deep copy of structs to and from device memory - cuda

Question

I am having trouble with the deep copy of an array of structs with dynamically allocated member variables in this cuda code. I think it is occurring because &deviceHistogram points to an address on the host instead of an address on the device. I tried making an intermediate pointer variable as in here, but that did not work; how do I properly copy this entire array of structs so I can modify it from the makeHistogram function?
#include <stdlib.h>
#include <stdio.h>
#include "cuda.h"
typedef struct histogramBin {
int* items;
int count;
} histogramBin;
__host__ __device__ void outputHistogram(histogramBin* histogram, int size) {
for (int i = 0; i < size; i++) {
printf("%d: ", i);
if (!histogram[i].count) {
printf("EMPTY");
} else {
for (int j = 0; j < histogram[i].count; j++) {
printf("%d ", histogram[i].items[j]);
}
}
printf("\n");
}
}
// This function embeds PTX code of CUDA to extract bit field from x.
__device__ uint bfe(uint x, uint start, uint nbits) {
uint bits;
asm("bfe.u32 %0, %1, %2, %3;"
: "=r"(bits)
: "r"(x), "r"(start), "r"(nbits));
return bits;
}
__global__ void makeHistogram(histogramBin** histogram, int* rH, int rSize, int bit) {
for (int r = 0; r < rSize; r++) {
int thisBin = bfe(rH[r], bit, 1);
int position = (*histogram)[thisBin].count; // **** out of memory access here****
(*histogram)[thisBin].items[position] = rH[r];
(*histogram)[thisBin].count++;
}
}
void histogramDriver(histogramBin* histogram, int* rH, int rSize, int bit) {
int n = 8;
int* deviceRH;
histogramBin* deviceHistogram;
cudaMalloc((void**)&deviceRH, rSize * sizeof(int));
cudaMemcpy(deviceRH, rH, rSize * sizeof(int), cudaMemcpyHostToDevice);
cudaMalloc((void**)&deviceHistogram, n * sizeof(histogramBin));
cudaMemcpy(deviceHistogram, histogram, n * sizeof(histogramBin), cudaMemcpyHostToDevice);
int* tempData[n];
for (int i = 0; i < n; i++) {
cudaMalloc(&(tempData[i]), rSize * sizeof(int));
}
for (int i = 0; i < n; i++) {
cudaMemcpy(&(deviceHistogram[i].items), &(tempData[i]), sizeof(int*), cudaMemcpyHostToDevice);
}
for (int i = 0; i < n; i++) {
cudaMemcpy(tempData[i], histogram[i].items, rSize * sizeof(int), cudaMemcpyHostToDevice);
}
makeHistogram<<<1, 1>>>(&deviceHistogram, deviceRH, rSize, bit);
cudaDeviceSynchronize();
}
int main(){
int rSize = 5;
int rH[rSize] = {1, 2, 3, 4, 5};
histogramBin * histogram = (histogramBin*)malloc(sizeof(histogramBin) * 8);
for(int i = 0; i < 8; i++){
histogram[i].items = (int*)calloc(sizeof(int), rSize);
histogram[i].count = 0;
}
histogramDriver(histogram, rH, rSize, 0);
return 0;
}
Once it has been copied properly to the device, how do I get it back on the host? For example, if I call outputHistogram(histogram, 5); from inside makeHistogram, I see the following:
0: 2 4
1: 1 3 5
2: EMPTY
3: EMPTY
4: EMPTY
5: EMPTY
6: EMPTY
7: EMPTY
Which is the output I am expecting.
When I call outputHistogram(histogram, 8) from histogramDriver (after the cudaDeviceSynchronize()) I see the following:
0: EMPTY
1: EMPTY
2: EMPTY
3: EMPTY
4: EMPTY
5: EMPTY
6: EMPTY
7: EMPTY
Clearly I am not properly copying the values back from the device to the host.
I have tried copying by doing the reverse procedure from the one in histogramDriver:
for(int i = 0; i < n; i++){
cudaMemcpy(&(tempData[i]), &(deviceHistogram[i].items), sizeof(int*), cudaMemcpyDeviceToHost);
}
for (int i = 0; i < n; i++) {
cudaMemcpy(histogram[i].items, tempData[i], rSize * sizeof(int), cudaMemcpyDeviceToHost);
}
But the output from the outputHistogram call in histogramDriver remains unchanged.

Answer 1

As #talonmies indicated, the biggest problem here is the design of your kernel. There is no reason/need to use a double-pointer for histogram (and indeed, the first iteration of the code you posted did not have that in the kernel prototype, although it was incomplete).
By removing the double-pointer aspect, your code runs without any runtime errors.
#include <stdlib.h>
#include <stdio.h>
#include "cuda.h"
typedef struct histogramBin {
int* items;
int count;
} histogramBin;
// This function embeds PTX code of CUDA to extract bit field from x.
__device__ uint bfe(uint x, uint start, uint nbits) {
uint bits;
asm("bfe.u32 %0, %1, %2, %3;"
: "=r"(bits)
: "r"(x), "r"(start), "r"(nbits));
return bits;
}
__global__ void makeHistogram(histogramBin* histogram, int* rH, int rSize, int bit) {
for (int r = 0; r < rSize; r++) {
int thisBin = bfe(rH[r], bit, 1);
int position = histogram[thisBin].count;
histogram[thisBin].items[position] = rH[r];
histogram[thisBin].count++;
}
}
void histogramDriver(histogramBin* histogram, int* rH, int rSize, int bit) {
int n = 8;
int* deviceRH;
histogramBin* deviceHistogram;
cudaMalloc((void**)&deviceRH, rSize * sizeof(int));
cudaMemcpy(deviceRH, rH, rSize * sizeof(int), cudaMemcpyHostToDevice);
cudaMalloc((void**)&deviceHistogram, n * sizeof(histogramBin));
cudaMemcpy(deviceHistogram, histogram, n * sizeof(histogramBin), cudaMemcpyHostToDevice);
int* tempData[n];
for (int i = 0; i < n; i++) {
cudaMalloc(&(tempData[i]), rSize * sizeof(int));
}
for (int i = 0; i < n; i++) {
cudaMemcpy(&(deviceHistogram[i].items), &(tempData[i]), sizeof(int*), cudaMemcpyHostToDevice);
}
for (int i = 0; i < n; i++) {
cudaMemcpy(tempData[i], histogram[i].items, rSize * sizeof(int), cudaMemcpyHostToDevice);
}
makeHistogram<<<1, 1>>>(deviceHistogram, deviceRH, rSize, bit);
cudaDeviceSynchronize();
}
int main(){
const int rSize = 5;
int rH[rSize] = {1, 2, 3, 4, 5};
histogramBin * histogram = (histogramBin*)malloc(sizeof(histogramBin) * 8);
for(int i = 0; i < 8; i++){
histogram[i].items = (int*)calloc(sizeof(int), rSize);
histogram[i].count = 0;
}
histogramDriver(histogram, rH, rSize, 0);
return 0;
}
$ nvcc t1452.cu -o t1452
$ cuda-memcheck ./t1452
========= CUDA-MEMCHECK
========= ERROR SUMMARY: 0 errors
$
Note that the only changes here are to the kernel code itself, plus removal of the ampersand on kernel call, plus I added const to the definition of rSize to get things to compile.
I have no idea if it produces correct output, because you've included no way to inspect the output, nor indicated what you expect the output to be. If you are interested in that, those would be good things to include in your MVE.