Tutorial¶

Warning

Under construction. Contributions very welcome!

Tip

Rolf Rabenseifner at HLRS developed a comprehensive MPI-3.1/4.0 course with slides and a large set of exercises including solutions. This material is available online for self-study. The slides and exercises show the C, Fortran, and Python (mpi4py) interfaces. For performance reasons, most Python exercises use NumPy arrays and communication routines involving buffer-like objects.

Tip

Victor Eijkhout at TACC authored the book Parallel Programming for Science and Engineering. This book is available online in PDF and HTML formats. The book covers parallel programming with MPI and OpenMP in C/C++ and Fortran, and MPI in Python using mpi4py.

MPI for Python supports convenient, pickle-based communication of generic Python object as well as fast, near C-speed, direct array data communication of buffer-provider objects (e.g., NumPy arrays).

Communication of generic Python objects

You have to use methods with all-lowercase names, like Comm.send, Comm.recv, Comm.bcast, Comm.scatter, Comm.gather . An object to be sent is passed as a parameter to the communication call, and the received object is simply the return value.

The Comm.isend and Comm.irecv methods return Request instances; completion of these methods can be managed using the Request.test and Request.wait methods.

The Comm.recv and Comm.irecv methods may be passed a buffer object that can be repeatedly used to receive messages avoiding internal memory allocation. This buffer must be sufficiently large to accommodate the transmitted messages; hence, any buffer passed to Comm.recv or Comm.irecv must be at least as long as the pickled data transmitted to the receiver.

Collective calls like Comm.scatter, Comm.gather, Comm.allgather, Comm.alltoall expect a single value or a sequence of Comm.size elements at the root or all process. They return a single value, a list of Comm.size elements, or None.

Note

MPI for Python uses the highest protocol version available in the Python runtime (see the HIGHEST_PROTOCOL constant in the pickle module). The default protocol can be changed at import time by setting the MPI4PY_PICKLE_PROTOCOL environment variable, or at runtime by assigning a different value to the PROTOCOL attribute of the pickle object within the MPI module.
Communication of buffer-like objects

You have to use method names starting with an upper-case letter, like Comm.Send, Comm.Recv, Comm.Bcast, Comm.Scatter, Comm.Gather.

In general, buffer arguments to these calls must be explicitly specified by using a 2/3-list/tuple like [data, MPI.DOUBLE], or [data, count, MPI.DOUBLE] (the former one uses the byte-size of data and the extent of the MPI datatype to define count).

For vector collectives communication operations like Comm.Scatterv and Comm.Gatherv, buffer arguments are specified as [data, count, displ, datatype], where count and displ are sequences of integral values.

Automatic MPI datatype discovery for NumPy/GPU arrays and PEP-3118 buffers is supported, but limited to basic C types (all C/C99-native signed/unsigned integral types and single/double precision real/complex floating types) and availability of matching datatypes in the underlying MPI implementation. In this case, the buffer-provider object can be passed directly as a buffer argument, the count and MPI datatype will be inferred.

If mpi4py is built against a GPU-aware MPI implementation, GPU arrays can be passed to upper-case methods as long as they have either the __dlpack__ and __dlpack_device__ methods or the __cuda_array_interface__ attribute that are compliant with the respective standard specifications. Moreover, only C-contiguous or Fortran-contiguous GPU arrays are supported. It is important to note that GPU buffers must be fully ready before any MPI routines operate on them to avoid race conditions. This can be ensured by using the synchronization API of your array library. mpi4py does not have access to any GPU-specific functionality and thus cannot perform this operation automatically for users.

Running Python scripts with MPI¶

Most MPI programs can be run with the command mpiexec. In practice, running Python programs looks like:

$ mpiexec -n 4 python script.py

to run the program with 4 processors.

