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POgetting started with cython by using cdef
 

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  1. POgetting started with cython by using cdef
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    <p>I dont understand how to setup and run code with cython.</p> <p>I added <code>cdef</code>, <code>double</code>, etc to pertinent pieces of my code.</p> <p>setup.py of course the name hello isn't being used. <a href="http://docs.cython.org/src/quickstart/build.html" rel="nofollow">cython doc</a></p> <pre><code>from distutils.core import setup from distutils.extension import Extension from Cython.Distutils import build_ext ext_modules = [Extension("hello", ["hello.pyx"])] setup( name = 'Hello world app', cmdclass = {'build_ext': build_ext}, ext_modules = ext_modules ) </code></pre> <p><strong>Edit</strong></p> <p>Redefining the question to make it more of a concrete example.</p> <p>I want to run this system of ODEs through Cython. I am not sure if <code>double</code> is the best choice but the numbers are on the order of magnitudes of 10 to the 10 and are non-integer.</p> <p>So I want to call this in a bigger code where <code>mus</code> is a variable defined in the script calling the module. I have my <code>setup.py</code> file to compile the pyx file. I am not sure with what I need to do so I can call this ode now. Say I name the module 3bodyproblem. I would then call it in the scipt as <code>import 3bodyproblem</code> and then do `3bodyproblem.3bodyproblem(what would this input be)'</p> <p>I have be reading <a href="http://hplgit.github.io/teamods/cyode/cyode-sphinx/main_cyode.html" rel="nofollow">intro to cython for odes</a> but I am not sure how to use their example with mine. Also, if it needs to be in rk format, see the code below the first code.</p> <p><strong>Code 1</strong></p> <pre><code>cdef deriv(double u, dt): cdef double u[0], u[1], u[2] return [u[3], u[4], u[5], -mus * u[0] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[1] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[2] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5] dt = np.linspace(0.0, t12sec, t12sec) u = odeint(deriv, u0, dt, atol = 1e-13, rtol = 1e-13) x, y, z, vx, vy, vz = u.T </code></pre> <p><strong>Code 2</strong></p> <pre><code>cdef deriv(dt, double u): cdef double u[0], u[1], u[2], u[3], u[4], u[5] return [u[3], u[4], u[5], -mus * u[0] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[1] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[2] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5] solver = ode(deriv).set_integrator('dop853') solver.set_initial_value(u0) z = np.zeros(300000) for ii in range(300000): z[ii] = solver.integrate(dt[ii])[0] x, y, z, x2, y2, z2 = z.T </code></pre> <p>If I just try to compile code 1, cython doesn't know about the variables defined the larger <code>.py</code> file. I want to avoid setting variables in the cython code so it can be used else where with out re compiling. Here are the errors:</p> <pre><code>Error compiling Cython file: ------------------------------------------------------------ ... import numpy as np from scipy.integrate import odeint cdef deriv(double u, dt): cdef double u[0], u[1], u[2] ^ ------------------------------------------------------------ ODEcython.pyx:7:17: 'u' redeclared Error compiling Cython file: ------------------------------------------------------------ ... import numpy as np from scipy.integrate import odeint cdef deriv(double u, dt): cdef double u[0], u[1], u[2] ^ ------------------------------------------------------------ ODEcython.pyx:7:23: 'u' redeclared Error compiling Cython file: ------------------------------------------------------------ ... import numpy as np from scipy.integrate import odeint cdef deriv(double u, dt): cdef double u[0], u[1], u[2] ^ ------------------------------------------------------------ ODEcython.pyx:7:29: 'u' redeclared Error compiling Cython file: ------------------------------------------------------------ ... -mus * u[0] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[1] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[2] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5] dt = np.linspace(0.0, t12sec, t12sec) ^ ------------------------------------------------------------ ODEcython.pyx:16:28: undeclared name not builtin: t12sec Error compiling Cython file: ------------------------------------------------------------ ... -mus * u[1] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[2] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5] dt = np.linspace(0.0, t12sec, t12sec) u = odeint(deriv, u0, dt, atol = 1e-13, rtol = 1e-13) ^ ------------------------------------------------------------ ODEcython.pyx:17:16: Cannot convert 'object (double, object)' to Python object Error compiling Cython file: ------------------------------------------------------------ ... -mus * u[1] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, -mus * u[2] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5] dt = np.linspace(0.0, t12sec, t12sec) u = odeint(deriv, u0, dt, atol = 1e-13, rtol = 1e-13) ^ ------------------------------------------------------------ ODEcython.pyx:17:20: undeclared name not builtin: u0 Error compiling Cython file: ------------------------------------------------------------ ... cdef deriv(double u, dt): cdef double u[0], u[1], u[2] return [u[3], u[4], u[5], -mus * u[0] / (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 1.5, ^ ------------------------------------------------------------ ODEcython.pyx:11:17: undeclared name not builtin: mus building 'ODEcython' extension creating build creating build/temp.linux-x86_64-2.7 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c ODEcython.c -o build/temp.linux-x86_64-2.7/ODEcython.o ODEcython.