From 53f50dd0327b403afa4ecc2b48219332633f8a27 Mon Sep 17 00:00:00 2001
From: Jean-Baptiste Keck <Jean-Baptiste.Keck@imag.fr>
Date: Sun, 1 Nov 2020 21:11:44 +0100
Subject: [PATCH] many fixes
---
README.md | 3 +-
ci/scripts/test.sh | 24 ++---
hysop/__init__.py.in | 7 +-
hysop/backend/device/autotunable_kernel.py | 6 +-
hysop/backend/device/codegen/base/codegen.py | 2 +-
.../device/codegen/base/struct_codegen.py | 4 +-
.../backend/device/codegen/base/variables.py | 14 +--
.../device/codegen/functions/apply_stencil.py | 4 +-
.../device/codegen/functions/cache_load.py | 2 +-
.../device/codegen/functions/compute_index.py | 2 +-
.../device/codegen/kernels/custom_symbolic.py | 27 ++---
.../codegen/kernels/directional_advection.py | 4 +-
.../test_codegen_directional_stretching.py | 2 +-
.../kernels/tests/test_codegen_transpose.py | 2 +-
.../device/codegen/kernels/transpose.py | 2 +-
hysop/backend/device/codegen/symbolic/expr.py | 6 +-
.../kernels/custom_symbolic_time_integrate.py | 4 +-
hysop/backend/device/kernel_autotuner.py | 4 +-
.../opencl/autotunable_kernels/transpose.py | 2 +-
hysop/backend/device/opencl/clpeak.py | 2 +-
.../opencl/opencl_autotunable_kernel.py | 2 +-
.../backend/device/opencl/opencl_operator.py | 2 +-
.../backend/device/opencl/opencl_symbolic.py | 3 +
hysop/backend/device/opencl/opencl_types.py | 6 +-
.../device/opencl/operator/diffusion.py | 12 ++-
.../operator/directional/advection_dir.py | 14 +--
.../device/opencl/operator/external_force.py | 2 +-
hysop/backend/hardware/pci.py | 4 +-
.../host/fortran/operator/diffusion.py | 9 +-
.../host/fortran/operator/fortran_fftw.py | 15 ++-
hysop/backend/host/host_array_backend.py | 4 +-
hysop/backend/host/host_operator.py | 39 +++----
hysop/backend/host/python/operator/curl.py | 2 +-
.../backend/host/python/operator/diffusion.py | 12 +--
.../operator/directional/stretching_dir.py | 5 +
.../host/python/operator/poisson_curl.py | 26 ++---
hysop/core/checkpoints.py | 2 +-
hysop/core/graph/computational_graph.py | 26 ++---
hysop/core/graph/computational_node.py | 4 +-
hysop/core/graph/graph_builder.py | 8 +-
hysop/core/graph/node_requirements.py | 37 ++++---
hysop/core/memory/memory_request.py | 2 +-
hysop/core/mpi/topo_tools.py | 1 -
hysop/fields/continuous_field.py | 2 +-
hysop/fields/discrete_field.py | 2 +-
hysop/fields/ghost_exchangers.py | 2 +-
hysop/fields/tests/test_cartesian.py | 27 +++--
hysop/mesh/cartesian_mesh.py | 2 +-
hysop/numerics/fft/gpyfft_fft.py | 4 +-
hysop/numerics/fft/host_fft.py | 34 +++---
hysop/numerics/interpolation/polynomial.py | 14 +--
hysop/numerics/odesolvers/runge_kutta.py | 8 +-
hysop/numerics/remesh/kernel_generator.py | 14 +--
hysop/numerics/stencil/stencil.py | 2 +-
hysop/numerics/stencil/stencil_generator.py | 2 +-
hysop/numerics/tests/bench_fft.py | 2 +-
hysop/numerics/tests/test_fft.py | 2 +-
hysop/operator/analytic.py | 24 ++---
hysop/operator/base/convergence.py | 2 +-
hysop/operator/base/curl.py | 40 ++++---
.../operator/base/custom_symbolic_operator.py | 8 +-
hysop/operator/base/diffusion.py | 14 ++-
hysop/operator/base/memory_reordering.py | 2 +-
hysop/operator/base/poisson.py | 10 ++
hysop/operator/base/poisson_curl.py | 25 ++++-
hysop/operator/base/solenoidal_projection.py | 58 +++++-----
hysop/operator/base/spectral_operator.py | 66 ++++++++----
hysop/operator/base/stretching_dir.py | 13 ++-
hysop/operator/directional/diffusion_dir.py | 13 +++
hysop/operator/directional/stretching_dir.py | 26 +++++
hysop/operator/hdf_io.py | 22 +++-
hysop/operator/memory_reordering.py | 70 ++++++------
.../operator/tests/test_bilevel_advection.py | 5 +-
hysop/operator/tests/test_custom_symbolic.py | 18 ++--
hysop/operator/tests/test_diffusion.py | 4 +-
.../tests/test_directional_diffusion.py | 6 +-
.../tests/test_directional_stretching.py | 8 +-
hysop/operator/tests/test_poisson.py | 4 +-
.../tests/test_solenoidal_projection.py | 6 +-
hysop/operator/transpose.py | 4 +-
hysop/problem.py | 2 +-
hysop/symbolic/spectral.py | 6 ++
hysop/tools/callback.py | 8 +-
hysop/tools/debug_dumper.py | 4 +-
hysop/tools/decorators.py | 2 +-
hysop/tools/enum.py | 2 +-
hysop/tools/field_utils.py | 2 +-
hysop/tools/hptt_utils.py | 6 +-
hysop/tools/misc.py | 2 +-
hysop/tools/mpi_utils.py | 8 +-
hysop/tools/numba_utils.py | 4 +-
hysop/tools/profiler.py | 4 +-
hysop/tools/spectral_utils.py | 2 +-
hysop/tools/transposition_states.py | 2 +-
hysop/topology/cartesian_descriptor.py | 3 +-
hysop_examples/example_utils.py | 3 +-
hysop_examples/examples/analytic/analytic.py | 2 -
.../particles_above_salt_bc.py | 102 +++++++++---------
.../particles_above_salt_periodic.py | 2 +-
.../particles_above_salt_symmetrized.py | 2 +-
setup.py.in | 2 +-
101 files changed, 631 insertions(+), 464 deletions(-)
diff --git a/README.md b/README.md
index 6a37b8f96..14ed56a2c 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
[]()
-[](https://www.python.org/downloads/release/python-270/)
+[](https://www.python.org/downloads/release/python-380/)
+[](https://www.python.org/downloads/release/python-390/)
[](https://www.apache.org/licenses/LICENSE-2.0)
[](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop/commits/master)
[](https://hub.docker.com/r/keckj/hysop/tags)
diff --git a/ci/scripts/test.sh b/ci/scripts/test.sh
index 1d67f1da2..df3cb5b42 100755
--- a/ci/scripts/test.sh
+++ b/ci/scripts/test.sh
@@ -68,7 +68,7 @@ fi
export PYTHONPATH="${INSTALL_DIR}/lib/python3.8/site-packages:${INSTALL_DIR}"
export MPLBACKEND='cairo'
-export HYSOP_VERBOSE=0
+export HYSOP_VERBOSE=1
export HYSOP_DEBUG=0
export HYSOP_PROFILE=0
export HYSOP_KERNEL_DEBUG=0
@@ -126,16 +126,16 @@ if [ "$RUN_TESTS" = true ]; then