Point-to-Point Communication¶

Python objects (pickle under the hood):

from mpi4py import MPI

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

if rank == 0:
    data = {'a': 7, 'b': 3.14}
    comm.send(data, dest=1, tag=11)
elif rank == 1:
    data = comm.recv(source=0, tag=11)

Python objects with non-blocking communication:

from mpi4py import MPI

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

if rank == 0:
    data = {'a': 7, 'b': 3.14}
    req = comm.isend(data, dest=1, tag=11)
    req.wait()
elif rank == 1:
    req = comm.irecv(source=0, tag=11)
    data = req.wait()

NumPy arrays (the fast way!):

from mpi4py import MPI
import numpy

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

# passing MPI datatypes explicitly
if rank == 0:
    data = numpy.arange(1000, dtype='i')
    comm.Send([data, MPI.INT], dest=1, tag=77)
elif rank == 1:
    data = numpy.empty(1000, dtype='i')
    comm.Recv([data, MPI.INT], source=0, tag=77)

# automatic MPI datatype discovery
if rank == 0:
    data = numpy.arange(100, dtype=numpy.float64)
    comm.Send(data, dest=1, tag=13)
elif rank == 1:
    data = numpy.empty(100, dtype=numpy.float64)
    comm.Recv(data, source=0, tag=13)

Collective Communication¶

Broadcasting a Python dictionary:

from mpi4py import MPI

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

if rank == 0:
    data = {'key1' : [7, 2.72, 2+3j],
            'key2' : ( 'abc', 'xyz')}
else:
    data = None
data = comm.bcast(data, root=0)

Scattering Python objects:

from mpi4py import MPI

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

if rank == 0:
    data = [(i+1)**2 for i in range(size)]
else:
    data = None
data = comm.scatter(data, root=0)
assert data == (rank+1)**2

Gathering Python objects:

from mpi4py import MPI

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

data = (rank+1)**2
data = comm.gather(data, root=0)
if rank == 0:
    for i in range(size):
        assert data[i] == (i+1)**2
else:
    assert data is None

Broadcasting a NumPy array:

from mpi4py import MPI
import numpy as np

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

if rank == 0:
    data = np.arange(100, dtype='i')
else:
    data = np.empty(100, dtype='i')
comm.Bcast(data, root=0)
for i in range(100):
    assert data[i] == i

Scattering NumPy arrays:

from mpi4py import MPI
import numpy as np

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

sendbuf = None
if rank == 0:
    sendbuf = np.empty([size, 100], dtype='i')
    sendbuf.T[:,:] = range(size)
recvbuf = np.empty(100, dtype='i')
comm.Scatter(sendbuf, recvbuf, root=0)
assert np.allclose(recvbuf, rank)

Gathering NumPy arrays:

from mpi4py import MPI
import numpy as np

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

sendbuf = np.zeros(100, dtype='i') + rank
recvbuf = None
if rank == 0:
    recvbuf = np.empty([size, 100], dtype='i')
comm.Gather(sendbuf, recvbuf, root=0)
if rank == 0:
    for i in range(size):
        assert np.allclose(recvbuf[i,:], i)

Parallel matrix-vector product:

from mpi4py import MPI
import numpy

def matvec(comm, A, x):
    m = A.shape[0] # local rows
    p = comm.Get_size()
    xg = numpy.zeros(m*p, dtype='d')
    comm.Allgather([x,  MPI.DOUBLE],
                   [xg, MPI.DOUBLE])
    y = numpy.dot(A, xg)
    return y

Input/Output (MPI-IO)¶

Collective I/O with NumPy arrays:

from mpi4py import MPI
import numpy as np

amode = MPI.MODE_WRONLY|MPI.MODE_CREATE
comm = MPI.COMM_WORLD
fh = MPI.File.Open(comm, "./datafile.contig", amode)

buffer = np.empty(10, dtype=np.int)
buffer[:] = comm.Get_rank()

offset = comm.Get_rank()*buffer.nbytes
fh.Write_at_all(offset, buffer)

fh.Close()

Non-contiguous Collective I/O with NumPy arrays and datatypes:

from mpi4py import MPI
import numpy as np

comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()

amode = MPI.MODE_WRONLY|MPI.MODE_CREATE
fh = MPI.File.Open(comm, "./datafile.noncontig", amode)

item_count = 10

buffer = np.empty(item_count, dtype='i')
buffer[:] = rank

filetype = MPI.INT.Create_vector(item_count, 1, size)
filetype.Commit()

displacement = MPI.INT.Get_size()*rank
fh.Set_view(displacement, filetype=filetype)

fh.Write_all(buffer)
filetype.Free()
fh.Close()

Dynamic Process Management¶

Compute Pi - Master (or parent, or client) side:

#!/usr/bin/env python
from mpi4py import MPI
import numpy
import sys

comm = MPI.COMM_SELF.Spawn(sys.executable,
                           args=['cpi.py'],
                           maxprocs=5)

