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ENH: try OpenMP in SetEffectiveMigration #20

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ENH: try OpenMP in SetEffectiveMigration #20

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b881e54
ENH: try OpenMP in SetEffectiveMigration
ev-br Jun 26, 2021
c59fc5f
BLD: guard OpenMP on MacOS
ev-br Jun 26, 2021
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7 changes: 5 additions & 2 deletions VGsim/_BirthDeath.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
# distutils: language = c++

cimport cython
from cython.parallel import prange

from libc.math cimport log, floor, abs
from libcpp.vector cimport vector
Expand Down Expand Up @@ -185,9 +186,11 @@ cdef class BirthDeathModel:
@cython.wraparound(False)
@cython.cdivision(True)
cdef void SetEffectiveMigration(self):
cdef Py_ssize_t i, j

for i in range(self.popNum):
self.pm_maxEffectiveMigration[i] = 0.0
for i in range(self.popNum):
for i in prange(self.popNum, nogil=True):
for j in range(self.popNum):
self.pm_effectiveMigration[i,j] = self.pm_migrationRates[i,j]*self.pm.contactDensity[j]/self.pm.sizes[j]+self.pm_migrationRates[j,i]*self.pm.contactDensity[i]/self.pm.sizes[i]
if self.pm_effectiveMigration[i,j] > self.pm_maxEffectiveMigration[j]:
Expand Down Expand Up @@ -497,7 +500,7 @@ cdef class BirthDeathModel:
for j in range(0, iterations):
self.SampleTime()
popId = self.GenerateEvent()
if self.totalRate == 0.0 or self.pm.globalInfectious == 0:
if self.totalRate == 0.0 or self.pm.globalInfectious == 0 or self.events.ptr == 20000000:
break
self.CheckLockdown(popId)
print("Total number of iterations: ", self.events.ptr)
Expand Down
9 changes: 9 additions & 0 deletions VGsim/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,19 @@

from Cython.Compiler import Options

import sys
import numpy

Options.annotate = True

PACKAGE_NAME = 'VGsim'

# enable openMP on linux, disable on MacOS
if sys.platform == "darwin":
openmp_args = []
else:
openmp_args = ['-fopenmp']


def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
Expand All @@ -20,6 +27,8 @@ def configuration(parent_package='', top_path=None):
'models.pxi', 'fast_choose.pxi'],
language='c++',
include_dirs=[numpy.get_include()],
extra_compile_args=openmp_args,
extra_link_args=openmp_args,
)

return config
Expand Down