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Added parallelization to _project.pyx code

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This commit is contained in:
Guilhem Lavaux 2014-06-11 11:14:33 +02:00
parent 5b133a9ac8
commit 401ddc8a8b
9 changed files with 173 additions and 122 deletions
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88
python/_project.pyx
View File

@ -1,5 +1,6 @@
from cpython cimport bool
from cython cimport view
from cython.parallel import prange, parallel
from libc.math cimport sin, cos, abs, floor, sqrt
import numpy as np
cimport numpy as npx
@ -621,11 +622,12 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
return cube_integral_trilin(u, u0, jumper, vertex_value)
@cython.boundscheck(False)
def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
npx.ndarray[DTYPE_t] a_u,
cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
DTYPE_t a_u[3],
DTYPE_t min_distance,
DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id=0):
DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id) nogil except? 0:
cdef DTYPE_t u[3], ifu0[3], u0[3], utot[3]
cdef int u_delta[3]
@ -657,14 +659,17 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
u0[i] = ifu0[i]-iu0[i]
u_delta[i] = 1 if iu0[i] > 0 else -1
if (not ((iu0[i]>= 0) and (iu0[i] < N))):
raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i]))
with gil:
raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i]))
if (not (u0[i]>=0 and u0[i]<=1)):
raise RuntimeError("u0[%d] = %g !" % (i,u0[i]))
with gil:
raise RuntimeError("u0[%d] = %g !" % (i,u0[i]))
completed = 0
if ((int(iu0[0]) >= N) or (int(iu0[0]) <= 0) or
(int(iu0[1]) >= N) or (int(iu0[1]) <= 0) or
(int(iu0[2]) >= N) or (int(iu0[2]) <= 0)):
if ((iu0[0] >= N) or (iu0[0] <= 0) or
(iu0[1] >= N) or (iu0[1] <= 0) or
(iu0[2] >= N) or (iu0[2] <= 0)):
completed = 1
I0 = 0
@ -681,9 +686,9 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
u0[jumper[0]] = 0
if ((int(iu0[0]) >= N) or (int(iu0[0]) <= 0) or
(int(iu0[1]) >= N) or (int(iu0[1]) <= 0) or
(int(iu0[2]) >= N) or (int(iu0[2]) <= 0)):
if ((iu0[0] >= N) or (iu0[0] <= 0) or
(iu0[1] >= N) or (iu0[1] <= 0) or
(iu0[2] >= N) or (iu0[2] <= 0)):
completed = 1
else:
dist2 = 0
@ -699,35 +704,72 @@ def line_of_sight_projection(npx.ndarray[DTYPE_t, ndim=3] density,
return I0
def line_of_sight_projection(DTYPE_t[:,:,:] density not None,
DTYPE_t[:] a_u not None,
DTYPE_t min_distance,
DTYPE_t max_distance, DTYPE_t[:] shifter not None, int integrator_id=0):
cdef DTYPE_t u[3]
u[0] = a_u[0]
u[1] = a_u[1]
u[2] = a_u[2]
C_line_of_sight_projection(density,
u,
min_distance,
max_distance, shifter, integrator_id)
cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density,
double min_distance, double max_distance,
DTYPE_t[:] shifter, int integrator_id) nogil:
cdef DTYPE_t u0[3]
stheta = sin(theta)
u0[0] = cos(phi)*stheta
u0[1] = sin(phi)*stheta
u0[2] = cos(theta)
return C_line_of_sight_projection(density, u0, min_distance, max_distance, shifter, integrator_id)
@cython.boundscheck(False)
def spherical_projection(int Nside,
npx.ndarray[DTYPE_t, ndim=3] density not None,
DTYPE_t min_distance,
DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None):
DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None, int booster=10):
import healpy as hp
import progressbar as pb
cdef int i
cdef npx.ndarray[DTYPE_t, ndim=1] u
cdef npx.ndarray[DTYPE_t, ndim=1] outm
cdef DTYPE_t[:] theta,phi
cdef DTYPE_t[:,:,:] density_view
cdef DTYPE_t[:] outm
cdef npx.ndarray[DTYPE_t, ndim=1] outm_array
cdef long N
cdef double stheta
if shifter is None:
shifter = view.array(shape=(3,), format=FORMAT_DTYPE, itemsize=sizeof(DTYPE_t))
shifter[:] = 0
outm = np.empty(hp.nside2npix(Nside),dtype=DTYPE)
outm_array = np.empty(hp.nside2npix(Nside),dtype=DTYPE)
outm = outm_array
density_view = density
if progress:
p = pb.ProgressBar(maxval=outm.size).start()
if progress != 0:
p = pb.ProgressBar(maxval=outm.size,widgets=[pb.BouncingBar(), pb.ETA()]).start()
for i in range(outm.size):
if progress:
p.update(i)
u = np.array(hp.pix2vec(Nside, i), dtype=DTYPE)
outm[i] = line_of_sight_projection(density, u, min_distance, max_distance, shifter, integrator_id=integrator_id)
N = outm.size
theta,phi = hp.pix2ang(Nside, np.arange(N))
with nogil, parallel():
for i in prange(N):
if progress != 0 and (i%booster) == 0:
with gil:
p.update(i)
outm[i] = _spherical_projloop(theta[i], phi[i], density_view, min_distance, max_distance, shifter, integrator_id)
if progress:
p.finish()
return outm
return outm_array