N = numpy.array(100, 'i')
comm.Bcast([N, MPI.INT], root=MPI.ROOT)
PI = numpy.array(0.0, 'd')
comm.Reduce(None, [PI, MPI.DOUBLE],
            op=MPI.SUM, root=MPI.ROOT)
print(PI)

comm.Disconnect()

Compute Pi - Worker (or child, or server) side:

#!/usr/bin/env python
from mpi4py import MPI
import numpy

comm = MPI.Comm.Get_parent()
size = comm.Get_size()
rank = comm.Get_rank()

N = numpy.array(0, dtype='i')
comm.Bcast([N, MPI.INT], root=0)
h = 1.0 / N; s = 0.0
for i in range(rank, N, size):
    x = h * (i + 0.5)
    s += 4.0 / (1.0 + x**2)
PI = numpy.array(s * h, dtype='d')
comm.Reduce([PI, MPI.DOUBLE], None,
            op=MPI.SUM, root=0)

comm.Disconnect()

GPU-aware MPI + Python GPU arrays¶

Reduce-to-all CuPy arrays:

from mpi4py import MPI
import cupy as cp

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

sendbuf = cp.arange(10, dtype='i')
recvbuf = cp.empty_like(sendbuf)
cp.cuda.get_current_stream().synchronize()
comm.Allreduce(sendbuf, recvbuf)

assert cp.allclose(recvbuf, sendbuf*size)

One-Sided Communication (RMA)¶

Read from (write to) the entire RMA window:

import numpy as np
from mpi4py import MPI
from mpi4py.util import dtlib

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

datatype = MPI.FLOAT
np_dtype = dtlib.to_numpy_dtype(datatype)
itemsize = datatype.Get_size()

N = 10
win_size = N * itemsize if rank == 0 else 0
win = MPI.Win.Allocate(win_size, comm=comm)

buf = np.empty(N, dtype=np_dtype)
if rank == 0:
    buf.fill(42)
    win.Lock(rank=0)
    win.Put(buf, target_rank=0)
    win.Unlock(rank=0)
    comm.Barrier()
else:
    comm.Barrier()
    win.Lock(rank=0)
    win.Get(buf, target_rank=0)
    win.Unlock(rank=0)
    assert np.all(buf == 42)

Accessing a part of the RMA window using the target argument, which is defined as (offset, count, datatype):

import numpy as np
from mpi4py import MPI
from mpi4py.util import dtlib

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

datatype = MPI.FLOAT
np_dtype = dtlib.to_numpy_dtype(datatype)
itemsize = datatype.Get_size()

N = comm.Get_size() + 1
win_size = N * itemsize if rank == 0 else 0
win = MPI.Win.Allocate(
    size=win_size,
    disp_unit=itemsize,
    comm=comm,
)
if rank == 0:
    mem = np.frombuffer(win, dtype=np_dtype)
    mem[:] = np.arange(len(mem), dtype=np_dtype)
comm.Barrier()

buf = np.zeros(3, dtype=np_dtype)
target = (rank, 2, datatype)
win.Lock(rank=0)
win.Get(buf, target_rank=0, target=target)
win.Unlock(rank=0)
assert np.all(buf == [rank, rank+1, 0])

Wrapping with SWIG¶

C source:

/* file: helloworld.c */
void sayhello(MPI_Comm comm)
{
  int size, rank;
  MPI_Comm_size(comm, &size);
  MPI_Comm_rank(comm, &rank);
  printf("Hello, World! "
         "I am process %d of %d.\n",
         rank, size);
}

SWIG interface file:

// file: helloworld.i
%module helloworld
%{
#include <mpi.h>
#include "helloworld.c"
}%

%include mpi4py/mpi4py.i
%mpi4py_typemap(Comm, MPI_Comm);
void sayhello(MPI_Comm comm);

Try it in the Python prompt:

>>> from mpi4py import MPI
>>> import helloworld
>>> helloworld.sayhello(MPI.COMM_WORLD)
Hello, World! I am process 0 of 1.

Wrapping with F2Py¶

Fortran 90 source:

! file: helloworld.f90
subroutine sayhello(comm)
  use mpi
  implicit none
  integer :: comm, rank, size, ierr
  call MPI_Comm_size(comm, size, ierr)
  call MPI_Comm_rank(comm, rank, ierr)
  print *, 'Hello, World! I am process ',rank,' of ',size,'.'
end subroutine sayhello

Compiling example using f2py

$ f2py -c --f90exec=mpif90 helloworld.f90 -m helloworld