get rid of prange

pyross/deterministic.pyx

@@ -2,7 +2,6 @@ import numpy as np
 cimport numpy as np
 cimport cython
 from libc.math cimport sqrt
-from cython.parallel import prange
 cdef double PI = 3.14159265359
 
 DTYPE = np.float
@@ -52,9 +51,9 @@ cdef class SIR:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - FM[i]
@@ -164,9 +163,9 @@ cdef class SIRS:
  double [:] iaa = self.iaa
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa + sa[i] + ep*(gIa*Ia[i] + gIs*Is[i])
@@ -254,9 +253,9 @@ cdef class SEIR:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - FM[i]
@@ -416,9 +415,9 @@ cdef class SEI5R:
  double [:] mm = self.mm
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j]+fh*Ih[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa + sa[i] 
@@ -516,9 +515,9 @@ cdef class SEAIR:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - FM[i]
@@ -626,9 +625,9 @@ cdef class SEAIRQ:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
- for j in prange(M):
+ for j in range(M):
  bb += beta*CM[i,j]*(Ia[j]+fsa*Is[j])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - tS *S[i] - FM[i]
@@ -716,10 +715,10 @@ cdef class SIkR:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
  for jj in range(kk):
- for j in prange(M):
+ for j in range(M):
  bb += beta*(CM[i,j]*I[j+jj*M])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - FM[i]
@@ -812,10 +811,10 @@ cdef class SEkIkR:
  double [:] FM = self.FM
  double [:] X = self.drpdt
 
- for i in prange(M, nogil=True):
+ for i in range(M):
  bb=0
  for jj in range(kk):
- for j in prange(M):
+ for j in range(M):
  bb += beta*(CM[i,j]*I[j+jj*M])/Ni[j]
  aa = bb*S[i]
  X[i] = -aa - FM[i]

setup.py

@@ -7,48 +7,6 @@
 Cython.Compiler.Options.annotate = True
 
 
-def checkOpenmpSupport():
- """ Adapted from https://stackoverflow.com/questions/16549893/programatically-testing-for-openmp-support-from-a-python-setup-script
- """ 
- ompTest = \
- r"""
- #include <omp.h>
- #include <stdio.h>
- int main() {
- #pragma omp parallel
- printf("Thread %d, Total number of threads %d\n", omp_get_thread_num(), omp_get_num_threads());
- }
- """
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
-
- filename = r'test.c'
- try:
- with open(filename, 'w') as file:
- file.write(ompTest)
- with open(os.devnull, 'w') as fnull:
- result = subprocess.call(['cc', '-fopenmp', filename],
- stdout=fnull, stderr=fnull)
- except:
- print("Failed to test for OpenMP support. Assuming unavailability");
- result = -1;
- os.chdir(curdir)
- shutil.rmtree(tmpdir) 
- if result == 0:
- return True
- else:
- return False
-
-
-if checkOpenmpSupport() == True:
- ompArgs = ['-fopenmp']
-else:
- ompArgs = None 
-
-
-
-
 setup(
  name='PyRoss',
  version='1.0.0',
@@ -60,8 +18,6 @@ def checkOpenmpSupport():
  platforms='works on all platforms (eg LINUX, macOS, and Microsoft Windows)',
  ext_modules=cythonize([ Extension("pyross/*", ["pyross/*.pyx"],
  include_dirs=[numpy.get_include()],
- extra_compile_args=ompArgs,
- extra_link_args=ompArgs 
  )],
  compiler_directives={"language_level": sys.version_info[0]},
  ),