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 </code></pre> <p><strong>Maybe this will help</strong></p> <p>So I want to use the module in a file like this: (different deriv function but just ignore that the idea is the same)</p> <pre><code>import numpy as np from scipy.integrate import ode import pylab from mpl_toolkits.mplot3d import Axes3D from scipy.optimize import brentq from scipy.optimize import fsolve me = 5.974 * 10 ** 24 # mass of the earth mm = 7.348 * 10 ** 22 # mass of the moon G = 6.67259 * 10 ** -20 # gravitational parameter re = 6378.0 # radius of the earth in km rm = 1737.0 # radius of the moon in km r12 = 384400.0 # distance between the CoM of the earth and moon rs = 66100.0 # distance to the moon SOI Lambda = np.pi / 6 # angle at arrival to SOI M = me + mm d = 300 # distance the spacecraft is above the Earth pi1 = me / M pi2 = mm / M mue = 398600.0 # gravitational parameter of earth km^3/sec^2 mum = G * mm # grav param of the moon mu = mue + mum omega = np.sqrt(mu / r12 ** 3) # distance from the earth to Lambda on the SOI r1 = np.sqrt(r12 ** 2 + rs ** 2 - 2 * r12 * rs * np.cos(Lambda)) vbo = 10.85 # velocity at burnout h = (re + d) * vbo # angular momentum energy = vbo ** 2 / 2 - mue / (re + d) # energy v1 = np.sqrt(2.0 * (energy + mue / r1)) # refer to the close up of moon diagram # refer to diagram for angles theta1 = np.arccos(h / (r1 * v1)) phi1 = np.arcsin(rs * np.sin(Lambda) / r1) # p = h ** 2 / mue # semi-latus rectum a = -mue / (2 * energy) # semi-major axis eccen = np.sqrt(1 - p / a) # eccentricity nu0 = 0 nu1 = np.arccos((p - r1) / (eccen * r1)) # Solving for the eccentric anomaly def f(E0): return np.tan(E0 / 2) - np.sqrt((1 - eccen) / (1 + eccen)) * np.tan(0) E0 = brentq(f, 0, 5) def g(E1): return np.tan(E1 / 2) - np.sqrt((1 - eccen) / (1 + eccen)) * np.tan(nu1 / 2) E1 = fsolve(g, 0) # Time of flight from r0 to SOI deltat = (np.sqrt(a ** 3 / mue) * (E1 - eccen * np.sin(E1) - (E0 - eccen * np.sin(E0)))) # Solve for the initial phase angle def s(phi0): return phi0 + deltat * 2 * np.pi / (27.32 * 86400) + phi1 - nu1 phi0 = fsolve(s, 0) nu = -phi0 gamma = 0 * np.pi / 180 # angle in radians of the flight path vx = vbo * (np.sin(gamma) * np.cos(nu) - np.cos(gamma) * np.sin(nu)) # velocity of the bo in the x direction vy = vbo * (np.sin(gamma) * np.sin(nu) + np.cos(gamma) * np.cos(nu)) # velocity of the bo in the y direction xrel = (re + 300.0) * np.cos(nu) - pi2 * r12 yrel = (re + 300.0) * np.sin(nu) u0 = [xrel, yrel, 0, vx, vy, 0] def deriv(u, dt): return [u[3], # dotu[0] = u[3] u[4], # dotu[1] = u[4] u[5], # dotu[2] = u[5] (2 * omega * u[4] + omega ** 2 * u[0] - mue * (u[0] + pi2 * r12) / np.sqrt(((u[0] + pi2 * r12) ** 2 + u[1] ** 2) ** 3) - mum * (u[0] - pi1 * r12) / np.sqrt(((u[0] - pi1 * r12) ** 2 + u[1] ** 2) ** 3)), # dotu[3] = that (-2 * omega * u[3] + omega ** 2 * u[1] - mue * u[1] / np.sqrt(((u[0] + pi2 * r12) ** 2 + u[1] ** 2) ** 3) - mum * u[1] / np.sqrt(((u[0] - pi1 * r12) ** 2 + u[1] ** 2) ** 3)), # dotu[4] = that 0] # dotu[5] = 0 dt = np.linspace(0.0, 259200.0, 259200.0) # secs to run the simulation u = odeint(deriv, u0, dt) x, y, z, x2, y2, z2 = u.T fig = pylab.figure() ax = fig.add_subplot(111, projection='3d') ax.plot(x, y, z, color = 'r') # adding the moon phi = np.linspace(0, 2 * np.pi, 100) theta = np.linspace(0, np.pi, 100) xm = rm * np.outer(np.cos(phi), np.sin(theta)) + r12 - pi2 * r12 ym = rm * np.outer(np.sin(phi), np.sin(theta)) zm = rm * np.outer(np.ones(np.size(phi)), np.cos(theta)) ax.plot_surface(xm, ym, zm, color = '#696969', linewidth = 0) ax.auto_scale_xyz([-8000, 385000], [-8000, 385000], [-8000, 385000]) # adding the earth xe = re * np.outer(np.cos(phi), np.sin(theta)) - pi2 * r12 ye = re * np.outer(np.sin(phi), np.sin(theta)) ze = re * np.outer(np.ones(np.size(phi)), np.cos(theta)) ax.plot_surface(xe, ye, ze, color = '#4169E1', linewidth = 0) ax.auto_scale_xyz([-8000, 385000], [-8000, 385000], [-8000, 385000]) pylab.show() </code></pre>
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    1. COCan you show how you compile and run the Cython code?
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      1. USKos
    2. CO@Kos I am using the shebang line `#!/usr/bin/env ipython` where in my bashrc I have `alias ipython='ipython --pylab=qt'`
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    3. COShebangs don't expand shell aliases. And Cython files cannot be run directly, they must be compiled. See the Cython documentation.
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      1. USFred Foo
 

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