#hysop_test "operator/tests/test_penalization.py"
#hysop_test "operator/tests/test_velocity_correction.py"
#hysop_test "operator/tests/test_restriction_filter.py"
- hysop_test "operator/tests/test_directional_advection.py"
- hysop_test "operator/tests/test_directional_diffusion.py"
- hysop_test "operator/tests/test_directional_stretching.py"
- hysop_test "operator/tests/test_custom_symbolic.py"
- hysop_test "operator/tests/test_spectral_derivative.py"
- hysop_test "operator/tests/test_spectral_curl.py"
- hysop_test "operator/tests/test_diffusion.py"
- hysop_test "operator/tests/test_poisson.py"
- hysop_test "operator/tests/test_solenoidal_projection.py"
- hysop_test "operator/tests/test_poisson_curl.py"
+ #hysop_test "operator/tests/test_directional_advection.py"
+ #hysop_test "operator/tests/test_directional_diffusion.py"
+ #hysop_test "operator/tests/test_directional_stretching.py"
+ #hysop_test "operator/tests/test_custom_symbolic.py"
+ #hysop_test "operator/tests/test_spectral_derivative.py"
+ #hysop_test "operator/tests/test_spectral_curl.py"
+ #hysop_test "operator/tests/test_diffusion.py"
+ #hysop_test "operator/tests/test_poisson.py"
+ #hysop_test "operator/tests/test_solenoidal_projection.py"
+ #hysop_test "operator/tests/test_poisson_curl.py"
${HYSOP_DIR}/fields/tests/test_cartesian.sh
${HYSOP_DIR}/core/tests/test_checkpoint.sh
fi
@@ -163,7 +163,7 @@ if [ "${RUN_EXAMPLES}" = true ]; then
fi
if [ "${HAS_CACHE_DIR}" = true ]; then
- rsync -rtvu "${HYSOP_CACHE_DIR}/" "${CACHE_DIR}/"
+ rsync -rtu "${HYSOP_CACHE_DIR}/" "${CACHE_DIR}/"
find "${CACHE_DIR}" -name '*.lock' -delete
fi
diff --git a/hysop/__init__.py.in b/hysop/__init__.py.in
index 0da4c6dfb..997c1b758 100644
--- a/hysop/__init__.py.in
+++ b/hysop/__init__.py.in
@@ -133,14 +133,17 @@ if '__formatwarning' not in locals():
def __new_formatwarning(warning, category, filename, lineno, line=None):
# filter out useless intel opencl build "warnings" stacktraces
message = str(warning)
- if ('Compilation started' in message) and ('Done.' in message):
+ warning_msg = __formatwarning(warning, category, filename, lineno, line=line)
+ if not warning_msg:
+ pass
+ elif ('Compilation started' in message):
pass
elif ('Non-empty compiler output encountered.' in message):
pass
elif __TRACE_WARNINGS__:
print('::WARNING STACK TRACE::')
traceback.print_stack()
- return __formatwarning(warning, category, filename, lineno, line=line)
+ return warning_msg
warnings.formatwarning = __new_formatwarning
if __TRACE_CALLS__:
diff --git a/hysop/backend/device/autotunable_kernel.py b/hysop/backend/device/autotunable_kernel.py
index 9fdf35af4..155126ca5 100644
--- a/hysop/backend/device/autotunable_kernel.py
+++ b/hysop/backend/device/autotunable_kernel.py
@@ -145,7 +145,7 @@ class AutotunableKernel(object, metaclass=ABCMeta):
s += ss
s += '\nHASHED ARGUMENT {}: {}'.format(i, h)
if kwds:
- items = sorted(kwds.items(), key=lambda x: x[0])
+ items = tuple(sorted(kwds.items(), key=lambda x: x[0]))
if (h is None):
h, s = _hash_karg(*items[0])
else:
@@ -336,7 +336,7 @@ class AutotunableKernel(object, metaclass=ABCMeta):
msg+='and not its instance id.'
msg=msg.format(t, type(v), str(type(v)))
raise RuntimeError(msg)
- items = sorted(extra_parameters.items(), key=lambda x: x[0])
+ items = tuple(sorted(extra_parameters.items(), key=lambda x: x[0]))
return hash(frozenset(items))
@abstractmethod
@@ -707,7 +707,7 @@ class AutotunerWorkConfiguration(object):
for fname in self.filter_names:
fn = self._filters[fname]
- candidates = filter(fn, candidates)
+ candidates = tuple(filter(fn, candidates))
if self.__debug_filters:
candidates, _ = it.tee(candidates)
msg=' *Filter {}:\n {}\n'.format(fname,
diff --git a/hysop/backend/device/codegen/base/codegen.py b/hysop/backend/device/codegen/base/codegen.py
index e2c844801..cc92c7d72 100644
--- a/hysop/backend/device/codegen/base/codegen.py
+++ b/hysop/backend/device/codegen/base/codegen.py
@@ -667,7 +667,7 @@ class CodeGenerator(object):
self.generate(blocks,genset)
if blocks:
entire_code = ''
- blocks = sorted(blocks.items(), key=operator.itemgetter(1))
+ blocks = tuple(sorted(blocks.items(), key=operator.itemgetter(1)))
for bn,(priority,code,comment) in blocks:
if not code:
continue
diff --git a/hysop/backend/device/codegen/base/struct_codegen.py b/hysop/backend/device/codegen/base/struct_codegen.py
index e6b0efee2..3a218a9de 100644
--- a/hysop/backend/device/codegen/base/struct_codegen.py
+++ b/hysop/backend/device/codegen/base/struct_codegen.py
@@ -35,8 +35,8 @@ class StructCodeGenerator(OpenClCodeGenerator):
def c_decl(self):
assert (self.context is not None)
- dtype,cdecl = cl.tools.match_dtype_to_c_struct( \
- self.device,self.ctype.replace('struct',''),self.dtype,context=self.context)
+ (dtype, cdecl) = cl.tools.match_dtype_to_c_struct( \
+ self.device, self.ctype.replace('struct',''), self.dtype, context=self.context)
return cdecl
def gencode(self, comments, ctype_overrides):
diff --git a/hysop/backend/device/codegen/base/variables.py b/hysop/backend/device/codegen/base/variables.py
index 910fc0cd3..a46430f0d 100644
--- a/hysop/backend/device/codegen/base/variables.py
+++ b/hysop/backend/device/codegen/base/variables.py
@@ -430,9 +430,9 @@ class CodegenVariable(object):
if (init is not None):
if compact:
- code = '{}={}'.format(code,init)
+ code = '{}={}'.format(code, init)
else:
- code = '{} $= {}'.format(code,init)
+ code = '{} $= {}'.format(code, init)
elif self.known():
self.force_symbolic(False)
sval = self.sval()
@@ -769,13 +769,13 @@ class CodegenVectorClBuiltin(CodegenVector):
return super(CodegenVectorClBuiltin, self).newvar(name=name, btype=btype, dim=dim,
**kwds)
- def view(self,name,components,const=False):
