def get_kernel_compile_files(self):
"""
Returns the correct src_file, lib_file, log_file for this kernel
"""
if MPI:
mpi_comm = MPI.COMM_WORLD
mpi_rank = mpi_comm.Get_rank()
cache_name = self._cache_key # only required here because loading is done by Kernel class instead of Compiler class
dyn_dir = get_cache_dir() if mpi_rank == 0 else None
dyn_dir = mpi_comm.bcast(dyn_dir, root=0)
basename = cache_name if mpi_rank == 0 else None
basename = mpi_comm.bcast(basename, root=0)
basename = basename + "_%d" % mpi_rank
else:
cache_name = self._cache_key # only required here because loading is done by Kernel class instead of Compiler class
dyn_dir = get_cache_dir()
basename = "%s_0" % cache_name
lib_path = "lib" + basename
src_file_or_files = None
if type(basename) in (list, dict, tuple, ndarray):
src_file_or_files = [
"",
] * len(basename)
for i, src_file in enumerate(basename):
src_file_or_files[i] = "%s.c" % path.join(dyn_dir, src_file)
else:
src_file_or_files = "%s.c" % path.join(dyn_dir, basename)
lib_file = "%s.%s" % (path.join(
dyn_dir, lib_path), 'dll' if platform == 'win32' else 'so')
log_file = "%s.log" % path.join(dyn_dir, basename)
return src_file_or_files, lib_file, log_file
def remove_lib(self):
# Unload the currently loaded dynamic linked library to be secure
if self._lib is not None:
_ctypes.FreeLibrary(self._lib._handle) if platform == 'win32' else _ctypes.dlclose(self._lib._handle)
del self._lib
self._lib = None
# deactivate the cleanup finalizers for the current set of files
if self._cleanup_files is not None:
self._cleanup_files.detach()
if self._cleanup_lib is not None:
self._cleanup_lib.detach()
# If file already exists, pull new names. This is necessary on a Windows machine, because
# Python's ctype does not deal in any sort of manner well with dynamic linked libraries on this OS.
if path.isfile(self.lib_file):
[remove(s) for s in [self.src_file, self.lib_file, self.log_file]]
if MPI:
mpi_comm = MPI.COMM_WORLD
mpi_rank = mpi_comm.Get_rank()
basename = path.join(get_cache_dir(), self._cache_key) if mpi_rank == 0 else None
basename = mpi_comm.bcast(basename, root=0)
basename = basename + "_%d" % mpi_rank
else:
basename = path.join(get_cache_dir(), "%s_0" % self._cache_key)
self.src_file = "%s.c" % basename
self.lib_file = "%s.%s" % (basename, 'dll' if platform == 'win32' else 'so')
self.log_file = "%s.log" % basename
def __init__(self, fieldset, ptype, pyfunc=None, funcname=None,
funccode=None, py_ast=None, funcvars=None, c_include="", delete_cfiles=True):
self.fieldset = fieldset
self.ptype = ptype
self._lib = None
self.delete_cfiles = delete_cfiles
self._cleanup_files = None
self._cleanup_lib = None
self.c_include = c_include
# Derive meta information from pyfunc, if not given
self.funcname = funcname or pyfunc.__name__
if pyfunc is AdvectionRK4_3D:
warning = False
if isinstance(fieldset.W, Field) and fieldset.W.creation_log != 'from_nemo' and \
fieldset.W._scaling_factor is not None and fieldset.W._scaling_factor > 0:
warning = True
if type(fieldset.W) in [SummedField, NestedField]:
for f in fieldset.W:
if f.creation_log != 'from_nemo' and f._scaling_factor is not None and f._scaling_factor > 0:
warning = True
if warning:
logger.warning_once('Note that in AdvectionRK4_3D, vertical velocity is assumed positive towards increasing z.\n'
' If z increases downward and w is positive upward you can re-orient it downwards by setting fieldset.W.set_scaling_factor(-1.)')
