我是C和MPI的新手。
我有下面的代码用于MPI。
#include "RabinKarp.c"
#include <stdio.h>
#include <stdlib.h>
#include<string.h>
#include<math.h>
#include </usr/include/mpi/mpi.h>
typedef struct {
int lowerOffset;
int upperOffset;
int processorNumber;
} patternPartitioning;
int rank;
FILE *fp;
char* filename = "/home/rohit/Downloads/10_seqs_2000_3000_bp.fasta";
int n = 0;
int d = 0;
//number of processors
int k, i = 0, lower_limit, upper_limit;
int main(int argc, char** argv) {
char* pattern= "taaat";
patternPartitioning partition[k];
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &k);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
fp = fopen(filename, "rb");
if (fp != '\0') {
fseek(fp, 0L, SEEK_END);
n = ftell(fp);
fseek(fp, 0L, SEEK_SET);
}
//Do for Master Processor
if(rank ==0){
int m = strlen(pattern);
printf("pattern length is %d \n", m);
d = (int)(n - m + 1) / k;
for (i = 0; i <= k - 2; i++) {
lower_limit = round(i * d);
upper_limit = round((i + 1) * d) + m - 1;
partition->lowerOffset = lower_limit;
partition->upperOffset = upper_limit;
partition->processorNumber = i+1;
// k-2 times calculate the limits like this
printf(" the lower limit is %d and upper limit is%d\n",
partition->lowerOffset, partition->upperOffset);
int mpi_send_block[2];
mpi_send_block[0]= lower_limit;
mpi_send_block[1] = upper_limit;
MPI_Send(mpi_send_block, 2, MPI_INT, i+1, i+1, MPI_COMM_WORLD);
//int MPI_Send(void *buf, int count, MPI_Datatype dtype, int dest, int tag, MPI_Comm comm);
}
// for the last processor calculate the index here
lower_limit = round((k - 1) * d);
upper_limit = n;
partition->lowerOffset = lower_limit;
partition->upperOffset = n;
partition->processorNumber = k;
printf("Processor : %d : has start : %d : and end : %d :\n",rank,partition->lowerOffset,partition->upperOffset);
//perform the search here
int size = partition->upperOffset-partition->lowerOffset;
char *text = (char*) malloc (size);
fseek(fp,partition->lowerOffset , SEEK_SET);
fread(&text, sizeof(char), size, fp);
printf("read in rank0");
fputs(text,stdout);
int number =0;
fputs(text,stdout);
fputs(pattern,stdout);
number = rabincarp(text,pattern);
for (i = 0; i <= k - 2; i++) {
int res[1];
res[0]=0;
MPI_Status status;
// MPI_Recv(res, 1, MPI_INT, i+1, i+1, MPI_COMM_WORLD, &status);
// number = number + res[0];
}
printf("\n\ntotal number of result found:%d\n", number);
} else {
patternPartitioning mypartition;
MPI_Status status;
int number[1];
int mpi_recv_block[2];
MPI_Recv(mpi_recv_block, 2, MPI_INT, 0, rank, MPI_COMM_WORLD,
&status);
printf("Processor : %d : has start : %d : and end : %d :\n",rank,mpi_recv_block[0],mpi_recv_block[1]);
//perform the search here
int size = mpi_recv_block[1]-mpi_recv_block[0];
char *text = (char*) malloc (size);
fseek(fp,mpi_recv_block[0] , SEEK_SET);
fread(&text, sizeof(char), size, fp);
printf("read in rank1");
// fread(text,size,size,fp);
printf("length of text segment by proc: %d is %d",rank,(int)strlen(text));
number[0] = rabincarp(text,pattern);
//MPI_Send(number, 1, MPI_INT, 0, rank, MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
fclose(fp);
return (EXIT_SUCCESS);
}
如果运行(mpirun-np 2 pnew),则会出现以下错误:
[localhost:03265] *** Process received signal ***
[localhost:03265] *** Process received signal ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 3265 on node localhost exited on signal 7 (Bus error).
所以如果我删除fread()语句,就不会得到错误。。有人能告诉我我缺了什么吗?
最佳答案
char *text = (char*) malloc (size);
fseek(fp,partition->lowerOffset , SEEK_SET);
fread(&text, sizeof(char), size, fp);
fread
的文档说明“函数从fread()
指向的流中读取nmemb
个字节长的数据元素,并将它们存储在size
指定的位置。”因为
stream
是aptr
,text
是achar *
的地址。这将没有足够的空间来保存你正在读取的数据。您要传递&text
您分配的内存的地址,而不是保存该地址的变量的地址!(因此删除char *
)关于c - MPI中的fread()给出信号7总线错误,我们在Stack Overflow上找到一个类似的问题:https://stackoverflow.com/questions/7744824/