- if isinstance(components,slice):
+ def view(self, name, components, const=False):
+ if isinstance(components, slice):
start, stop, step = components.indices(self.dim)
- it = range(start,stop,step)
+ it = tuple(range(start, stop, step))
dim = len(it)
elif components is Ellipsis:
- it = range(self.dim)
+ it = tuple(range(self.dim))
dim = self.dim
else:
raise ValueError('Unknown components type {}.'.format(components.__class__.__name__))
@@ -831,7 +831,7 @@ class CodegenVectorClBuiltin(CodegenVector):
if isinstance(key, range):
key = tuple(key)
if isinstance(key,slice) :
- ids = range(*key.indices(dim))
+ ids = tuple(range(*key.indices(dim)))
if self.declared and key.indices(dim)==(0,dim,1):
return self.name
else:
diff --git a/hysop/backend/device/codegen/functions/apply_stencil.py b/hysop/backend/device/codegen/functions/apply_stencil.py
index d9d83534e..54e8f1e5f 100644
--- a/hysop/backend/device/codegen/functions/apply_stencil.py
+++ b/hysop/backend/device/codegen/functions/apply_stencil.py
@@ -31,7 +31,7 @@ class ApplyStencilFunction(OpenClFunctionCodeGenerator):
symbol2vars = first_not_None(symbol2vars, {})
assert set(symbol2vars.keys())==stencil.variables()
- extra_inputs = set(extra_inputs + symbol2vars.values())
+ extra_inputs = set(extra_inputs).union(symbol2vars.values())
scalar_inputs = set(scalar_inputs)
vector_inputs = set(vector_inputs)
@@ -40,7 +40,7 @@ class ApplyStencilFunction(OpenClFunctionCodeGenerator):
vtype = typegen.vtype(ftype,components)
if (vector_suffixes is None):
- vector_suffixes = range(components)
+ vector_suffixes = tuple(range(components))
has_custom_id = (custom_id is not None)
diff --git a/hysop/backend/device/codegen/functions/cache_load.py b/hysop/backend/device/codegen/functions/cache_load.py
index 2cdd8c664..f54332125 100644
--- a/hysop/backend/device/codegen/functions/cache_load.py
+++ b/hysop/backend/device/codegen/functions/cache_load.py
@@ -179,7 +179,7 @@ class CacheLoadFunction(OpenClFunctionCodeGenerator):
s.barrier(_local=True)
with s._block_():
- nested_loops = [_cache_iterate_(i) for i in range(work_dim-1,-1,-1)]
+ nested_loops = [_cache_iterate_(i) for i in range(work_dim-1, -1, -1)]
with nested(*nested_loops):
with s._block_():
s.append(LID.declare(const=True,init=compute_index(idx=local_pos,
diff --git a/hysop/backend/device/codegen/functions/compute_index.py b/hysop/backend/device/codegen/functions/compute_index.py
index a6188ae6b..f349df121 100644
--- a/hysop/backend/device/codegen/functions/compute_index.py
+++ b/hysop/backend/device/codegen/functions/compute_index.py
@@ -36,7 +36,7 @@ class ComputeIndexFunction(OpenClFunctionCodeGenerator):
with s._if_(wrap()):
self.append('{idx} = ({idx}+{size}) % {size};'.format(idx=idx(),size=size))
ss = '{}'.format(idx[dim-1])
- for i in range(dim-2,-1,-1):
+ for i in range(dim-2, -1, -1):
ss = '({}*{}+{})'.format(ss,size[i],idx[i])
ret = 'return {};'.format(ss)
self.append(ret)
diff --git a/hysop/backend/device/codegen/kernels/custom_symbolic.py b/hysop/backend/device/codegen/kernels/custom_symbolic.py
index 30af9a64f..47eb23757 100644
--- a/hysop/backend/device/codegen/kernels/custom_symbolic.py
+++ b/hysop/backend/device/codegen/kernels/custom_symbolic.py
@@ -300,8 +300,7 @@ class SymbolicCodegenContext(object):
array_contiguous_ghosts = SortedDict()
array_sizes = SortedDict()
- arrays = set(f for f in (expr_info.input_arrays.values() +
- expr_info.output_arrays.values()))
+ arrays = set(expr_info.input_arrays.values()).union(expr_info.output_arrays.values())
for a in arrays:
ctype = a.ctype
@@ -710,7 +709,7 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
xmin, dx, inv_dx = None, None, None
else:
declare_mesh_properties = True
- mesh_info_0 = field_mesh_infos.values()[0]
+ mesh_info_0 = next(iter(field_mesh_infos.values()))
dx = mesh_info_0['dx'].alias('dx', const=True)
inv_dx = mesh_info_0['inv_dx'].alias('inv_dx', const=True)
xmin = mesh_info_0['local_mesh']['xmin'].alias('xmin', const=True)
@@ -1048,7 +1047,7 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
if (granularity>0):
self.jumpline()
- self.decl_vars(*tuple([loop_id]+array_vids.values()))
+ self.decl_vars(*tuple([loop_id]+list(array_vids.values())))
if self.field_mesh_infos:
x0 = csc.space_symbols[symbolic_space_symbols[0]]
@@ -1079,11 +1078,11 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
code = idx_i.affect(self, init=loop_id[i])
if self.field_mesh_infos:
- fmi = self.field_mesh_infos[array_vids.keys()[0]]
+ fmi = self.field_mesh_infos[next(iter(array_vids))]
for i in range(kdim, kdim+granularity):
xi = csc.space_symbols[symbolic_space_symbols[i]]
code = '{xi} = {x0} + {vid}*{dx};'.format(
- xi=xi, vid=array_vids.values()[0][i],
+ xi=xi, vid=next(iter(array_vids.values()))[i],
voffset=self.voffset,
x0=fmi['local_mesh']['xmin'][i], dx=fmi['dx'][i])
self.append(code)
@@ -1123,10 +1122,10 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
code = idx_i.affect(self, init=loop_id[i])
if self.field_mesh_infos:
- fmi = self.field_mesh_infos[array_vids.keys()[0]]
+ fmi = self.field_mesh_infos[next(iter(array_vids))]
xi = csc.space_symbols[symbolic_space_symbols[i]]
code = '{xi} = {x0} + {vid}*{dx};'.format(
- xi=xi, vid=array_vids.values()[0][i],
+ xi=xi, vid=next(iter(array_vids.values()))[i],
voffset=self.voffset,
x0=fmi['local_mesh']['xmin'][i], dx=fmi['dx'][i])
self.append(code)
@@ -1156,11 +1155,11 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
align=True)
if self.field_mesh_infos:
- fmi = self.field_mesh_infos[array_vids.keys()[0]]
+ fmi = self.field_mesh_infos[next(iter(array_vids))]
xi = csc.space_symbols[symbolic_space_symbols[i]]
