25f);
h_f[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 45; ++i) {
shiftVec[i] = Float3(1.0f, 0.5f, 0.25f);
h_shiftVec[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 45; ++i) {
fShift[i] = Float3(1.0f, 0.5f, 0.25f);
h_fShift[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 56881; ++i) {
cj4[i] = get_cj4(i);
h_cj4[i] = get_cj4(i);
}
for (int i = 0; i < 4806; ++i) {
sci[i] = get_sci(i);
h_sci[i] = get_sci(i);
}
for (int i = 0; i < 19205; ++i) {
excl[i] = get_excl(i);
h_excl[i] = get_excl(i);
}
for (int i = 0; i < NUM_ATOMS; ++i) {
atomTypes[i] = (i % 2);
h_atomTypes[i] = (i % 2);
}
for (int i = 0; i < 1024; ++i) {
nbfp[i] = make_float2(0.5f, 0.25f);
h_nbfp[i] = make_float2(0.5f, 0.25f);
}

hipMemcpy(a_xq, h_xq, sizeof(Float4) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(a_f, h_f, sizeof(Float3) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(shiftVec, h_shiftVec, sizeof(Float3) * 45, hipMemcpyHostToDevice);
hipMemcpy(fShift, h_fShift, sizeof(Float3) * 45, hipMemcpyHostToDevice);
hipMemcpy(cj4, h_cj4, sizeof(nbnxn_cj4_t) * 56881, hipMemcpyHostToDevice);
hipMemcpy(sci, h_sci, sizeof(nbnxn_sci_t) * 4806, hipMemcpyHostToDevice);
hipMemcpy(excl, h_excl, sizeof(nbnxn_excl_t) * 19205, hipMemcpyHostToDevice);
hipMemcpy(atomTypes, h_atomTypes, sizeof(int) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(nbfp, h_nbfp, sizeof(Float2) * 1024, hipMemcpyHostToDevice);

// Warming-up
hipLaunchKernelGGL(nbnxmKernelTest, grids, blocks, 0, 0,
a_xq,
Expand Down Expand Up @@ -498,51 +521,63 @@ int main(int argc, char* argv[]) {
printf("Average kernel execution time (w/o shift): %f (us)\n", (time * 1e-3f) / repeat);

#ifdef DEBUG
hipMemcpy(h_f, a_f, sizeof(Float3) * NUM_ATOMS, hipMemcpyDeviceToHost);
hipMemcpy(h_fShift, fShift, sizeof(Float3) * 45, hipMemcpyDeviceToHost);
float f0 = 0, f1 = 0, f2 = 0;
for (int i = 0; i < NUM_ATOMS; ++i) {
f0 += a_f[i][0];
f1 += a_f[i][1];
f2 += a_f[i][2];
f0 += h_f[i][0];
f1 += h_f[i][1];
f2 += h_f[i][2];
}
printf("Checksum (a_f): %f %f %f\n", f0, f1, f2);

f0 = 0, f1 = 0, f2 = 0;
for (int i = 0; i < 45; ++i) {
f0 += fShift[i][0];
f1 += fShift[i][1];
f2 += fShift[i][2];
f0 += h_fShift[i][0];
f1 += h_fShift[i][1];
f2 += h_fShift[i][2];
}
printf("Checksum (fShift): %f %f %f\n", f0, f1, f2);
#endif

for (int i = 0; i < NUM_ATOMS; ++i) {
a_xq[i] = make_float4(1.0f, 0.5f, 0.25f, 0.125f);
h_xq[i] = make_float4(1.0f, 0.5f, 0.25f, 0.125f);
}
for (int i = 0; i < NUM_ATOMS; ++i) {
a_f[i] = Float3(1.0f, 0.5f, 0.25f);
h_f[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 45; ++i) {
shiftVec[i] = Float3(1.0f, 0.5f, 0.25f);
h_shiftVec[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 45; ++i) {
fShift[i] = Float3(1.0f, 0.5f, 0.25f);
h_fShift[i] = Float3(1.0f, 0.5f, 0.25f);
}
for (int i = 0; i < 56881; ++i) {
cj4[i] = get_cj4(i);
h_cj4[i] = get_cj4(i);
}
for (int i = 0; i < 4806; ++i) {
sci[i] = get_sci(i);
h_sci[i] = get_sci(i);
}
for (int i = 0; i < 19205; ++i) {
excl[i] = get_excl(i);
h_excl[i] = get_excl(i);
}
for (int i = 0; i < NUM_ATOMS; ++i) {
atomTypes[i] = (i % 2);
h_atomTypes[i] = (i % 2);
}
for (int i = 0; i < 1024; ++i) {
nbfp[i] = make_float2(0.5f, 0.25f);
h_nbfp[i] = make_float2(0.5f, 0.25f);
}

hipMemcpy(a_xq, h_xq, sizeof(Float4) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(a_f, h_f, sizeof(Float3) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(shiftVec, h_shiftVec, sizeof(Float3) * 45, hipMemcpyHostToDevice);
hipMemcpy(fShift, h_fShift, sizeof(Float3) * 45, hipMemcpyHostToDevice);
hipMemcpy(cj4, h_cj4, sizeof(nbnxn_cj4_t) * 56881, hipMemcpyHostToDevice);
hipMemcpy(sci, h_sci, sizeof(nbnxn_sci_t) * 4806, hipMemcpyHostToDevice);
hipMemcpy(excl, h_excl, sizeof(nbnxn_excl_t) * 19205, hipMemcpyHostToDevice);
hipMemcpy(atomTypes, h_atomTypes, sizeof(int) * NUM_ATOMS, hipMemcpyHostToDevice);
hipMemcpy(nbfp, h_nbfp, sizeof(Float2) * 1024, hipMemcpyHostToDevice);

start = std::chrono::steady_clock::now();

for (int i = 0; i < repeat; ++i) {
Expand All @@ -569,19 +604,21 @@ int main(int argc, char* argv[]) {
printf("Average kernel execution time (w/ shift): %f (us)\n", (time * 1e-3f) / repeat);

#ifdef DEBUG
hipMemcpy(h_f, a_f, sizeof(Float3) * NUM_ATOMS, hipMemcpyDeviceToHost);
hipMemcpy(h_fShift, fShift, sizeof(Float3) * 45, hipMemcpyDeviceToHost);
f0 = 0, f1 = 0, f2 = 0;
for (int i = 0; i < NUM_ATOMS; ++i) {
f0 += a_f[i][0];
f1 += a_f[i][1];
f2 += a_f[i][2];
f0 += h_f[i][0];
f1 += h_f[i][1];
f2 += h_f[i][2];
}
printf("Checksum (a_f): %f %f %f\n", f0, f1, f2);

f0 = 0, f1 = 0, f2 = 0;
for (int i = 0; i < 45; ++i) {
f0 += fShift[i][0];
f1 += fShift[i][1];
f2 += fShift[i][2];
f0 += h_fShift[i][0];
f1 += h_fShift[i][1];
f2 += h_fShift[i][2];
}
printf("Checksum (fShift): %f %f %f\n", f0, f1, f2);
#endif
Expand All @@ -596,5 +633,15 @@ int main(int argc, char* argv[]) {
hipFree(a_f);
hipFree(a_xq);

delete[] h_nbfp;
delete[] h_atomTypes;
delete[] h_excl;
delete[] h_sci;
delete[] h_cj4;
delete[] h_fShift;
delete[] h_shiftVec;
delete[] h_f;
delete[] h_xq;

return 0;
}