5
python/cosmotool/__init__.py
View File

@ -1,8 +1,7 @@
from _cosmotool import *
from _project import *
from grafic import writeGrafic, writeWhitePhase, readGrafic
from grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
from borg import read_borg_vol
from cic import cicParticles
from simu import loadRamsesAll, simpleWriteGadget, SimulationBare
from timing import timeit

26
python/cosmotool/grafic.py
View File

@ -42,9 +42,9 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
bad, bad, bad,
scalefac,
cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h'], checkPoint))
checkPoint = 4*Ny*Nx
checkPoint = 4*Ny*Nz
field = field.reshape(field.shape, order='F')
for i in xrange(Nz):
for i in xrange(Nx):
f.write(struct.pack("I", checkPoint))
f.write(field[i].astype(np.float32).tostring())
f.write(struct.pack("I", checkPoint))
@ -58,9 +58,29 @@ def writeWhitePhase(filename, field):
checkPoint = 4*4
f.write(struct.pack("IIIIII", checkPoint, Nx, Ny, Nz, 0, checkPoint))
checkPoint = struct.pack("I", 4*Ny*Nz)
field = field.reshape(field.shape, order='F')
checkPoint = struct.pack("I", 4*Nx*Ny)
for i in xrange(Nx):
f.write(checkPoint)
f.write(field[i].astype(np.float32).tostring())
f.write(checkPoint)
def readWhitePhase(filename):
with file(filename, mode="rb") as f:
_, Nx, Ny, Nz, _, _ = struct.unpack("IIIIII", f.read(4*4+2*4))
a = np.empty((Nx,Ny,Nz), dtype=np.float32)
checkPoint_ref = 4*Ny*Nz
for i in xrange(Nx):
if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
raise ValueError("Invalid unformatted access")
a[i, :, :] = np.fromfile(f, dtype=np.float32, count=Ny*Nz).reshape((Ny, Nz), order='F')
if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
raise ValueError("Invalid unformatted access")
return a

15
python/cosmotool/timing.py Normal file
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@ -0,0 +1,15 @@
import time
def timeit(method):
def timed(*args, **kw):
ts = time.time()
result = method(*args, **kw)
te = time.time()
print '%r (%r, %r) %2.2f sec' % \
(method.__name__, args, kw, te-ts)
return result
return timed

