c - How to use MPI to transfer a custom struct with a dynamic array？

Question

There is a simple example to describe my question. I have a custom struct which contains a dynamic array

struct my_data_type {
    int c;
    int d[];
};

and the root process (process 0) has an array of such struct nums[4].

I want to send chunks of the array to different processes (for example, 2 processes) via MPI_Scatter. The main problem here is that I want this array d[] to be dynamic.

The main code is the following:

int main(int argc, char* argv[]) {

    MPI_Init(NULL, NULL);

    int my_size; MPI_Comm_size(MPI_COMM_WORLD, &my_size);
    int my_rank; MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);

    int len = 2; //example: the dynamic array d contains len=2 elements
    my_data_type *nums //nums[4]
        = (my_data_type*)malloc((sizeof(my_data_type) + sizeof(int) * len) * 4);
    my_data_type *sub_nums //sub_nums[2]
        = (my_data_type*)malloc((sizeof(my_data_type) + sizeof(int) * len) * 2);

    if (my_rank == 0) { //just some examples
        nums[0].c = 0; nums[1].c = 1; nums[2].c = 2; nums[3].c = 3;
        nums[0].d[0] = 10; nums[1].d[0] = 11; nums[2].d[0] = 12; nums[3].d[0] = 13;
        nums[0].d[1] = 14; nums[1].d[1] = 15; nums[2].d[1] = 16; nums[3].d[1] = 17;
    }

    MPI_Datatype mpi_data_type; //new datatype
    int blocklens[2];
    MPI_Datatype old_types[2];
    MPI_Aint indices[2];

    blocklens[0] = 1; blocklens[1] = len;
    old_types[0] = MPI_INT; old_types[1] = MPI_INT;
    MPI_Address(&nums[0].c, &indices[0]);
    MPI_Address(&nums[0].d[0], &indices[1]);
    indices[1] = indices[1] - indices[0];
    indices[0] = 0;

    MPI_Type_create_struct(2, blocklens, indices, old_types, &mpi_data_type);
    MPI_Type_commit(&mpi_data_type);

    MPI_Scatter(nums, 2, mpi_data_type,
                sub_nums, 2, mpi_data_type,
                0, MPI_COMM_WORLD);

    cout << "rank " << my_rank << ": " << endl;
    cout << "c: " << sub_nums[0].c << ", " << sub_nums[1].c << endl;
    cout << "d: " << sub_nums[0].d[0] << ", " << sub_nums[0].d[1] << ", ";
    cout << sub_nums[1].d[0] << ", " << sub_nums[1].d[1] << endl;

    MPI_Finalize();

    return 0;
}

If I change the int d[]; into int d[2]; in the definition of struct my_data_type, I will certainly get the expected results like

rank 0: 
c: 0, 1
d: 10, 14, 11, 15
rank 1: 
c: 2, 3
d: 12, 16, 13, 17

But if not, the results are the following:

rank 0: 
c: 0, 10
d: 10, 14, 14, 15
rank 1: 
c: 33, 0
d: 0, 0, 0, 1

As you can see, I know the problem is about the dynamic array, but I cannot use a static one in my project. So how can I change my code above to get the expected results?

标签： carraysstructmpi

Answer 1

您的基本问题不是 mpi，而是使用具有灵活数组成员的 struct 数组。这是一个示例程序来说明问题

#include <assert.h>
#include <stdlib.h>
#include <stdint.h>

typedef struct s s;
struct s
{
    int c;
    int d[];
};

int main(int argc, char* argv[])
{
    assert(sizeof(s) == sizeof(int));

    int len = 4;
    s* okay = malloc(sizeof(*okay) + sizeof(int)*len);

    intptr_t true_size = (intptr_t)&okay->d[len] -(intptr_t)(okay);
    assert(true_size == ((len+1)*sizeof(int)));

    int nbad = 6;
    s* bad = malloc((sizeof(*bad) + sizeof(int)*len)*nbad);


    intptr_t bad_size = (intptr_t)&bad[1] -(intptr_t)&bad[0];

    /* this size mismatch means arrays of `s` do not do what you think they do */
    assert(bad_size != true_size);
    assert(bad_size == sizeof(int));

    assert((char*)&bad[1] == (char*)&bad[0].d[0]);
    assert((char*)&bad[2] == (char*)&bad[0].d[1]);
    assert((char*)&bad[3] == (char*)&bad[0].d[2]);

    assert((char*)&bad[1].d[0] == (char*)&bad[0].d[1]);
    assert((char*)&bad[2].d[0] == (char*)&bad[0].d[2]);
    assert((char*)&bad[3].d[0] == (char*)&bad[0].d[3]);
}

要处理具有灵活数组成员的结构数组，您需要手动计算用于索引的内存偏移量，而不是依赖编译器。所以你可以像这样定义一个辅助函数：

s* s_index(const s* a, int len, int index)
{
    uintptr_t true_size = sizeof(*a) + len*sizeof(int);
    return (s*)((char*)a + index * true_size);
}

然后用于s_index访问所需的数组成员，而不是bad[0],bad[1]构造：

s* first = s_index(bad, len, 0);
s* second = s_index(bad, len, 1);
assert((char*)&first->d[len] == (char *)second);