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1 .. _parallelmpi:
1 .. _parallelmpi:
2
2
3 =======================
3 =======================
4 Using MPI with IPython
4 Using MPI with IPython
5 =======================
5 =======================
6
6
7 Often, a parallel algorithm will require moving data between the engines. One
7 Often, a parallel algorithm will require moving data between the engines. One
8 way of accomplishing this is by doing a pull and then a push using the
8 way of accomplishing this is by doing a pull and then a push using the
9 multiengine client. However, this will be slow as all the data has to go
9 multiengine client. However, this will be slow as all the data has to go
10 through the controller to the client and then back through the controller, to
10 through the controller to the client and then back through the controller, to
11 its final destination.
11 its final destination.
12
12
13 A much better way of moving data between engines is to use a message passing
13 A much better way of moving data between engines is to use a message passing
14 library, such as the Message Passing Interface (MPI) [MPI]_. IPython's
14 library, such as the Message Passing Interface (MPI) [MPI]_. IPython's
15 parallel computing architecture has been designed from the ground up to
15 parallel computing architecture has been designed from the ground up to
16 integrate with MPI. This document describes how to use MPI with IPython.
16 integrate with MPI. This document describes how to use MPI with IPython.
17
17
18 Additional installation requirements
18 Additional installation requirements
19 ====================================
19 ====================================
20
20
21 If you want to use MPI with IPython, you will need to install:
21 If you want to use MPI with IPython, you will need to install:
22
22
23 * A standard MPI implementation such as OpenMPI [OpenMPI]_ or MPICH.
23 * A standard MPI implementation such as OpenMPI [OpenMPI]_ or MPICH.
24 * The mpi4py [mpi4py]_ package.
24 * The mpi4py [mpi4py]_ package.
25
25
26 .. note::
26 .. note::
27
27
28 The mpi4py package is not a strict requirement. However, you need to
28 The mpi4py package is not a strict requirement. However, you need to
29 have *some* way of calling MPI from Python. You also need some way of
29 have *some* way of calling MPI from Python. You also need some way of
30 making sure that :func:`MPI_Init` is called when the IPython engines start
30 making sure that :func:`MPI_Init` is called when the IPython engines start
31 up. There are a number of ways of doing this and a good number of
31 up. There are a number of ways of doing this and a good number of
32 associated subtleties. We highly recommend just using mpi4py as it
32 associated subtleties. We highly recommend just using mpi4py as it
33 takes care of most of these problems. If you want to do something
33 takes care of most of these problems. If you want to do something
34 different, let us know and we can help you get started.
34 different, let us know and we can help you get started.
35
35
36 Starting the engines with MPI enabled
36 Starting the engines with MPI enabled
37 =====================================
37 =====================================
38
38
39 To use code that calls MPI, there are typically two things that MPI requires.
39 To use code that calls MPI, there are typically two things that MPI requires.
40
40
41 1. The process that wants to call MPI must be started using
41 1. The process that wants to call MPI must be started using
42 :command:`mpiexec` or a batch system (like PBS) that has MPI support.
42 :command:`mpiexec` or a batch system (like PBS) that has MPI support.
43 2. Once the process starts, it must call :func:`MPI_Init`.
43 2. Once the process starts, it must call :func:`MPI_Init`.
44
44
45 There are a couple of ways that you can start the IPython engines and get
45 There are a couple of ways that you can start the IPython engines and get
46 these things to happen.
46 these things to happen.
47
47
48 Automatic starting using :command:`mpiexec` and :command:`ipcluster`
48 Automatic starting using :command:`mpiexec` and :command:`ipcluster`
49 --------------------------------------------------------------------
49 --------------------------------------------------------------------
50
50
51 The easiest approach is to use the `MPI` Launchers in :command:`ipcluster`,
51 The easiest approach is to use the `MPI` Launchers in :command:`ipcluster`,
52 which will first start a controller and then a set of engines using
52 which will first start a controller and then a set of engines using
53 :command:`mpiexec`::
53 :command:`mpiexec`::
54
54
55 $ ipcluster start -n 4 --engines=MPIEngineSetLauncher
55 $ ipcluster start -n 4 --engines=MPIEngineSetLauncher
56
56
57 This approach is best as interrupting :command:`ipcluster` will automatically
57 This approach is best as interrupting :command:`ipcluster` will automatically
58 stop and clean up the controller and engines.
58 stop and clean up the controller and engines.
59
59
60 Manual starting using :command:`mpiexec`
60 Manual starting using :command:`mpiexec`
61 ----------------------------------------
61 ----------------------------------------
62
62
63 If you want to start the IPython engines using the :command:`mpiexec`, just
63 If you want to start the IPython engines using the :command:`mpiexec`, just
64 do::
64 do::
65
65
66 $ mpiexec -n 4 ipengine --mpi=mpi4py
66 $ mpiexec -n 4 ipengine --mpi=mpi4py
67
67
68 This requires that you already have a controller running and that the FURL
68 This requires that you already have a controller running and that the FURL
69 files for the engines are in place. We also have built in support for
69 files for the engines are in place. We also have built in support for
70 PyTrilinos [PyTrilinos]_, which can be used (assuming is installed) by
70 PyTrilinos [PyTrilinos]_, which can be used (assuming is installed) by
71 starting the engines with::
71 starting the engines with::
72
72
73 $ mpiexec -n 4 ipengine --mpi=pytrilinos
73 $ mpiexec -n 4 ipengine --mpi=pytrilinos
74
74
75 Automatic starting using PBS and :command:`ipcluster`
75 Automatic starting using PBS and :command:`ipcluster`
76 ------------------------------------------------------
76 ------------------------------------------------------
77
77
78 The :command:`ipcluster` command also has built-in integration with PBS. For
78 The :command:`ipcluster` command also has built-in integration with PBS. For
79 more information on this approach, see our documentation on :ref:`ipcluster
79 more information on this approach, see our documentation on :ref:`ipcluster
80 <parallel_process>`.