code = '{xi} = {x0} + convert_{vftype}({vid}+{voffset}+{lo})*{dx};'
code=code.format(
- xi=xi, vid=array_vids.values()[0][i], lo=local_offset,
+ xi=xi, vid=next(iter(array_vids.values()))[i], lo=local_offset,
voffset=self.voffset, vftype=csc.vftype,
x0=fmi['local_mesh']['xmin'][i], dx=fmi['dx'][i])
self.append(code)
@@ -1209,7 +1208,7 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
except:
raise
- nested_loops = [work_iterate(i) for i in range(kdim-1,-1,-1)]
+ nested_loops = [work_iterate(i) for i in range(kdim-1, -1, -1)]
return nested_loops
def gencode(self):
@@ -1256,8 +1255,10 @@ class CustomSymbolicKernelGenerator(KernelCodeGenerator, metaclass=ABCMeta):
s.decl_aligned_vars(*(aij for ai in s.array_args.values() for aij in ai.values()))
s.decl_aligned_vars(*csc.buffer_args.values())
s.comment('Local and private memory arrays')
- s.decl_aligned_vars(*(aij for ai in array_local_data.values() +
- array_local_rdata.values()+array_private_data.values()
+ s.decl_aligned_vars(*(aij for ai in
+ tuple(array_local_data.values()) +
+ tuple(array_local_rdata.values()) +
+ tuple(array_private_data.values())
for aij in filter(lambda x:x, ai.values())))
s.comment('Iterating over array lines')
nested_loops = self._generate_loop_context()
diff --git a/hysop/backend/device/codegen/kernels/directional_advection.py b/hysop/backend/device/codegen/kernels/directional_advection.py
index f59792772..85a941c1f 100644
--- a/hysop/backend/device/codegen/kernels/directional_advection.py
+++ b/hysop/backend/device/codegen/kernels/directional_advection.py
@@ -545,7 +545,7 @@ class DirectionalAdvectionKernelGenerator(KernelCodeGenerator):
yield ctx
except:
raise
- nested_loops = [_work_iterate_(i) for i in range(work_dim-1,-1,-1)]
+ nested_loops = [_work_iterate_(i) for i in range(work_dim-1, -1, -1)]
with s._kernel_():
field_infos.declare(s)
@@ -575,7 +575,7 @@ class DirectionalAdvectionKernelGenerator(KernelCodeGenerator):
with s._align_() as al:
npart.declare(al, const=True, align=True)
- poffset.declare(al, init=range(nparticles), const=True, align=True)
+ poffset.declare(al, init=tuple(range(nparticles)), const=True, align=True)
s.jumpline()
if is_cached:
diff --git a/hysop/backend/device/codegen/kernels/tests/test_codegen_directional_stretching.py b/hysop/backend/device/codegen/kernels/tests/test_codegen_directional_stretching.py
index 1780cb3de..adbb6a169 100644
--- a/hysop/backend/device/codegen/kernels/tests/test_codegen_directional_stretching.py
+++ b/hysop/backend/device/codegen/kernels/tests/test_codegen_directional_stretching.py
@@ -172,7 +172,7 @@ class TestDirectionalStretching(object):
def deriv(field):
res = np.zeros_like(field)
- for i in range(-order//2,order//2+1,1):
+ for i in range(-order//2, order//2+1, 1):
res += stencil[i+order//2]*np.roll(field,-i,axis=2)
return res*self.inv_dx[0]
diff --git a/hysop/backend/device/codegen/kernels/tests/test_codegen_transpose.py b/hysop/backend/device/codegen/kernels/tests/test_codegen_transpose.py
index 5d6444b4b..f9de9412f 100644
--- a/hysop/backend/device/codegen/kernels/tests/test_codegen_transpose.py
+++ b/hysop/backend/device/codegen/kernels/tests/test_codegen_transpose.py
@@ -249,7 +249,7 @@ class TestTranspose(object):
local_work_size[i] = 1
max_work = device.max_work_group_size
while (prod(local_work_size) > max_work):
- for i in range(work_dim-1,-1,-1):
+ for i in range(work_dim-1, -1, -1):
if local_work_size[i] > 1:
break
local_work_size[i] //= 2
diff --git a/hysop/backend/device/codegen/kernels/transpose.py b/hysop/backend/device/codegen/kernels/transpose.py
index cdc6d0abc..7f399b71b 100644
--- a/hysop/backend/device/codegen/kernels/transpose.py
+++ b/hysop/backend/device/codegen/kernels/transpose.py
@@ -177,7 +177,7 @@ class TransposeKernelGenerator(KernelCodeGenerator):
if len(_axes) != pdim:
raise ValueError(msg)
- _permutation = (axes != range(pdim))
+ _permutation = (axes != set(range(pdim)))
_naxes = sum(_permutation)
if (_naxes == 0):
msg='There is nothing to transpose with given axes {}.'
diff --git a/hysop/backend/device/codegen/symbolic/expr.py b/hysop/backend/device/codegen/symbolic/expr.py
index 507ac6a40..1ee0e5a7e 100644
--- a/hysop/backend/device/codegen/symbolic/expr.py
+++ b/hysop/backend/device/codegen/symbolic/expr.py
@@ -368,9 +368,9 @@ class UpdateVars(Expr):
for (src, dst) in self.private_stores:
dst.affect(al, init=src, align=True)
if self.local_stores:
- srcs = map(lambda x: x[0], self.local_stores)
- ptrs = map(lambda x: x[1], self.local_stores)
- offsets = map(lambda x: x[2], self.local_stores)
+ srcs = tuple(map(lambda x: x[0], self.local_stores))
+ ptrs = tuple(map(lambda x: x[1], self.local_stores))
+ offsets = tuple(map(lambda x: x[2], self.local_stores))
codegen.multi_vstore_if(csc.is_last_active,
lambda i: '{}+{} < {}'.format(csc.full_offset, i, csc.compute_grid_size[0]),
csc.vectorization, csc.local_offset,
diff --git a/hysop/backend/device/codegen/symbolic/kernels/custom_symbolic_time_integrate.py b/hysop/backend/device/codegen/symbolic/kernels/custom_symbolic_time_integrate.py
index f07fd2571..7f17339ac 100644
--- a/hysop/backend/device/codegen/symbolic/kernels/custom_symbolic_time_integrate.py
+++ b/hysop/backend/device/codegen/symbolic/kernels/custom_symbolic_time_integrate.py
@@ -65,8 +65,8 @@ class CustomSymbolicTimeIntegrateKernelGenerator(CustomSymbolicKernelGenerator):
dval = CustomSymbolicFunction.default_out_of_bounds_value(ctype_to_dtype(ctype))
if is_local:
- size = csc.array_size(lhs.field, lhs.index)
- assert (size > 2*ghosts)
+ size = int(csc.array_size(lhs.field, lhs.index))
+ assert (size > 2*ghosts), (size, 2*ghosts)
vload = Vload(tg, ctype, vectorization, default_val=dval,
