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Lecture Note

MPI for Python Part 1

  • University:

    Boston University
  • Course:

    MET CS 201 | Introduction to Programming
  • Academic year:

    2024

  • Views:

    350

    Pages:

    15

  • Author:

    Naomi Whitehead

MPI for Python Outline Communicators Point to Point Communication Collective Operations Compute Pi Mandelbrot Set Dynamic Process Management What is mpi4py? I I I Full-featured Python bindings for MPI. API based on the standard MPI-2 C++ bindings. Almost all MPI calls are supported. I I targeted to MPI-2 implementations. also works with MPI-1 implementations. Implementation Implemented with Cython I Code base far easier to write, maintain, and extend. I Faster than other solutions (mixed Python and C codes). I A pythonic API that runs at C speed ! Features – MPI-1 I Process groups and communication domains. I I I Point to point communication. I I I intracommunicators intercommunicators blocking (send/recv) nonblocking (isend/irecv + test/wait) Collective operations. I I I Synchronization (barrier) Communication (broadcast, scatter/gather) Global reductions (reduce, scan) Features – MPI-2 I Dynamic process management (spawn, connect/accept). I Parallel I/O (read/write). I One sided operations, a.k.a. RMA (put/get/accumulate). I Extended collective operations. Features – Python I Communication of Python objects. I I high level and very convenient, based in pickle serialization can be slow for large data (CPU and memory consuming) −→ pickle.dump() −→ send() ↓ ←− pickle.load() ←− recv() I Communication of array data (e.g. NumPy arrays). I I lower level, slightly more verbose very fast, almost C speed (for messages above 5-10 KB) message = [, (count, displ), datatype] Point to Point Throughput – Gigabit Ethernet 120 Throughput [MiB/s] 100 PingPong Pickle Buffer C 80 60 40 20 0 100 101 102 103 104 105 Array Size [Bytes] 106 107 Throughput [MiB/s] Point to Point Throughput – Shared Memory 4500 4000 3500 3000 2500 2000 1500 1000 500 0 100 PingPong Pickle Buffer C 101 102 103 104 105 Array Size [Bytes] 106 107 Features – IPython Integration with IPython enables MPI to be used interactively. I Start engines with MPI enabled $ ipcluster mpiexec -n 16 --mpi=mpi4py I Connect to the engines $ ipython In [1]: from IPython.kernel import client In [2]: mec = client.MultiEngineClient() In [3]: mec.activate() I Execute commands using %px In [4]: %px from mpi4py import MPI In [5]: %px print(MPI.Get_processor_name()) Features – Interoperability Good support for wrapping other MPI-based codes. I You can use Cython (cimport statement). I You can use SWIG (typemaps provided). I You can use F2Py (py2f()/f2py() methods). I You can use Boost::Python or hand-written C extensions. mpi4py will allow you to use virtually any MPI based C/C++/Fortran code from Python. Hello World! 1 from mpi4py import MPI 2 3 4 5 rank = MPI.COMM_WORLD.Get_rank() size = MPI.COMM_WORLD.Get_size() name = MPI.Get_processor_name() 6 7 8 9 print ("Hello, World! " "I am process %d of %d on %s" % (rank, size, name)) Hello World! – Wrapping with SWIG C source 1 2 3 4 5 6 7 8 9 10 11 /* 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 1 2 3 4 5 6 // file: helloworld.i %module helloworld %{ # include # include "helloworld.c" }% 7 8 9 %include mpi4py/mpi4py.i %mpi4py_typemap(Comm, MPI_Comm); 10 11 void sayhello(MPI_Comm comm); At the Python prompt . . . >>> from mpi4py import MPI >>> import helloworld >>> helloworld.sayhello(MPI.COMM_WORLD) Hello, World! I am process 0 of 1. Hello World! – Wrapping with Boost.Python 1 2 3 4 // file: helloworld.cxx # include # include using namespace boost::python; 5 6 7 8 9 10 11 12 # include "helloworld.c" static void wrap_sayhello(object py_comm) { PyObject* py_obj = py_comm.ptr(); MPI_Comm *comm_p = PyMPIComm_Get(py_obj); if (comm_p == NULL) throw_error_already_set(); sayhello(*comm_p); } 13 14 15 16 17 BOOST_PYTHON_MODULE(helloworld) { if (import_mpi4py() < 0) return; def("sayhello", wrap_sayhello); } Hello World! – Wrapping with F2Py Fortran 90 source 1 2 3 4 5 6 7 8 9 ! 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 At 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.

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MPI for Python Part 1

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