Fix GCC 5 Builds

setup.py

@@ -1,6 +1,7 @@
 import glob
 import os
 import sys
+from collections import defaultdict
 from distutils.ccompiler import get_default_compiler
 from distutils.version import LooseVersion
 
@@ -36,20 +37,24 @@
 with open("README.md") as file:
     long_description = file.read()
 
-if check_for_openmp():
-    omp_args = ["-fopenmp"]
-else:
-    omp_args = []
+CPP14_CONFIG = defaultdict(
+    lambda: ["-std=c++14"], {"unix": ["-std=c++14"], "msvc": ["/std:c++14"]}
+)
+CPP03_CONFIG = defaultdict(
+    lambda: ["-std=c++03"], {"unix": ["-std=c++03"], "msvc": ["/std:c++03"]}
+)
+
+_COMPILER = get_default_compiler()
+
+omp_args, _ = check_for_openmp()
 
 if os.name == "nt":
     std_libs = []
 else:
     std_libs = ["m"]
 
-if get_default_compiler() == "msvc":
-    CPP14_FLAG = ["/std:c++14"]
-else:
-    CPP14_FLAG = ["--std=c++14"]
+CPP14_FLAG = CPP14_CONFIG[_COMPILER]
+CPP03_FLAG = CPP03_CONFIG[_COMPILER]
 
 cythonize_aliases = {
     "LIB_DIR": "yt/utilities/lib/",
@@ -65,6 +70,7 @@
     "FIXED_INTERP": "yt/utilities/lib/fixed_interpolator.cpp",
     "ARTIO_SOURCE": glob.glob("yt/frontends/artio/artio_headers/*.c"),
     "CPP14_FLAG": CPP14_FLAG,
+    "CPP03_FLAG": CPP03_FLAG,
 }
 
 lib_exts = [

setupext.py

@@ -59,7 +59,8 @@ def stdchannel_redirected(stdchannel, dest_filename):
 
 
 def check_for_openmp():
-    """Returns True if local setup supports OpenMP, False otherwise
+    """Returns OpenMP compiler and linker flags if local setup supports
+    OpenMP or [], [] otherwise
 
     Code adapted from astropy_helpers, originally written by Tom
     Robitaille and Curtis McCully.
@@ -72,15 +73,17 @@ def check_for_openmp():
     tmp_dir = tempfile.mkdtemp()
     start_dir = os.path.abspath(".")
 
+    # TODO: test more known compilers:
+    # MinGW, AppleClang with libomp, MSVC, ICC, XL, PGI, ...
     if os.name == "nt":
         # TODO: make this work with mingw
         # AFAICS there's no easy way to get the compiler distutils
         # will be using until compilation actually happens
-        compile_flag = "-openmp"
-        link_flag = ""
+        compile_flags = ["-openmp"]
+        link_flags = [""]
     else:
-        compile_flag = "-fopenmp"
-        link_flag = "-fopenmp"
+        compile_flags = ["-fopenmp"]
+        link_flags = ["-fopenmp"]
 
     try:
         os.chdir(tmp_dir)
@@ -93,12 +96,12 @@ def check_for_openmp():
         # Compile, link, and run test program
         with stdchannel_redirected(sys.stderr, os.devnull):
             ccompiler.compile(
-                ["test_openmp.c"], output_dir="objects", extra_postargs=[compile_flag]
+                ["test_openmp.c"], output_dir="objects", extra_postargs=compile_flags
             )
             ccompiler.link_executable(
                 glob.glob(os.path.join("objects", "*")),
                 "test_openmp",
-                extra_postargs=[link_flag],
+                extra_postargs=link_flags,
             )
             output = (
                 subprocess.check_output("./test_openmp")
@@ -136,7 +139,10 @@ def check_for_openmp():
             "extensions will be compiled without parallel support"
         )
 
-    return using_openmp
+    if using_openmp:
+        return compile_flags, link_flags
+    else:
+        return [], []
 
 
 def check_for_pyembree(std_libs):

yt/geometry/particle_oct_container.pyx

@@ -1,5 +1,6 @@
 # distutils: include_dirs = LIB_DIR_EWAH
 # distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG
 # distutils: libraries = STD_LIBS
 """
 Oct container tuned for Particles

yt/utilities/lib/cykdtree/kdtree.pyx

@@ -3,7 +3,7 @@
 # distutils: sources = yt/utilities/lib/cykdtree/c_utils.cpp
 # distutils: depends = yt/utilities/lib/cykdtree/c_kdtree.hpp, yt/utilities/lib/cykdtree/c_utils.hpp
 # distutils: language = c++
-# distutils: extra_compile_args = -std=c++03
+# distutils: extra_compile_args = CPP03_FLAG
 import cython
 import numpy as np
 

yt/utilities/lib/cykdtree/utils.pyx

@@ -2,7 +2,7 @@
 # distutils: sources = yt/utilities/lib/cykdtree/c_utils.cpp
 # distutils: depends = yt/utilities/lib/cykdtree/c_utils.hpp
 # distutils: language = c++
-# distutils: extra_compile_args = -std=c++03
+# distutils: extra_compile_args = CPP03_FLAG
 import numpy as np
 
 cimport cython

yt/utilities/lib/cyoctree.pyx

@@ -1,6 +1,6 @@
 # distutils: libraries = STD_LIBS
-# distutils: extra_link_args = OMP_ARGS
-# distutils: extra_compile_args = OMP_ARGS
+# distutils: extra_link_args = CPP14_FLAG OMP_ARGS
+# distutils: extra_compile_args = CPP14_FLAG OMP_ARGS
 # distutils: include_dirs = LIB_DIR
 # distutils: language = c++
 """

yt/utilities/lib/field_interpolation_tables.pxd

@@ -1,3 +1,6 @@
+# distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG
+# distutils: extra_link_args = CPP14_FLAG
 """
 Field Interpolation Tables
 