57
python_sample/build_nbody_skymap.py
View File

@ -1,57 +0,0 @@
import healpy as hp
import numpy as np
import cosmotool as ct
import h5py as h5
from matplotlib import pyplot as plt
L=600.
Nside=128
INDATA="/nethome/lavaux/Copy/PlusSimulation/BORG/Input_Data/2m++.npy"
tmpp = np.load(INDATA)
def build_sky_proj(density, dmax=60.,dmin=0):
N = density.shape[0]
ix = (np.arange(N)-0.5)*L/N - 0.5 * L
dist2 = (ix[:,None,None]**2 + ix[None,:,None]**2 + ix[None,None,:]**2)
flux = density.transpose().astype(ct.DTYPE) # / dist2
dmax=N*dmax/L
dmin=N*dmin/L
projsky1 = ct.spherical_projection(Nside, flux, dmin, dmax, integrator_id=1)
# projsky0 = ct.spherical_projection(Nside, flux, 0, 52, integrator_id=0)
return projsky1*L/N#,projsky0
l,b = tmpp['gal_long'],tmpp['gal_lat']
l = np.radians(l)
b = np.pi/2 - np.radians(b)
dcmb = tmpp['velcmb']/100.
idx = np.where((dcmb>10)*(dcmb<60))
plt.figure(1)
plt.clf()
if False:
with h5.File("fields.h5", mode="r") as f:
d = f["density"][:]
d /= np.average(np.average(np.average(d,axis=0),axis=0),axis=0)
proj = build_sky_proj(f["density"][:], dmin=10,dmax=60.)
else:
d = np.load("icgen/dcic0.npy")
proj0 = build_sky_proj(1+d, dmin=10,dmax=60.)
d = np.load("icgen/dcic1.npy")
proj1 = build_sky_proj(1+d, dmin=10,dmax=60.)
hp.mollview(proj0, fig=1, coord='CG', max=60, cmap=plt.cm.coolwarm)
hp.projscatter(b[idx], l[idx], lw=0, color='g', s=5.0, alpha=0.8)
plt.figure(2)
plt.clf()
hp.mollview(proj1, fig=2, coord='CG', max=60, cmap=plt.cm.coolwarm)
hp.projscatter(b[idx], l[idx], lw=0, color='g', s=5.0, alpha=0.8)

1
python_sample/build_nbody_skymap.py Symbolic link
View File

@ -0,0 +1 @@
/nethome/lavaux/wuala/WualaDrive/g_lavaux/PythonCode/BORG/build_nbody_skymap.py

72
python_sample/icgen/borgicgen.py
View File

@ -93,17 +93,67 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
density = np.fft.irfftn(lpt.dhat*D1_0)*(supersample*N/L)**3
return posx,vel,density,N*supersample,L,a_ic
return posx,vel,density,N*supersample,L,a_ic,cosmo
def write_icfiles(*generated_ic, **cosmo):
"""Write the initial conditions from the tuple returned by run_generation"""
posx,vel,density,N,L,a_ic = generated_ic
def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
N = density.shape[0]
ik = np.fft.fftfreq(N, d=L/N)*2*np.pi
ct.simpleWriteGadget("borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic)
for i,c in enumerate(["x","y","z"]):
ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
# This used to be necessary. However this has been fixed in writeGrafic now
# ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)).transpose(), L, a_ic, **cosmo)
k = np.sqrt(ik[:,None,None]**2 + ik[None,:,None]**2 + ik[None,None,:(N/2+1)]**2)
p = ct.CosmologyPower(**cosmo)
p.setFunction(func)
p.normalize(cosmo['SIGMA8'])
Pk = p.compute(k)*cosmo['h']**3*L**3
Pk[0,0,0]=1
density_hat = np.fft.rfftn(density)/N**3/np.sqrt(Pk)
Ns = N*supergenerate
density_hat_super = np.zeros((Ns,Ns,Ns/2+1), dtype=np.complex128)
density_hat_super[:] = np.nan
# Copy density hat in place
hN = N/2
density_hat_super[:hN, :hN, :hN+1] = density_hat[:hN, :hN, :]
density_hat_super[:hN, (Ns-hN):Ns, :hN+1] = density_hat[:hN, hN:, :]
density_hat_super[(Ns-hN):Ns, (Ns-hN):Ns, :hN+1] = density_hat[hN:, hN:, :]
density_hat_super[(Ns-hN):Ns, :hN, :hN+1] = density_hat[hN:, :hN, :]
# The moved nyquist place is untouched (so loss of "noise") to keep the structure
# now we just add some noise term
cond=np.isnan(density_hat_super)
x = np.random.randn(np.count_nonzero(cond),2)/np.sqrt(2.0)
density_hat_super[cond] = x[:,0] + 1j * x[:,1]
# Now we have to fix the Nyquist plane
hNs = Ns/2
nyquist = density_hat_super[:, :, :hNs]
Nplane = nyquist.size
nyquist.flat[:Nplane/2] = nyquist.flat[Nplane:Nplane/2:-1].conj()
return np.fft.irfftn(density_hat_super)
def write_icfiles(*generated_ic, **kwargs):
"""Write the initial conditions from the tuple returned by run_generation"""
supergenerate=1
if 'supergenerate' in kwargs:
supergenerate=kwargs['supergenerate']
posx,vel,density,N,L,a_ic,cosmo = generated_ic
ct.simpleWriteGadget("borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic)
for i,c in enumerate(["x","y","z"]):
ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
ct.writeGrafic("ic_deltab", density, L, a_ic, **cosmo)
ct.writeWhitePhase("white.dat", whitify(density, L, cosmo, supergenerate=supergenerate))
with file("white_params", mode="w") as f:
f.write("4\n%lg, %lg, %lg\n" % (cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h']))
f.write("%lg\n%lg\n-%lg\n0,0\n" % (cosmo['omega_B_0'],cosmo['ns'],cosmo['SIGMA8']))
f.write("-%lg\n1\n0\n\n\n\n\n" % L)
f.write("2\n\n0\nwhite.dat\n0\npadding_white.dat\n")
ct.writeGrafic("ic_deltab", density, L, a_ic, **cosmo)
ct.writeWhitePhase("white.dat", density)

