MPI: Distributing segments of large file does not speedup execution - c

Question

I have a large bioinformatics file (fasta), and I am using MPI to open the file at specific regions depending on the current program's ID. Then, I transcribe the amino acid sequence into their corresponding proteins.
#include <mpi.h>
int main(int argc, char* argv[]){
MPI_File in;
int id;
int p;
long buffersize = 3000000000/p;
MPI_Offset fileStart = buffersize * id;
char* nucleotides = (char*)malloc(buffersize);
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &id);
MPI_Comm_size(MPI_COMM_WORLD, &p);
MPI_File_open(MPI_COMM_WORLD, argv[1], MPI_MODE_RDONLY, MPI_INFO_NULL, &in);
MPI_File_read_at(in, fileStart, nucleotides, buffersize, MPI_CHAR, MPI_STATUS_IGNORE);
/* Calculations */
/* Write result */
MPI_File_close(&in);
free(nucleotides);
MPI_Finalize();
return 0;
}
I expect a speedup correlated with number of machines running the algorithm. However, I observe running my applications across multiple machines does not change execution time. Execution time appears to be independent of number of machines listed in my hostfile.
Any ideas how to get the expected behavior of more machines decreasing the read time?

Answer 1

To turn the comments into an answer:
Turn this
#include <mpi.h>
int main(int argc, char* argv[]){
MPI_File in;
int id;
int p;
//you are using p uninitialized here!!!
long buffersize = 3000000000/p;
//same applies to id
MPI_Offset fileStart = buffersize * id;
char* nucleotides = (char*)malloc(buffersize);
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &id);
MPI_Comm_size(MPI_COMM_WORLD, &p);
MPI_File_open(MPI_COMM_WORLD, argv[1], MPI_MODE_RDONLY, MPI_INFO_NULL, &in);
MPI_File_read_at(in, fileStart, nucleotides, buffersize, MPI_CHAR, MPI_STATUS_IGNORE);
/* Calculations */
/* Write result */
MPI_File_close(&in);
free(nucleotides);
MPI_Finalize();
return 0;
}
into this:
#include <mpi.h>
int main(int argc, char* argv[]){
MPI_File in;
MPI_Init(&argc, &argv);
int id;
int p;
MPI_Comm_rank(MPI_COMM_WORLD, &id);
MPI_Comm_size(MPI_COMM_WORLD, &p);
long buffersize = 3000000000/p;
MPI_Offset fileStart = buffersize * id;
char* nucleotides = (char*)malloc(buffersize);
MPI_File_open(MPI_COMM_WORLD, argv[1], MPI_MODE_RDONLY, MPI_INFO_NULL, &in);
MPI_File_read_at(in, fileStart, nucleotides, buffersize, MPI_CHAR, MPI_STATUS_IGNORE);
/* Calculations */
/* Write result */
MPI_File_close(&in);
free(nucleotides);
MPI_Finalize();
return 0;
}
No guarantee about whether the rest will work above.
I would highly recommend to make yourself comfortable with C programming before starting to write MPI code because you might end up lost. MPI issues are difficult to debug.