Tutorial — MPI for Python 3.1.4 documentation

# 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

## 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()

## CUDA-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)
      assert hasattr(sendbuf, '__cuda_array_interface__')
      assert hasattr(recvbuf, '__cuda_array_interface__')
      cp.cuda.get_current_stream().synchronize()
      comm.Allreduce(sendbuf, recvbuf)

      assert cp.allclose(recvbuf, sendbuf*size)

## One-Sided Communications

- 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

- Try it in the Python prompt:

      >>> from mpi4py import MPI
      >>> import helloworld
      >>> fcomm = MPI.COMM_WORLD.py2f()
      >>> helloworld.sayhello(fcomm)
      Hello, World! I am process 0 of 1.