2
python_sample/icgen/gen_ic_from_borg.py
View File

@ -14,4 +14,4 @@ astart=1/(1.+zstart)
halfPixelShift=True
if __name__=="__main__":
bic.write_icfiles(*bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=2, shiftPixel=halfPixelShift, do_lpt2=False), **cosmo)
bic.write_icfiles(*bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=2, shiftPixel=halfPixelShift, do_lpt2=False))

6
python_sample/icgen/test_ic_from_borg.py
View File

@ -10,7 +10,7 @@ cosmo['omega_k_0'] = 0
cosmo['omega_B_0']=0.049
cosmo['SIGMA8']=0.8344
cosmo['ns']=0.9624
N0=256
N0=128
doSimulation=True
@ -29,7 +29,7 @@ if doSimulation:
dsim_hat = np.fft.rfftn(dsim)*(L/N0)**3
Psim, bsim = bic.bin_power(np.abs(dsim_hat)**2/L**3, L, range=(0,1.), bins=150)
pos,_,density,N,L,_ = bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=2, do_lpt2=True)
pos,_,density,N,L,_,_ = bic.run_generation("initial_density_1380.dat", 0.001, astart, cosmo, supersample=2, do_lpt2=True)
dcic = ct.cicParticles(pos, L, N0)
dcic /= np.average(np.average(np.average(dcic, axis=0), axis=0), axis=0)
@ -50,5 +50,5 @@ Pref, bref = bic.compute_ref_power(L, N0, cosmo, range=(0,1.), bins=150)
Pcic /= D1_0**2
Pdens /= D1_0**2
borg_evolved = ct.read_borg_vol("final_density_380.dat")
borg_evolved = ct.read_borg_vol("final_density_1380.dat")

20
python_sample/test_spheric_proj.py
View File

@ -1,20 +0,0 @@
import cosmotool as ct
import numpy as np
import healpy as hp
d = np.zeros((64,64,64), ct.DTYPE)
d[32,32,32] = 1
ii=np.arange(256)*64/256.-32
xx = ii[:,None,None].repeat(256,axis=1).repeat(256,axis=2).reshape(256**3)
yy = ii[None,:,None].repeat(256,axis=0).repeat(256,axis=2).reshape(256**3)
zz = ii[None,None,:].repeat(256,axis=0).repeat(256,axis=1).reshape(256**3)
d_high = ct.interp3d(xx, yy, zz, d, 64, periodic=True)
d_high = d_high.reshape((256,256,256))
proj0 = ct.spherical_projection(64, d, 0, 20, integrator_id=0, shifter=np.array([0.5,0.5,0.5]))
proj1 = ct.spherical_projection(64, d, 0, 20, integrator_id=1)
proj0_high = ct.spherical_projection(256, d_high, 0, 30, integrator_id=0, shifter=np.array([0.5,0.5,0.5]))

1
python_sample/test_spheric_proj.py Symbolic link
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@ -0,0 +1 @@
/nethome/lavaux/wuala/WualaDrive/g_lavaux/PythonCode/BORG/test_spheric_proj.py