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Added fast parallel interpolator. Some adjustment to BORG icgen

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This commit is contained in:
Guilhem Lavaux 2015-08-28 11:56:35 +02:00
parent 21507e3013
commit 8d4ee1bfdd
6 changed files with 48 additions and 7 deletions
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9
python/CMakeLists.txt
View file

@ -13,6 +13,11 @@ IF(CYTHON)
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx)
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_fast_interp.pyx
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_fast_interp.pyx)
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx
@ -29,6 +34,7 @@ ENDIF(CYTHON)
add_library(_cosmotool MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp)
add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp)
add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
@ -37,6 +43,7 @@ target_link_libraries(_cosmotool ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LI
target_link_libraries(_cosmo_power ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
target_link_libraries(_cosmo_cic ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
target_link_libraries(_project ${PYTHON_LIBRARIES})
target_link_libraries(_fast_interp ${CosmoTool_local} ${PYTHON_LIBRARIES})
# Discover where to put packages
if (NOT PYTHON_SITE_PACKAGES)
@ -62,7 +69,7 @@ if (WIN32 AND NOT CYGWIN)
SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
endif (WIN32 AND NOT CYGWIN)
INSTALL(TARGETS _cosmotool _project _cosmo_power _cosmo_cic
INSTALL(TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp
LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
)

32
python/_fast_interp.pyx Normal file
View file

@ -0,0 +1,32 @@
from cpython cimport bool
from cython cimport view
from cython.parallel import prange, parallel
from libc.math cimport sin, cos, abs, floor, round, sqrt
import numpy as np
cimport numpy as npx
cimport cython
__all__=["fast_interp"]
@cython.boundscheck(False)
@cython.cdivision(True)
def fast_interp(npx.float64_t xmin, npx.float64_t dx, npx.float64_t[:] A, npx.float64_t[:] y, npx.float64_t[:] out, npx.float64_t beyond_val=npx.nan):
cdef double rq, q
cdef int iq
cdef long i, Asize, ysize
cdef npx.float64_t[:] out0
ysize = y.size
out0 = out
Asize = A.size
with nogil:
for i in prange(ysize):
q = (y[i] - xmin) / dx
iq = int(floor(q))
rq = (q-iq)
if iq+1 >= Asize or iq < 0:
out0[i] = beyond_val
else:
out0[i] = rq * A[iq+1] + (1-rq)*A[iq]

1
python/cosmotool/__init__.py
View file

@ -2,6 +2,7 @@ from _cosmotool import *
from _project import *
from _cosmo_power import *
from _cosmo_cic import *
from _fast_interp import *
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
from .borg import read_borg_vol
from .cic import cicParticles

2
python/cosmotool/fftw.py
View file

@ -8,7 +8,7 @@ class CubeFT(object):
self.N = N
self.align = pyfftw.simd_alignment
self.L = L
self.L = float(L)
self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype='complex64')
self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype='float32')