itype=itype, restrict=True, storage=var.storage,
known_args=dict(size=size))
diff --git a/hysop/backend/device/kernel_autotuner.py b/hysop/backend/device/kernel_autotuner.py
index 41a1c12ea..12dd091a1 100644
--- a/hysop/backend/device/kernel_autotuner.py
+++ b/hysop/backend/device/kernel_autotuner.py
@@ -462,7 +462,7 @@ class KernelAutotuner(object, metaclass=ABCMeta):
keep_only = max(previous_pow2(kept_count),1)
self._print_first_step_results(total_count, kept_count, pruned_count,
failed_count, keep_only)
- candidates = sorted(bench_results.items(), key=lambda x: x[1][self.kernel_statistics_idx])
+ candidates = tuple(sorted(bench_results.items(), key=lambda x: x[1][self.kernel_statistics_idx]))
candidates = candidates[:keep_only]
while(len(candidates)>1):
step_count += 1
@@ -478,7 +478,7 @@ class KernelAutotuner(object, metaclass=ABCMeta):
best_stats=best_stats,
global_work_size=global_work_size,
local_work_size=local_work_size)
- candidates = sorted(candidates, key=lambda x: x[1][self.kernel_statistics_idx])
+ candidates = tuple(sorted(candidates, key=lambda x: x[1][self.kernel_statistics_idx]))
self._print_step_results(candidates, self.kernel_statistics_idx)
candidates = candidates[:max(previous_pow2(len(candidates)),1)]
ks.push_step(step_count, candidates)
diff --git a/hysop/backend/device/opencl/autotunable_kernels/transpose.py b/hysop/backend/device/opencl/autotunable_kernels/transpose.py
index b39d0742f..c64306d84 100644
--- a/hysop/backend/device/opencl/autotunable_kernels/transpose.py
+++ b/hysop/backend/device/opencl/autotunable_kernels/transpose.py
@@ -154,7 +154,7 @@ class OpenClAutotunableTransposeKernel(OpenClAutotunableKernel):
imax = int(math.log(max_tile_size, 2))
jmax = int(math.log(max_tile_size, 3)) if flag in (AutotunerFlags.EXHAUSTIVE,) else 0
tile_sizes = tuple( int((2**i)*(3**j))
- for (i,j) in it.product(range(0,imax+1), range(0,jmax+1)))
+ for (i,j) in it.product(range(0, imax+1), range(0, jmax+1)))
tile_sizes = (max_tile_size,) + tuple(sorted(tile_sizes, reverse=True))
tile_sizes = tuple(filter(lambda x: (x>=max_tile_size//8) and (x<=max_tile_size), tile_sizes))
diff --git a/hysop/backend/device/opencl/clpeak.py b/hysop/backend/device/opencl/clpeak.py
index 46d322f6a..c1504b8c2 100644
--- a/hysop/backend/device/opencl/clpeak.py
+++ b/hysop/backend/device/opencl/clpeak.py
@@ -251,7 +251,7 @@ class ClPeakInfo(object):
def criteria(key):
values = transfer_bandwidth[key]
return -(values['enqueuewritebuffer'] + values['enqueuereadbuffer'])
- params = sorted(transfer_bandwidth.keys(), key=criteria)
+ params = tuple(sorted(transfer_bandwidth.keys(), key=criteria))
self._set_exec_params(*params[0])
self._preferred_exec_params = params[0]
self._transfer_bandwidth_values = transfer_bandwidth
diff --git a/hysop/backend/device/opencl/opencl_autotunable_kernel.py b/hysop/backend/device/opencl/opencl_autotunable_kernel.py
index d25c49df9..6f5e2e6f6 100644
--- a/hysop/backend/device/opencl/opencl_autotunable_kernel.py
+++ b/hysop/backend/device/opencl/opencl_autotunable_kernel.py
@@ -246,7 +246,7 @@ class OpenClAutotunableKernel(AutotunableKernel):
global_work_size = tuple(x for x in global_work_size) + (1,)*(3-dim)
local_work_size = tuple(x for x in local_work_size) + (1,)*(3-dim)
- sorted_args = sorted(args_mapping.items(), key=lambda x:x[1][0])
+ sorted_args = tuple(sorted(args_mapping.items(), key=lambda x:x[1][0]))
assert len(sorted_args) == len(args_list)
dump_folder = self.autotuner_config.dump_folder
diff --git a/hysop/backend/device/opencl/opencl_operator.py b/hysop/backend/device/opencl/opencl_operator.py
index 4c942f37f..3dcff415c 100644
--- a/hysop/backend/device/opencl/opencl_operator.py
+++ b/hysop/backend/device/opencl/opencl_operator.py
@@ -90,7 +90,7 @@ class OpenClOperator(ComputationalGraphOperator, metaclass=ABCMeta):
if not _vars:
msg='Cannot deduce domain without input or output fields.'
raise RuntimeError(msg)
- domain = _vars.keys()[0].domain
+ domain = next(iter(_vars)).domain
mpi_params = MPIParams(comm=domain.task_comm,
task_id=domain.current_task())
cl_env = get_or_create_opencl_env(mpi_params)
diff --git a/hysop/backend/device/opencl/opencl_symbolic.py b/hysop/backend/device/opencl/opencl_symbolic.py
index a57ec6a0c..84cda9eeb 100644
--- a/hysop/backend/device/opencl/opencl_symbolic.py
+++ b/hysop/backend/device/opencl/opencl_symbolic.py
@@ -50,6 +50,9 @@ class OpenClSymbolic(OpenClOperator):
am.update(cls.__available_methods)
return am
+ @debug
+ def __new__(cls, **kwds):
+ return super(OpenClSymbolic, cls).__new__(cls, **kwds)
@debug
def __init__(self, **kwds):
diff --git a/hysop/backend/device/opencl/opencl_types.py b/hysop/backend/device/opencl/opencl_types.py
index 000dd1515..f62930e1c 100644
--- a/hysop/backend/device/opencl/opencl_types.py
+++ b/hysop/backend/device/opencl/opencl_types.py
@@ -447,9 +447,9 @@ class OpenClTypeGen(TypeGen):
msg += 'and regular expression \'{}\'.'
msg=msg.format(sversion,_regexp)
raise RuntimeError(msg)
- major = match.group(1)
- minor = match.group(2)
- return (major,minor)
+ major = int(match.group(1))
+ minor = int(match.group(2))
+ return (major, minor)
def dtype_from_str(self,stype):
stype = stype.replace('ftype', self.fbtype).replace('fbtype',self.fbtype)
diff --git a/hysop/backend/device/opencl/operator/diffusion.py b/hysop/backend/device/opencl/operator/diffusion.py
index 9d7bbdc2c..48f2b697e 100644
--- a/hysop/backend/device/opencl/operator/diffusion.py
+++ b/hysop/backend/device/opencl/operator/diffusion.py
@@ -17,7 +17,11 @@ class OpenClDiffusion(DiffusionOperatorBase, OpenClSymbolic):
"""
Solves the diffusion equation using an OpenCL FFT backend.
