Added parallelization to _project.pyx code
This commit is contained in:
Guilhem Lavaux
parent
5b133a9ac8
commit
401ddc8a8b
9 changed files with 173 additions and 122 deletions
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@ -1,5 +1,6 @@
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from cpython cimport bool
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from cython cimport view
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from cython.parallel import prange, parallel
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from libc.math cimport sin, cos, abs, floor, sqrt
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import numpy as np
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cimport numpy as npx
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@ -620,12 +621,13 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
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# return cube_integral(u, u0, jumper)*d
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return cube_integral_trilin(u, u0, jumper, vertex_value)
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@cython.boundscheck(False)
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def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
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npx.ndarray[DTYPE_t] a_u,
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cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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DTYPE_t a_u[3],
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DTYPE_t min_distance,
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DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id=0):
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DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id) nogil except? 0:
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cdef DTYPE_t u[3], ifu0[3], u0[3], utot[3]
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cdef int u_delta[3]
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@ -657,14 +659,17 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
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u0[i] = ifu0[i]-iu0[i]
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u_delta[i] = 1 if iu0[i] > 0 else -1
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if (not ((iu0[i]>= 0) and (iu0[i] < N))):
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raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i]))
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with gil:
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raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i]))
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if (not (u0[i]>=0 and u0[i]<=1)):
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raise RuntimeError("u0[%d] = %g !" % (i,u0[i]))
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with gil:
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raise RuntimeError("u0[%d] = %g !" % (i,u0[i]))
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completed = 0
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if ((int(iu0[0]) >= N) or (int(iu0[0]) <= 0) or
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(int(iu0[1]) >= N) or (int(iu0[1]) <= 0) or
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(int(iu0[2]) >= N) or (int(iu0[2]) <= 0)):
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if ((iu0[0] >= N) or (iu0[0] <= 0) or
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(iu0[1] >= N) or (iu0[1] <= 0) or
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(iu0[2] >= N) or (iu0[2] <= 0)):
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completed = 1
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I0 = 0
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@ -681,9 +686,9 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
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u0[jumper[0]] = 0
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if ((int(iu0[0]) >= N) or (int(iu0[0]) <= 0) or
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(int(iu0[1]) >= N) or (int(iu0[1]) <= 0) or
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(int(iu0[2]) >= N) or (int(iu0[2]) <= 0)):
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if ((iu0[0] >= N) or (iu0[0] <= 0) or
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(iu0[1] >= N) or (iu0[1] <= 0) or
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(iu0[2] >= N) or (iu0[2] <= 0)):
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completed = 1
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else:
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dist2 = 0
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@ -699,35 +704,72 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
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return I0
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def line_of_sight_projection(DTYPE_t[:,:,:] density not None,
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DTYPE_t[:] a_u not None,
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DTYPE_t min_distance,
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DTYPE_t max_distance, DTYPE_t[:] shifter not None, int integrator_id=0):
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cdef DTYPE_t u[3]
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u[0] = a_u[0]
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u[1] = a_u[1]
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u[2] = a_u[2]
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C_line_of_sight_projection(density,
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u,
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min_distance,
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max_distance, shifter, integrator_id)
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cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density,
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double min_distance, double max_distance,
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DTYPE_t[:] shifter, int integrator_id) nogil:
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cdef DTYPE_t u0[3]
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stheta = sin(theta)
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u0[0] = cos(phi)*stheta
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u0[1] = sin(phi)*stheta
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u0[2] = cos(theta)
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return C_line_of_sight_projection(density, u0, min_distance, max_distance, shifter, integrator_id)
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@cython.boundscheck(False)
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def spherical_projection(int Nside,
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npx.ndarray[DTYPE_t, ndim=3] density not None,
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DTYPE_t min_distance,
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DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None):
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DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None, int booster=10):
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import healpy as hp
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import progressbar as pb
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cdef int i
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cdef npx.ndarray[DTYPE_t, ndim=1] u
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cdef npx.ndarray[DTYPE_t, ndim=1] outm
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cdef DTYPE_t[:] theta,phi
