Python: Sending discontinuous data with mpi4py

Question

I have a C-ordered matrix of dimensions (N,M)

mat = np.random.randn(N, M)

of which I want to send a column through a persistent MPI request to another node. However, using mpi4py,

sreq = MPI.COMM_WORLD.Send_Init((mat[:,idx], MPI.DOUBLE), send_id, tag)

fails on account of the slice being non-contiguous. Can someone suggest a way of going about this? I believe in C that MPI_Type_vector allows for one to specify a stride when creating a type. How can I accomplish this with mpi4py?

Answer 1

create a sendbuffer! look at this example:

  1 #!/usr/bin/python2
  2 # -*- coding: utf-8 -*-
  3
  4 from mpi4py import MPI
  5 import numpy as np
  6
  7 comm = MPI.COMM_WORLD
  8 rank = comm.Get_rank()
  9
 10 matrix = np.empty((5, 10), dtype='f')
 11 for y in xrange(len(matrix)):
 12     for x in xrange(len(matrix[0])):
 13         matrix[y,x] = rank * 10 + x * y
 14
 15 sendbuf = np.empty(5, dtype='f')
 16
 17 #column 1
 18 sendbuf[:] = matrix[:,1]
 19
 20 result = comm.gather(sendbuf, root=0)
 21
 22 if rank == 0:
 23     for res in result:
 24         print res

this will give you:

$ mpirun -np 4 column.py
[ 0.  1.  2.  3.  4.]
[ 10.  11.  12.  13.  14.]
[ 20.  21.  22.  23.  24.]
[ 30.  31.  32.  33.  34.]