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fperez/BackgroundLoop.ipynb

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Created May 31, 2012 06:52
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Sample notebook for backgrounding a simulation on IPython engines
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BackgroundLoop.ipynb
{
"metadata": {
"name": "BackgroundLoop"
},
"nbformat": 3,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"source": [
"Real-time monitoring of a parallel MPI simulation"
]
},
{
"cell_type": "markdown",
"source": [
"In this notebook, we show how IPython can be used to monitor a running MPI simulation by connecting to the IPython engines and reading data from them for display in the notebook.",
"",
"The toy example we use to illustrate things here is a plot of the sine function with an increasingly fine grid, that sleeps for 1 second in each 'timestep', but does so *while holding the GIL*. It is thus a realistic example of how a computationally-intensive process would work.",
"",
"For optimal results, this demo assumes you have configured an MPI profile [as explained in our documentation](http://ipython.org/ipython-doc/rel-0.12.1/parallel/parallel_process.html#using-ipcluster-in-mpiexec-mpirun-mode), you should consult that document and configure your MPI profile first if that's not the case. If you don't have MPI you can still run the demo, as we supply a few dummy stand-in methods for the MPI facilities, though some results may get out of sync in this dummy mode.",
"",
"Once your MPI profile is ready, use it to start a cluster from the [clusters tab](/#tab2) of the Notebook Dashboard."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%pylab inline",
"",
"import sys, time",
"import numpy as np",
"import matplotlib.pyplot as plt"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"",
"Welcome to pylab, a matplotlib-based Python environment [backend: module://IPython.zmq.pylab.backend_inline].",
"For more information, type 'help(pylab)'.",
""
]
}
],
"prompt_number": 1
},
{
"cell_type": "markdown",
"source": [
"Create the Client and View:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from IPython import parallel",
"rc = parallel.Client(profile=\"mpi\")",
"dv = rc[:]",
"dv.block = True",
"dv.activate()",
"dv"
],
"language": "python",
"outputs": [
{
"output_type": "pyout",
"prompt_number": 2,
"text": [
"<DirectView [0, 1]>"
]
}
],
"prompt_number": 2
},
{
"cell_type": "markdown",
"source": [
"Check for MPI. It's fine for this example if we don't have it, but it will technically be possible for",
"simulation nodes to get slightly out of sync."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%px",
"try:",
" from mpi4py import MPI",
"except ImportError:",
" bcast = lambda buf: buf",
" barrier = lambda : None",
" rank = 0",
" print \"No MPI, dummy sims may get slightly out of sync\"",
"else:",
" mpi = MPI.COMM_WORLD",
" bcast = mpi.bcast",
" barrier = mpi.barrier",
" rank = mpi.rank",
" print \"MPI rank: %i/%i\" % (mpi.rank,mpi.size)"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
"[stdout:0] MPI rank: 0/2",
"[stdout:1] MPI rank: 1/2",
""
]
}
],
"prompt_number": 3
},
{
"cell_type": "markdown",
"source": [
"Quick test of the broadcast:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%px bcast(rank)"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
},
{
"output_type": "display_data",
"text": [
"[0] \u001b[0;31mOut[39]: \u001b[0m0"
]
},
{
"output_type": "display_data",
"text": [
"[1] \u001b[0;31mOut[39]: \u001b[0m0"
]
}
],
"prompt_number": 4
},
{
"cell_type": "markdown",
"source": [
"Define a function on the engines that holds the GIL for a period of time",
"(like time.sleep, but holding the GIL to simulate blocking computation):"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%px",
"from cython import inline",
"",
"def gilsleep(t):",
" \"\"\"gil-holding sleep with cython.inline\"\"\"",
" code = '\\n'.join([",
" 'from posix cimport unistd',",
" 'unistd.sleep(t)',",
" ])",
" inline(code, quiet=True, t=t)",
"",
"gilsleep(1)"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
}
],
"prompt_number": 5
},
{
"cell_type": "markdown",
"source": [
"And define our dummy simulation, which just refines the appropriate slice of sin(x),",
"after grabbing the GIL for a period of time:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%px",
"import numpy as np",
"",
"class DummySimulation(object):",
" def __init__(self, x1, x2, n, p, dt=1):",
" self.x1 = x1",
" self.x2 = x2",
" self.n = n",
" self.p = p",
" self.dt = dt",
" self.y = None",
" self.step = 0",
" ",
" def advance(self):",
" # include mpi barrier, for good measure",
" barrier()",
" self.step += 1",
" n = self.n",
" p = self.p",
" gilsleep(self.dt)",
" npoints = p * self.step",
" X = np.linspace(x1, x2, npoints)",
" x = X[n * npoints / p : (n+1) * npoints / p]",
" self.y = np.sin(x)",
" return self.step",
""
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
}
],
"prompt_number": 6
},
{
"cell_type": "markdown",
"source": [
"Set up the global state (we are just sampling sin(x) on an interval), and instantiate the Simulation objects:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"x1 = 0",
"x2 = 10*np.pi",
"dv['x1'] = x1",
"dv['x2'] = x2",
"",
"dv.scatter('n', range(len(dv)), flatten=True)",
"dv['p'] = len(dv)",
"dv['step'] = 0",
"",
"%px sim = DummySimulation(x1, x2, n, p, dt=1)"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
}
],
"prompt_number": 7
},
{
"cell_type": "markdown",
"source": [
"Take the first step, to make sure everything is in working order:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%px sim.advance()"
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
},
{
"output_type": "display_data",
"text": [
"[0] \u001b[0;31mOut[43]: \u001b[0m1"
]
},
{
"output_type": "display_data",
"text": [
"[1] \u001b[0;31mOut[43]: \u001b[0m1"
]
}
],
"prompt_number": 8
},
{
"cell_type": "markdown",
"source": [
"This is the function we are going to use to inspect our intermediate result.",
"It fetches the current value of the simulation step, and the value of 'y',",
"and makes a plot."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from IPython.core.display import display, clear_output",
"",
"def check_y():",
" \"\"\"fetch and plot the current state of the simulation\"\"\"",
" states = dv.apply_sync(lambda : (sim.step, sim.y))",
" steps, ys = zip(*states)",
" Y = np.concatenate(ys)",
" X = linspace(0, 10*np.pi, len(Y))",
" ",
" fig = plt.figure()",
" plt.title(\"step %i (%i points)\" % (steps[0], len(X)))",
" plt.plot(X, Y, 'o-')",
" clear_output()",
" display(fig)",
" plt.close(fig)"
],
"language": "python",
"outputs": [],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"check_y()"
],
"language": "python",
"outputs": [
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{
"cell_type": "heading",
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"source": [
"Now the interesting part"
]
},
{
"cell_type": "markdown",
"source": [
"Here we start a Thread that advances the simulation *in the background*.",
"",
"The engines should be responsive on the timescale of the gilsleep threshold (**1 seconds**, here):"
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{
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" Thread.__init__(self)",
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" self._paused = True",
" ",
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"sim_thread = BackgroundAdvance(sim.advance)",
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""
],
"language": "python",
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Parallel execution on engine(s): [0, 1]",
""
]
}
],
"prompt_number": 11
},
{
"cell_type": "markdown",
"source": [
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"Now the simulation is running in a background thread, and we can check in on it with out check_y():"
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"input": [
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" check_y()",
" time.sleep(2)"
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},
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