@@ -8,12 +11,19 @@ Field Interpolation Tables
 
 cimport cython
 cimport numpy as np
-from libc.math cimport isnormal
 from libc.stdlib cimport malloc
 
 from yt.utilities.lib.fp_utils cimport fabs, fclip, fmax, fmin, iclip, imax, imin
 
 
+cdef extern from "<cmath>" namespace "std":
+    bint isnormal(double x) nogil
+
+
+cdef extern from "platform_dep_math.hpp":
+    bint __isnormal(double) nogil
+
+
 cdef struct FieldInterpolationTable:
     # Note that we make an assumption about retaining a reference to values
     # externally.
@@ -58,7 +68,7 @@ cdef inline np.float64_t FIT_get_value(const FieldInterpolationTable *fit,
     cdef np.float64_t dd, dout
     cdef int bin_id
     if dvs[fit.field_id] >= fit.bounds[1] or dvs[fit.field_id] <= fit.bounds[0]: return 0.0
-    if not isnormal(dvs[fit.field_id]): return 0.0
+    if not __isnormal(dvs[fit.field_id]): return 0.0
     bin_id = <int> ((dvs[fit.field_id] - fit.bounds[0]) * fit.idbin)
     bin_id = iclip(bin_id, 0, fit.nbins-2)
 

yt/utilities/lib/geometry_utils.pyx

@@ -1,6 +1,7 @@
 # distutils: libraries = STD_LIBS
-# distutils: extra_compile_args = OMP_ARGS
-# distutils: extra_link_args = OMP_ARGS
+# distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG OMP_ARGS
+# distutils: extra_link_args = CPP14_FLAG OMP_ARGS
 """
 Simple integrators for the radiative transfer equation
 

yt/utilities/lib/grid_traversal.pyx

@@ -1,6 +1,9 @@
 # distutils: include_dirs = LIB_DIR
 # distutils: libraries = STD_LIBS
 # distutils: sources = FIXED_INTERP
+# distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG
+# distutils: extra_link_args = CPP14_FLAG
 """
 Simple integrators for the radiative transfer equation
 
@@ -13,12 +16,6 @@ import numpy as np
 
 cimport cython
 cimport numpy as np
-from field_interpolation_tables cimport (
-    FieldInterpolationTable,
-    FIT_eval_transfer,
-    FIT_eval_transfer_with_light,
-    FIT_initialize_table,
-)
 from fixed_interpolator cimport *
 from libc.math cimport (
     M_PI,

yt/utilities/lib/image_samplers.pyx

@@ -1,6 +1,6 @@
 # distutils: include_dirs = LIB_DIR
-# distutils: extra_compile_args = OMP_ARGS
-# distutils: extra_link_args = OMP_ARGS
+# distutils: extra_compile_args = CPP14_FLAG OMP_ARGS
+# distutils: extra_link_args = CPP14_FLAG OMP_ARGS
 # distutils: libraries = STD_LIBS
 # distutils: sources = FIXED_INTERP
 # distutils: language = c++

yt/utilities/lib/misc_utilities.pyx

@@ -1,6 +1,7 @@
 # distutils: libraries = STD_LIBS
-# distutils: extra_compile_args = OMP_ARGS
-# distutils: extra_link_args = OMP_ARGS
+# distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG OMP_ARGS
+# distutils: extra_link_args = CPP14_FLAG OMP_ARGS
 """
 Simple utilities that don't fit anywhere else
 

yt/utilities/lib/partitioned_grid.pyx

@@ -2,6 +2,8 @@
 # distutils: include_dirs = LIB_DIR
 # distutils: libraries = STD_LIBS
 # distutils: language = c++
+# distutils: extra_compile_args = CPP14_FLAG
+# distutils: extra_link_args = CPP14_FLAG
 """
 Image sampler definitions
 

yt/utilities/lib/pixelization_routines.pyx

@@ -1,6 +1,6 @@
 # distutils: include_dirs = LIB_DIR
-# distutils: extra_compile_args = OMP_ARGS
-# distutils: extra_link_args = OMP_ARGS
+# distutils: extra_compile_args = CPP14_FLAG OMP_ARGS
+# distutils: extra_link_args = CPP14_FLAG OMP_ARGS
 # distutils: language = c++
 # distutils: libraries = STD_LIBS
 # distutils: sources = yt/utilities/lib/pixelization_constants.cpp

yt/utilities/lib/platform_dep.h

@@ -59,6 +59,4 @@ double erf(double x)
 #include <stdint.h>
 #include "alloca.h"
 #include <math.h>
-#endif
-
-
+#endif

yt/utilities/lib/platform_dep_math.hpp

@@ -0,0 +1,18 @@
+/*
+This file provides a compatibility layout between MSVC, and different version of GCC.
+
+MSVC does not define isnormal in the std:: namespace, so we cannot import it from <cmath>, but from <math.h> instead.
+However with GCC-5, there is a clash between the definition of isnormal in <math.h> and using C++14, so we need to import from cmath instead.
+*/
+
+#if _MSC_VER
+#include <math.h>
+inline bool __isnormal(double x) {
+    return isnormal(x);
+}
+#else
+#include <cmath>
+inline bool __isnormal(double x) {
+    return std::isnormal(x);
+}
+#endif