Refactoring compiler

parcels/__init__.py

@@ -8,6 +8,7 @@
 from parcels.kernel import *  # noqa
 import parcels.rng as ParcelsRandom  # noqa
 from parcels.particlefile import *  # noqa
+from parcels.compilation import *  # noqa
 from parcels.kernels import *  # noqa
 from parcels.scripts import *  # noqa
 from parcels.gridset import *  # noqa

parcels/compilation/__init__.py

@@ -0,0 +1,2 @@
+from .codegenerator import *  # noqa
+from .codecompiler import *  # noqa

parcels/compilation/codecompiler.py

@@ -0,0 +1,271 @@
+import os
+import subprocess
+from struct import calcsize
+
+try:
+    from mpi4py import MPI
+except:
+    MPI = None
+
+
+class Compiler_parameters(object):
+    def __init__(self):
+        self._compiler = ""
+        self._cppargs = []
+        self._ldargs = []
+        self._incdirs = []
+        self._libdirs = []
+        self._libs = []
+        self._dynlib_ext = ""
+        self._stclib_ext = ""
+        self._obj_ext = ""
+        self._exe_ext = ""
+
+    @property
+    def compiler(self):
+        return self._compiler
+
+    @property
+    def cppargs(self):
+        return self._cppargs
+
+    @property
+    def ldargs(self):
+        return self._ldargs
+
+    @property
+    def incdirs(self):
+        return self._incdirs
+
+    @property
+    def libdirs(self):
+        return self._libdirs
+
+    @property
+    def libs(self):
+        return self._libs
+
+    @property
+    def dynlib_ext(self):
+        return self._dynlib_ext
+
+    @property
+    def stclib_ext(self):
+        return self._stclib_ext
+
+    @property
+    def obj_ext(self):
+        return self._obj_ext
+
+    @property
+    def exe_ext(self):
+        return self._exe_ext
+
+
+class GNU_parameters(Compiler_parameters):
+    def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None):
+        super(GNU_parameters, self).__init__()
+        if cppargs is None:
+            cppargs = []
+        if ldargs is None:
+            ldargs = []
+        if incdirs is None:
+            incdirs = []
+        if libdirs is None:
+            libdirs = []
+        if libs is None:
+            libs = []
+
+        Iflags = []
+        if isinstance(incdirs, list):
+            for i, dir in enumerate(incdirs):
+                Iflags.append("-I"+dir)
+        Lflags = []
+        if isinstance(libdirs, list):
+            for i, dir in enumerate(libdirs):
+                Lflags.append("-L"+dir)
+        lflags = []
+        if isinstance(libs, list):
+            for i, lib in enumerate(libs):
+                lflags.append("-l" + lib)
+
+        cc_env = os.getenv('CC')
+        self._compiler = "mpicc" if MPI else "gcc" if cc_env is None else cc_env
+        opt_flags = ['-g', '-O3']
+        arch_flag = ['-m64' if calcsize("P") == 8 else '-m32']
+        self._cppargs = ['-Wall', '-fPIC']
+        self._cppargs += Iflags
+        self._cppargs += opt_flags + cppargs + arch_flag
+        self._ldargs = ['-shared']
+        self._ldargs += Lflags
+        self._ldargs += lflags
+        self._ldargs += ldargs
+        if len(Lflags) > 0:
+            self._ldargs += ['-Wl, -rpath=%s' % (":".join(libdirs))]
+        self._ldargs += arch_flag
+        self._incdirs = incdirs
+        self._libdirs = libdirs
+        self._libs = libs
+        self._dynlib_ext = "so"
+        self._stclib_ext = "a"
+        self._obj_ext = "o"
+        self._exe_ext = ""
+
+
+class Clang_parameters(Compiler_parameters):
+    def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None):
+        super(Clang_parameters, self).__init__()
+        if cppargs is None:
+            cppargs = []
+        if ldargs is None:
+            ldargs = []
+        if incdirs is None:
+            incdirs = []
+        if libdirs is None:
+            libdirs = []
+        if libs is None:
+            libs = []
+        self._compiler = "cc"
+        self._cppargs = cppargs
+        self._ldargs = ldargs
+        self._incdirs = incdirs
+        self._libdirs = libdirs
+        self._libs = libs
+        self._dynlib_ext = "dynlib"
+        self._stclib_ext = "a"
+        self._obj_ext = "o"
+        self._exe_ext = "exe"
+
+
+class MinGW_parameters(Compiler_parameters):
+    def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None):
+        super(MinGW_parameters, self).__init__()
+        if cppargs is None:
+            cppargs = []
+        if ldargs is None:
+            ldargs = []
+        if incdirs is None:
+            incdirs = []
+        if libdirs is None:
+            libdirs = []
+        if libs is None:
+            libs = []
+        self._compiler = "gcc"
+        self._cppargs = cppargs
+        self._ldargs = ldargs
+        self._incdirs = incdirs
+        self._libdirs = libdirs
+        self._libs = libs
+        self._dynlib_ext = "so"
+        self._stclib_ext = "a"
+        self._obj_ext = "o"
+        self._exe_ext = "exe"
+
+
+class VS_parameters(Compiler_parameters):
+    def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None):
+        super(VS_parameters, self).__init__()
+        if cppargs is None:
+            cppargs = []
+        if ldargs is None:
+            ldargs = []
+        if incdirs is None:
+            incdirs = []
+        if libdirs is None:
+            libdirs = []
+        if libs is None:
+            libs = []
+        self._compiler = "cl"
+        self._cppargs = cppargs
+        self._ldargs = ldargs
+        self._incdirs = incdirs
+        self._libdirs = libdirs
+        self._libs = libs
+        self._dynlib_ext = "dll"
+        self._stclib_ext = "lib"
+        self._obj_ext = "obj"
+        self._exe_ext = "exe"
+
+
+class CCompiler(object):
+    """A compiler object for creating and loading shared libraries.
+
+    :arg cc: C compiler executable (uses environment variable ``CC`` if not provided).
+    :arg cppargs: A list of arguments to the C compiler (optional).
+    :arg ldargs: A list of arguments to the linker (optional)."""
+
+    def __init__(self, cc=None, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None, tmp_dir=os.getcwd()):
+        if cppargs is None:
+            cppargs = []
+        if ldargs is None:
+            ldargs = []
+
+        self._cc = os.getenv('CC') if cc is None else cc
+        self._cppargs = cppargs
+        self._ldargs = ldargs
+        self._dynlib_ext = ""
+        self._stclib_ext = ""
+        self._obj_ext = ""
+        self._exe_ext = ""
+        self._tmp_dir = tmp_dir
+
+    def compile(self, src, obj, log):
+        pass
+
+    def _create_compile_process_(self, cmd, src, log):
+        with open(log, 'w') as logfile:
+            try:
+                subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
+            except OSError:
+                err = """OSError during compilation
+Please check if compiler exists: %s""" % self._cc
+                raise RuntimeError(err)
+            except subprocess.CalledProcessError:
+                with open(log, 'r') as logfile2:
+                    err = """Error during compilation:
+Compilation command: %s
+Source/Destination file: %s
+Log file: %s
+
+Log output: %s""" % (" ".join(cmd), src, logfile.name, logfile2.read())
+                raise RuntimeError(err)
+        return True
+
+
+class CCompiler_SS(CCompiler):
+    """
+    single-stage C-compiler; used for a SINGLE source file
+    """
+    def __init__(self, cc=None, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None, tmp_dir=os.getcwd()):
+        super(CCompiler_SS, self).__init__(cc=cc, cppargs=cppargs, ldargs=ldargs, incdirs=incdirs, libdirs=libdirs, libs=libs, tmp_dir=tmp_dir)
+
+    def compile(self, src, obj, log):
+        cc = [self._cc] + self._cppargs + ['-o', obj, src] + self._ldargs
+        with open(log, 'w') as logfile:
+            logfile.write("Compiling: %s\n" % " ".join(cc))
+        self._create_compile_process_(cc, src, log)
+
+
+class GNUCompiler_SS(CCompiler_SS):
+    """A compiler object for the GNU Linux toolchain.
+
+    :arg cppargs: A list of arguments to pass to the C compiler
+         (optional).
+    :arg ldargs: A list of arguments to pass to the linker (optional)."""
+    def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=None, tmp_dir=os.getcwd()):
+        c_params = GNU_parameters(cppargs, ldargs, incdirs, libdirs, libs)
+        super(GNUCompiler_SS, self).__init__(c_params.compiler, cppargs=c_params.cppargs, ldargs=c_params.ldargs, incdirs=c_params.incdirs, libdirs=c_params.libdirs, libs=c_params.libs, tmp_dir=tmp_dir)
+        self._dynlib_ext = c_params.dynlib_ext
+        self._stclib_ext = c_params.stclib_ext
+        self._obj_ext = c_params.obj_ext
+        self._exe_ext = c_params.exe_ext
+
+    def compile(self, src, obj, log):
+        lib_pathfile = os.path.basename(obj)
+        lib_pathdir = os.path.dirname(obj)
+        obj = os.path.join(lib_pathdir, lib_pathfile)
+
+        super(GNUCompiler_SS, self).compile(src, obj, log)
+
+
+GNUCompiler = GNUCompiler_SS

parcels/examples/tutorial_sampling.ipynb

@@ -599,8 +599,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.6.11"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}