80 <parallel_process>`.
81
81
82 Actually using MPI
82 Actually using MPI
83 ==================
83 ==================
84
84
85 Once the engines are running with MPI enabled, you are ready to go. You can
85 Once the engines are running with MPI enabled, you are ready to go. You can
86 now call any code that uses MPI in the IPython engines. And, all of this can
86 now call any code that uses MPI in the IPython engines. And, all of this can
87 be done interactively. Here we show a simple example that uses mpi4py
87 be done interactively. Here we show a simple example that uses mpi4py
88 [mpi4py]_ version 1.1.0 or later.
88 [mpi4py]_ version 1.1.0 or later.
89
89
90 First, lets define a simply function that uses MPI to calculate the sum of a
90 First, lets define a simply function that uses MPI to calculate the sum of a
91 distributed array. Save the following text in a file called :file:`psum.py`:
91 distributed array. Save the following text in a file called :file:`psum.py`:
92
92
93 .. sourcecode:: python
93 .. sourcecode:: python
94
94
95 from mpi4py import MPI
95 from mpi4py import MPI
96 import numpy as np
96 import numpy as np
97
97
98 def psum(a):
98 def psum(a):
99 locsum = np.sum(a)
99 locsum = np.sum(a)
100 rcvBuf = np.array(0.0,'d')
100 rcvBuf = np.array(0.0,'d')
101 MPI.COMM_WORLD.Allreduce([locsum, MPI.DOUBLE],
101 MPI.COMM_WORLD.Allreduce([locsum, MPI.DOUBLE],
102 [rcvBuf, MPI.DOUBLE],
102 [rcvBuf, MPI.DOUBLE],
103 op=MPI.SUM)
103 op=MPI.SUM)
104 return rcvBuf
104 return rcvBuf
105
105
106 Now, start an IPython cluster::
106 Now, start an IPython cluster::
107
107
108 $ ipcluster start --profile=mpi -n 4
108 $ ipcluster start --profile=mpi -n 4
109
109
110 .. note::
110 .. note::
111
111
112 It is assumed here that the mpi profile has been set up, as described :ref:`here
112 It is assumed here that the mpi profile has been set up, as described :ref:`here
113 <parallel_process>`.
113 <parallel_process>`.
114
114
115 Finally, connect to the cluster and use this function interactively. In this
115 Finally, connect to the cluster and use this function interactively. In this
116 case, we create a random array on each engine and sum up all the random arrays
116 case, we create a random array on each engine and sum up all the random arrays
117 using our :func:`psum` function:
117 using our :func:`psum` function:
118
118
119 .. sourcecode:: ipython
119 .. sourcecode:: ipython
120
120
121 In [1]: from IPython.parallel import Client
121 In [1]: from IPython.parallel import Client
122
122
123 In [2]: c = Client(profile='mpi')
123 In [2]: c = Client(profile='mpi')
124
124
125 In [3]: view = c[:]
125 In [3]: view = c[:]
126
126
127 In [4]: view.activate() # enabe magics
127 In [4]: view.activate() # enable magics
128
128
129 # run the contents of the file on each engine:
129 # run the contents of the file on each engine:
130 In [5]: view.run('psum.py')
130 In [5]: view.run('psum.py')
131
131
132 In [6]: view.scatter('a',np.arange(16,dtype='float'))
132 In [6]: view.scatter('a',np.arange(16,dtype='float'))
133
133
134 In [7]: view['a']
134 In [7]: view['a']
135 Out[7]: [array([ 0., 1., 2., 3.]),
135 Out[7]: [array([ 0., 1., 2., 3.]),
136 array([ 4., 5., 6., 7.]),
136 array([ 4., 5., 6., 7.]),
137 array([ 8., 9., 10., 11.]),
137 array([ 8., 9., 10., 11.]),
138 array([ 12., 13., 14., 15.])]
138 array([ 12., 13., 14., 15.])]
139
139
140 In [7]: %px totalsum = psum(a)
140 In [7]: %px totalsum = psum(a)
141 Parallel execution on engines: [0,1,2,3]
141 Parallel execution on engines: [0,1,2,3]
142
142
143 In [8]: view['totalsum']
143 In [8]: view['totalsum']
144 Out[8]: [120.0, 120.0, 120.0, 120.0]
144 Out[8]: [120.0, 120.0, 120.0, 120.0]
145
145
146 Any Python code that makes calls to MPI can be used in this manner, including
146 Any Python code that makes calls to MPI can be used in this manner, including
147 compiled C, C++ and Fortran libraries that have been exposed to Python.
147 compiled C, C++ and Fortran libraries that have been exposed to Python.
148
148
149 .. [MPI] Message Passing Interface. http://www-unix.mcs.anl.gov/mpi/
149 .. [MPI] Message Passing Interface. http://www-unix.mcs.anl.gov/mpi/
150 .. [mpi4py] MPI for Python. mpi4py: http://mpi4py.scipy.org/
150 .. [mpi4py] MPI for Python. mpi4py: http://mpi4py.scipy.org/
151 .. [OpenMPI] Open MPI. http://www.open-mpi.org/
151 .. [OpenMPI] Open MPI. http://www.open-mpi.org/
152 .. [PyTrilinos] PyTrilinos. http://trilinos.sandia.gov/packages/pytrilinos/
152 .. [PyTrilinos] PyTrilinos. http://trilinos.sandia.gov/packages/pytrilinos/
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