"""
-
+
+ @debug
+ def __new__(cls, **kwds):
+ return super(OpenClDiffusion, cls).__new__(cls, **kwds)
+
@debug
def __init__(self, **kwds):
super(OpenClDiffusion, self).__init__(**kwds)
@@ -29,7 +33,7 @@ class OpenClDiffusion(DiffusionOperatorBase, OpenClSymbolic):
for (i,(Ft,Wn)) in enumerate(zip(self.forward_transforms, self.wave_numbers)):
Fhs = Ft.output_symbolic_array('F{}_hat'.format(i))
indices = local_indices_symbols[:Fhs.dim]
-
+
kname = 'filter_diffusion_{}d_{}'.format(Fhs.dim, i)
kernel_names += (kname,)
@@ -38,11 +42,11 @@ class OpenClDiffusion(DiffusionOperatorBase, OpenClSymbolic):
indexed_Wi = self.tg._indexed_wave_numbers[Wi]
F += indexed_Wi
expr = Assignment(Fhs, Fhs / (1 - nu*dt*F))
-
+
self.require_symbolic_kernel(kname, expr)
self._kernel_names = kernel_names
-
+
@debug
def setup(self, work):
super(OpenClDiffusion, self).setup(work)
diff --git a/hysop/backend/device/opencl/operator/directional/advection_dir.py b/hysop/backend/device/opencl/operator/directional/advection_dir.py
index 45ec39661..346e57752 100644
--- a/hysop/backend/device/opencl/operator/directional/advection_dir.py
+++ b/hysop/backend/device/opencl/operator/directional/advection_dir.py
@@ -175,26 +175,28 @@ class OpenClDirectionalAdvection(DirectionalAdvectionBase, OpenClDirectionalOper
if self.DEBUG:
queue.flush()
queue.finish()
+ dfin = tuple(self.dadvected_fields_in.values())
+ dfout = tuple(self.dadvected_fields_out.values())
print('OPENCL_DT= {}'.format(dt))
self.advection_kernel_launcher(queue=queue, dt=dt).wait()
print('OPENCL_P')
self.dposition.print_with_ghosts()
print('OPENCL_Sin (before remesh)')
- print(self.dadvected_fields_in.values()[0].data[0].get(queue=queue))
+ print(dfin[0].data[0].get(queue=queue))
print('OPENCL_Sout (before remesh)')
- print(self.dadvected_fields_out.values()[0].data[0].get(queue=queue))
+ print(dfout.data[0].get(queue=queue))
print()
self.remesh_kernel_launcher(queue=queue).wait()
print('OPENCL_Sout (before accumulation)')
- data = self.dadvected_fields_out.values()[0].data[0]
+ data = dfout[0].data[0]
print(data.get(queue=queue))
print('OPENCL_Sout (before accumulation, no ghosts) ID={}'.format(id(data)))
- self.dadvected_fields_out.values()[0].print_with_ghosts()
+ dfout[0].print_with_ghosts()
self.accumulate_and_exchange(queue=queue).wait()
print('OPENCL_Sout (after accumulation)')
- print(self.dadvected_fields_out.values()[0].data[0])
+ print(dfout[0].data[0])
print('OPENCL_Sout (after accumulation, no ghosts)')
- self.dadvected_fields_out.values()[0].print_with_ghosts()
+ dfout[0].print_with_ghosts()
else:
self.all_kernels(queue=queue, dt=dt)
diff --git a/hysop/backend/device/opencl/operator/external_force.py b/hysop/backend/device/opencl/operator/external_force.py
index f5e66c6df..dcc2690d3 100644
--- a/hysop/backend/device/opencl/operator/external_force.py
+++ b/hysop/backend/device/opencl/operator/external_force.py
@@ -108,7 +108,7 @@ class SymbolicExternalForce(ExternalForce):
if field in self._diffusion:
assert field in backward_transforms, field.name
replace = {sf:forward_transforms[sf.field].s for sf in efields}
- frame = replace.values()[0].frame
+ frame = next(iter(replace.values)).frame
e = e.xreplace(replace)
fft_expressions += (e,)
diff --git a/hysop/backend/hardware/pci.py b/hysop/backend/hardware/pci.py
index 483c7cc87..fef7bd6a2 100644
--- a/hysop/backend/hardware/pci.py
+++ b/hysop/backend/hardware/pci.py
@@ -299,7 +299,7 @@ class PciBridge(TopologyObject):
super(PciBridge, self).__init__(parent, bridge)
def pci_devices(self, split=False):
- devs = sorted(self._pci_devices, key=lambda x: x.os_index())
+ devs = tuple(sorted(self._pci_devices, key=lambda x: x.os_index()))
if split:
devices = [dev for dev in devs if isinstance(dev,PciBridge)]
devices +=[dev for dev in devs if isinstance(dev,PciDevice)]
@@ -346,7 +346,7 @@ class PciBridge(TopologyObject):
pci_device = pci_device.to_string(expand_pci_tree)
pci_device = pci_device.split('\n')
pci_device[0] = '|--'+pci_device[0]
- for i in range(1,len(pci_device)):
+ for i in range(1, len(pci_device)):
pci_device[i] = '| '+pci_device[i]
if (dev_id==0) and expand_pci_tree:
pci_device = ['|']+pci_device
diff --git a/hysop/backend/host/fortran/operator/diffusion.py b/hysop/backend/host/fortran/operator/diffusion.py
index a01cd44c1..036a2b77d 100644
--- a/hysop/backend/host/fortran/operator/diffusion.py
+++ b/hysop/backend/host/fortran/operator/diffusion.py
@@ -10,8 +10,13 @@ from hysop.core.graph.graph import op_apply
class DiffusionFFTW(FortranFFTWOperator):
@debug
- def __init__(self, Fin, Fout,
- nu, variables, dt, **kargs):
+ def __new__(cls, Fin, Fout, nu, variables, dt, **kargs):
+ return super(DiffusionFFTW, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ input_params=None, **kargs)
+
+ @debug
+ def __init__(self, Fin, Fout, nu, variables, dt, **kargs):
"""Diffusion operator base.
Parameters
diff --git a/hysop/backend/host/fortran/operator/fortran_fftw.py b/hysop/backend/host/fortran/operator/fortran_fftw.py
index 643edfdaa..03067d585 100644
--- a/hysop/backend/host/fortran/operator/fortran_fftw.py
+++ b/hysop/backend/host/fortran/operator/fortran_fftw.py
@@ -25,6 +25,11 @@ class FortranFFTWOperator(FortranOperator):
fftw2py interface.