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cdef DTYPE_t[:,:,:] density_view
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cdef DTYPE_t[:] outm
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cdef npx.ndarray[DTYPE_t, ndim=1] outm_array
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cdef long N
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cdef double stheta
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if shifter is None:
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shifter = view.array(shape=(3,), format=FORMAT_DTYPE, itemsize=sizeof(DTYPE_t))
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shifter[:] = 0
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outm = np.empty(hp.nside2npix(Nside),dtype=DTYPE)
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outm_array = np.empty(hp.nside2npix(Nside),dtype=DTYPE)
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outm = outm_array
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density_view = density
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if progress:
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p = pb.ProgressBar(maxval=outm.size).start()
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for i in range(outm.size):
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if progress:
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p.update(i)
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u = np.array(hp.pix2vec(Nside, i), dtype=DTYPE)
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outm[i] = line_of_sight_projection(density, u, min_distance, max_distance, shifter, integrator_id=integrator_id)
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if progress != 0:
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p = pb.ProgressBar(maxval=outm.size,widgets=[pb.BouncingBar(), pb.ETA()]).start()
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N = outm.size
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theta,phi = hp.pix2ang(Nside, np.arange(N))
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with nogil, parallel():
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for i in prange(N):
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if progress != 0 and (i%booster) == 0:
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with gil:
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p.update(i)
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outm[i] = _spherical_projloop(theta[i], phi[i], density_view, min_distance, max_distance, shifter, integrator_id)
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if progress:
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p.finish()
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return outm
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return outm_array
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@ -1,8 +1,7 @@
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from _cosmotool import *
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from _project import *
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from grafic import writeGrafic, writeWhitePhase, readGrafic
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from grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
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from borg import read_borg_vol
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from cic import cicParticles
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from simu import loadRamsesAll, simpleWriteGadget, SimulationBare
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from timing import timeit
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@ -42,9 +42,9 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
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bad, bad, bad,
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scalefac,
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cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h'], checkPoint))
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checkPoint = 4*Ny*Nx
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checkPoint = 4*Ny*Nz
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field = field.reshape(field.shape, order='F')
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for i in xrange(Nz):
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for i in xrange(Nx):
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f.write(struct.pack("I", checkPoint))
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f.write(field[i].astype(np.float32).tostring())
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f.write(struct.pack("I", checkPoint))
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@ -58,9 +58,29 @@ def writeWhitePhase(filename, field):
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checkPoint = 4*4
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f.write(struct.pack("IIIIII", checkPoint, Nx, Ny, Nz, 0, checkPoint))
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checkPoint = struct.pack("I", 4*Ny*Nz)
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field = field.reshape(field.shape, order='F')
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checkPoint = struct.pack("I", 4*Nx*Ny)
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for i in xrange(Nx):
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f.write(checkPoint)
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f.write(field[i].astype(np.float32).tostring())
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f.write(checkPoint)
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def readWhitePhase(filename):
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with file(filename, mode="rb") as f:
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_, Nx, Ny, Nz, _, _ = struct.unpack("IIIIII", f.read(4*4+2*4))
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a = np.empty((Nx,Ny,Nz), dtype=np.float32)
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checkPoint_ref = 4*Ny*Nz
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for i in xrange(Nx):
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if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
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raise ValueError("Invalid unformatted access")
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a[i, :, :] = np.fromfile(f, dtype=np.float32, count=Ny*Nz).reshape((Ny, Nz), order='F')
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if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
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raise ValueError("Invalid unformatted access")
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return a
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15
python/cosmotool/timing.py
Normal file
15
python/cosmotool/timing.py
Normal file
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@ -0,0 +1,15 @@
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import time
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def timeit(method):
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def timed(*args, **kw):
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ts = time.time()
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result = method(*args, **kw)
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te = time.time()
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print '%r (%r, %r) %2.2f sec' % \
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(method.__name__, args, kw, te-ts)
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return result
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return timed
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