elif pyfunc is AdvectionAnalytical:
if ptype.uses_jit:
raise NotImplementedError('Analytical Advection only works in Scipy mode')
if fieldset.U.interp_method != 'cgrid_velocity':
raise NotImplementedError('Analytical Advection only works with C-grids')
if fieldset.U.grid.gtype not in [GridCode.CurvilinearZGrid, GridCode.RectilinearZGrid]:
raise NotImplementedError('Analytical Advection only works with Z-grids in the vertical')
if funcvars is not None:
self.funcvars = funcvars
elif hasattr(pyfunc, '__code__'):
self.funcvars = list(pyfunc.__code__.co_varnames)
else:
self.funcvars = None
self.funccode = funccode or inspect.getsource(pyfunc.__code__)
# Parse AST if it is not provided explicitly
self.py_ast = py_ast or parse(fix_indentation(self.funccode)).body[0]
if pyfunc is None:
# Extract user context by inspecting the call stack
stack = inspect.stack()
try:
user_ctx = stack[-1][0].f_globals
user_ctx['math'] = globals()['math']
user_ctx['ParcelsRandom'] = globals()['ParcelsRandom']
user_ctx['random'] = globals()['random']
user_ctx['StateCode'] = globals()['StateCode']
user_ctx['OperationCode'] = globals()['OperationCode']
user_ctx['ErrorCode'] = globals()['ErrorCode']
except:
logger.warning("Could not access user context when merging kernels")
user_ctx = globals()
finally:
del stack # Remove cyclic references
# Compile and generate Python function from AST
py_mod = parse("")
py_mod.body = [self.py_ast]
exec(compile(py_mod, "<ast>", "exec"), user_ctx)
self.pyfunc = user_ctx[self.funcname]
else:
self.pyfunc = pyfunc
if version_info[0] < 3:
numkernelargs = len(inspect.getargspec(self.pyfunc).args)
else:
numkernelargs = len(inspect.getfullargspec(self.pyfunc).args)
assert numkernelargs == 3, \
'Since Parcels v2.0, kernels do only take 3 arguments: particle, fieldset, time !! AND !! Argument order in field interpolation is time, depth, lat, lon.'
self.name = "%s%s" % (ptype.name, self.funcname)
# Generate the kernel function and add the outer loop
if self.ptype.uses_jit:
kernelgen = KernelGenerator(fieldset, ptype)
kernel_ccode = kernelgen.generate(deepcopy(self.py_ast),
self.funcvars)
self.field_args = kernelgen.field_args
self.vector_field_args = kernelgen.vector_field_args
fieldset = self.fieldset
for f in self.vector_field_args.values():
Wname = f.W.ccode_name if f.W else 'not_defined'
for sF_name, sF_component in zip([f.U.ccode_name, f.V.ccode_name, Wname], ['U', 'V', 'W']):
if sF_name not in self.field_args:
if sF_name != 'not_defined':
self.field_args[sF_name] = getattr(f, sF_component)
self.const_args = kernelgen.const_args
loopgen = LoopGenerator(fieldset, ptype)
if path.isfile(c_include):
with open(c_include, 'r') as f:
c_include_str = f.read()
else:
c_include_str = c_include
self.ccode = loopgen.generate(self.funcname, self.field_args, self.const_args,
kernel_ccode, c_include_str)
if MPI:
mpi_comm = MPI.COMM_WORLD
mpi_rank = mpi_comm.Get_rank()
basename = path.join(get_cache_dir(), self._cache_key) if mpi_rank == 0 else None
basename = mpi_comm.bcast(basename, root=0)
basename = basename + "_%d" % mpi_rank
else:
basename = path.join(get_cache_dir(), "%s_0" % self._cache_key)
self.src_file = "%s.c" % basename
self.lib_file = "%s.%s" % (basename, 'dll' if platform == 'win32' else 'so')
self.log_file = "%s.log" % basename