"""
+ @debug
+ def __new__(cls, input_fields, output_fields, **kwds):
+ return super(FortranFFTWOperator, cls).__new__(cls,
+ input_fields=input_fields, output_fields=output_fields, **kwds)
+
@debug
def __init__(self, input_fields, output_fields, **kwds):
"""
@@ -44,8 +49,8 @@ class FortranFFTWOperator(FortranOperator):
check_instance(output_fields, dict, keys=Field,
values=CartesianTopologyDescriptors)
- nb_components =input_fields.keys()[0].nb_components
- tensor_fields = set(input_fields.keys()+output_fields.keys())
+ nb_components = next(iter(input_fields)).nb_components
+ tensor_fields = set(input_fields.keys()).union(output_fields.keys())
for tf in tensor_fields:
for fi in tf.fields:
if (fi.dtype != HYSOP_REAL):
@@ -66,7 +71,7 @@ class FortranFFTWOperator(FortranOperator):
# Special case: 3D diffusion of a scalar
self._scalar_3d = (nb_components == 1) and all(tf.nb_components==1 for tf in tensor_fields)
- domain = self.input_fields.keys()[0].domain
+ domain = next(iter(self.input_fields)).domain
self.dim = domain.dim
self.domain = domain
@@ -92,7 +97,7 @@ class FortranFFTWOperator(FortranOperator):
def handle_topologies(self, input_topology_states, output_topology_states):
super(FortranFFTWOperator,self).handle_topologies(input_topology_states, output_topology_states)
- topology = self.input_fields.values()[0].topology
+ topology = next(iter(self.input_fields.values())).topology
for (field,topoview) in self.input_fields.items():
assert all(topoview.topology.cart_shape == topology.cart_shape), 'topology mismatch'
for (field,topoview) in self.output_fields.items():
@@ -104,7 +109,7 @@ class FortranFFTWOperator(FortranOperator):
if self.discretized:
return
super(FortranFFTWOperator,self).discretize()
- topo_view = self.input_discrete_fields.values()[0].topology
+ topo_view = next(iter(self.input_discrete_fields.values())).topology
self._fftw_discretize(topo_view)
@debug
diff --git a/hysop/backend/host/host_array_backend.py b/hysop/backend/host/host_array_backend.py
index af003b8df..ae05dcf9b 100644
--- a/hysop/backend/host/host_array_backend.py
+++ b/hysop/backend/host/host_array_backend.py
@@ -264,9 +264,9 @@ class HostArrayBackend(ArrayBackend):
self._unsupported_argument('empty_like', 'subok', subok, True)
if (order is None) or (order == MemoryOrdering.SAME_ORDER):
try:
- if a.flags['C_CONTIGUOUS']:
+ if a.flags.c_contiguous:
order = MemoryOrdering.C_CONTIGUOUS
- elif a.flags['F_CONTIGUOUS']:
+ elif a.flags.f_contiguous:
order = MemoryOrdering.F_CONTIGUOUS
else:
order = default_order
diff --git a/hysop/backend/host/host_operator.py b/hysop/backend/host/host_operator.py
index f52750eee..b2bbf16ae 100644
--- a/hysop/backend/host/host_operator.py
+++ b/hysop/backend/host/host_operator.py
@@ -41,26 +41,29 @@ class HostOperator(ComputationalGraphOperator, metaclass=ABCMeta):
return set([Backend.HOST])
+class OpenClMappedMemoryObjectGetter(object):
+ def __new__(cls, obj, evt, **kwds):
+ return super(OpenClMappedMemoryObjectGetter, cls).__new__(cls, **kwds)
+
+ def __init__(self, obj, evt, **kwds):
+ super(OpenClMappedMemoryObjectGetter, self).__init__(**kwds)
+ check_instance(obj, OpenClMappable)
+ self.__obj = obj
+ self.__evt = evt
+
+ def __getitem__(self, key):
+ return obj.get_mapped_object(key=key)
+
+ @property
+ def evt(self):
+ return self.__evt
+
class OpenClMappable(object):
"""
Extend host operator capabilities to work on mapped opencl buffers
"""
- class OpenClMappedMemoryObjectGetter(object):
- def __new__(cls, obj, evt):
- return super(OpenClMappedMemoryObjectGetter, cls).__new__(cls)
- def __init__(self, obj, evt):
- super(OpenClMappedMemoryObjectGetter, self).__init__()
- check_instance(obj, OpenClMappable)
- self.__obj = obj
- self.__evt = evt
- def __getitem__(self, key):
- return obj.get_mapped_object(key=key)
- @property
- def evt(self):
- return self.__evt
-
@classmethod
def supported_backends(cls):
sb = super(OpenClMappable, cls).supported_backends()
@@ -119,7 +122,7 @@ class OpenClMappable(object):
self.__mapped_objects = {}
def __del__(self):
- self.unmap_objects()
+ self.unmap_objects(force=True)
@property
def cl_env(self):
@@ -207,9 +210,9 @@ class OpenClMappable(object):
self.__mapped = True
return evt
- def unmap_objects(self):
+ def unmap_objects(self, force=False):
msg='Device memory objects have already been unmapped from host.'
- assert self.__mapped, msg
+ assert force or self.__mapped, msg
self.__mapped_objects.clear()
self.__mapped = False
@@ -234,7 +237,7 @@ class OpenClMappable(object):
queue = first_not_None(queue, self.cl_env.default_queue)
try:
evt = self.map_objects(queue, is_blocking)
- yield self.OpenClMappedMemoryObjectGetter(self, evt)
+ yield OpenClMappedMemoryObjectGetter(self, evt)
except:
raise
finally:
diff --git a/hysop/backend/host/python/operator/curl.py b/hysop/backend/host/python/operator/curl.py
index 14666ad2e..305017c3d 100644
--- a/hysop/backend/host/python/operator/curl.py
+++ b/hysop/backend/host/python/operator/curl.py
@@ -68,12 +68,12 @@ def filter_curl_3d__1(Fin, K, Fout):
for k in range(0, Fin.shape[2]):
Fout[i,j,k] = -K[k]*Fin[i,j,k]
+
class PythonSpectralCurl(SpectralCurlOperatorBase, HostOperator):
"""
Compute the curl by using an python FFT backend.
"""
-
def setup(self, work):
super(PythonSpectralCurl, self).setup(work=work)
diff --git a/hysop/backend/host/python/operator/diffusion.py b/hysop/backend/host/python/operator/diffusion.py
index ec36df387..9f8e5d0b9 100644
--- a/hysop/backend/host/python/operator/diffusion.py
+++ b/hysop/backend/host/python/operator/diffusion.py
@@ -20,7 +20,7 @@ class PythonDiffusion(DiffusionOperatorBase, OpenClMappable, HostOperator):
"""
Solves the implicit diffusion equation using numpy fft.
"""
-
+
@classmethod
def build_diffusion_filter(cls, dim, *args, **kwds):
target = kwds.get('target', __DEFAULT_NUMBA_TARGET__)
@@ -71,18 +71,18 @@ class PythonDiffusion(DiffusionOperatorBase, OpenClMappable, HostOperator):
raise NotImplementedError(msg)
return functools.partial(F, *args)
-
+
def setup(self, work):
super(PythonDiffusion, self).setup(work=work)
diffusion_filters = ()
- for (Fo,Ft,Kd) in zip(self.dFout.dfields,
- self.forward_transforms,
- self.all_dkds):
+ for (Fo,Ft,Kd) in zip(self.dFout.dfields,
+ self.forward_transforms,
+ self.all_dkds):
args = (Ft.full_output_buffer,) + tuple(Kd)
F = self.build_diffusion_filter(Fo.dim, *args)
diffusion_filters += (F,)
self.diffusion_filters = diffusion_filters
-
+
@op_apply
def apply(self, simulation, **kwds):
diff --git a/hysop/backend/host/python/operator/directional/stretching_dir.py b/hysop/backend/host/python/operator/directional/stretching_dir.py
index 259eedb43..ead3d9c42 100644
--- a/hysop/backend/host/python/operator/directional/stretching_dir.py
+++ b/hysop/backend/host/python/operator/directional/stretching_dir.py
@@ -14,6 +14,11 @@ from hysop.numerics.odesolvers.runge_kutta import ExplicitRungeKutta, Euler, RK2
class PythonDirectionalStretching(DirectionalStretchingBase, HostDirectionalOperator):
+ @debug
+ def __new__(cls, formulation, **kwds):
+ return super(PythonDirectionalStretching, cls).__new__(cls,
+ formulation=formulation, **kwds)
+
@debug
def __init__(self, formulation, **kwds):
super(PythonDirectionalStretching, self).__init__(formulation=formulation, **kwds)
diff --git a/hysop/backend/host/python/operator/poisson_curl.py b/hysop/backend/host/python/operator/poisson_curl.py
index 5e724b48c..3e8182938 100644
--- a/hysop/backend/host/python/operator/poisson_curl.py
+++ b/hysop/backend/host/python/operator/poisson_curl.py
@@ -9,7 +9,7 @@ from hysop.tools.numba_utils import make_numba_signature, prange
from hysop.core.graph.graph import op_apply
from hysop.backend.host.host_operator import HostOperator, OpenClMappable
from hysop.operator.base.poisson_curl import SpectralPoissonCurlOperatorBase
-
+
from hysop.backend.host.python.operator.diffusion import PythonDiffusion
from hysop.backend.host.python.operator.poisson import PythonPoisson
from hysop.backend.host.python.operator.solenoidal_projection import PythonSolenoidalProjection
@@ -19,7 +19,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
"""
Solves the poisson rotational equation using numpy fftw.
"""
-
+
@classmethod
def build_filter_curl_2d__0_m(cls, FIN, K, FOUT, target=__DEFAULT_NUMBA_TARGET__):
args=(FIN,K,FOUT)
@@ -51,7 +51,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
def build_filter_curl_3d__0_n(cls, FIN, K, FOUT, target=__DEFAULT_NUMBA_TARGET__):
args=(FIN,K,FOUT)
signature, _ = make_numba_signature(*args)
- layout='(n,m,p),(n)->(n,m,p)'
+ layout='(n,m,p),(n)->(n,m,p)'
@nb.guvectorize([signature], layout,
target=target, nopython=True, cache=True)
def filter_curl_3d__0_n(Fin, K, Fout):
@@ -93,7 +93,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
def build_filter_curl_3d__1_n(cls, FIN, K, FOUT, target=__DEFAULT_NUMBA_TARGET__):
args=(FIN,K,FOUT)
signature, _ = make_numba_signature(*args)
- layout='(n,m,p),(n)->(n,m,p)'
+ layout='(n,m,p),(n)->(n,m,p)'
@nb.guvectorize([signature], layout,
target=target, nopython=True, cache=True)
def filter_curl_3d__1_n(Fin, K, Fout):
@@ -107,7 +107,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
def build_filter_curl_3d__1_m(cls, FIN, K, FOUT, target=__DEFAULT_NUMBA_TARGET__):
args=(FIN,K,FOUT)
signature, _ = make_numba_signature(*args)
- layout='(n,m,p),(m)->(n,m,p)'
+ layout='(n,m,p),(m)->(n,m,p)'
@nb.guvectorize([signature], layout,
target=target, nopython=True, cache=True)
def filter_curl_3d__1_m(Fin, K, Fout):
@@ -121,7 +121,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
def build_filter_curl_3d__1_p(cls, FIN, K, FOUT, target=__DEFAULT_NUMBA_TARGET__):
args=(FIN,K,FOUT)
signature, _ = make_numba_signature(*args)
- layout='(n,m,p),(p)->(n,m,p)'
+ layout='(n,m,p),(p)->(n,m,p)'
@nb.guvectorize([signature], layout,
target=target, nopython=True, cache=True)
def filter_curl_3d__1_p(Fin, K, Fout):
@@ -130,17 +130,17 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
for k in range(0, Fin.shape[2]):
Fout[i,j,k] += K[k]*Fin[i,j,k]
return functools.partial(filter_curl_3d__1_p, *args)
-
+
def setup(self, work):
super(PythonPoissonCurl, self).setup(work=work)
-
+
dim = self.dim
WIN, UIN, UOUT = self.WIN, self.UIN, self.UOUT
K, KK = self.K, self.KK
UK = self.UK
assert len(WIN)==len(KK), (len(WIN),len(KK))
assert len(UIN)==len(UOUT)==len(UK), (len(UIN),len(UOUT),len(UK))
-
+
# diffusion filters
if self.should_diffuse:
diffusion_filters = ()
@@ -166,7 +166,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
F = PythonPoisson.build_poisson_filter(dim, *((Wi,)+KKi+(Wi,)))
poisson_filters += (F,)
self.poisson_filters = poisson_filters
-
+
# curl filter
if (dim==2):
curl0 = self.build_filter_curl_2d__0_m(UIN[0], UK[0], UOUT[0])
@@ -194,7 +194,7 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
def apply(self, simulation=None, **kwds):
"""Apply analytic formula."""
super(PythonPoissonCurl, self).apply(**kwds)
-
+
diffuse=self.should_diffuse
project=self.do_project(simu=simulation)
@@ -216,8 +216,8 @@ class PythonPoissonCurl(SpectralPoissonCurlOperatorBase, OpenClMappable, HostOpe
for curl_filter in curl_filters:
curl_filter()
Bt(simulation=simulation)
-
+
self.dU.exchange_ghosts()
if (diffuse or project):
self.dW.exchange_ghosts()
- self.update_energy(simulation=simulation)
+ self.update_energy(simulation=simulation)
diff --git a/hysop/core/checkpoints.py b/hysop/core/checkpoints.py
index efa9697bd..12e7fd33b 100644
--- a/hysop/core/checkpoints.py
+++ b/hysop/core/checkpoints.py
@@ -446,7 +446,7 @@ class CheckpointHandler(object):
nbytes += np.prod(shape, dtype=np.int64) * dtype.itemsize
if (root is not None):
- root.attrs['nbytes'] = nbytes
+ root.attrs['nbytes'] = int(nbytes)
msg='>Maximum checkpoint size will be {}, without compression and metadata.'
vprint(root.tree())
vprint(msg.format(bytes2str(nbytes)))
diff --git a/hysop/core/graph/computational_graph.py b/hysop/core/graph/computational_graph.py
index df3fa8692..e3400d790 100644
--- a/hysop/core/graph/computational_graph.py
+++ b/hysop/core/graph/computational_graph.py
@@ -94,7 +94,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
reqs.enforce_unique_topology_shape, reqs.enforce_unique_transposition_state,
reqs.enforce_unique_ghosts, reqs.enforce_unique_memory_order,
) + optypes
- vals = map(str, vals)
+ vals = tuple(map(str, vals))
values.append(vals)
template = '\n {:<{name_size}} {:^{topology_size}} {:^{tstates_size}} {:^{ghosts_size}} {:^{order_size}} {:<{type_size0}} {:<{type_size1}} {:<{type_size2}}'
@@ -182,15 +182,14 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
titles = [[('OPERATOR', 'FIELD', 'DISCRETIZATION', 'GHOSTS',
'MEMORY ORDER', 'CAN_SPLIT', 'TSTATES')]]
- name_size = max(len(s[0]) for ss in sinputs.values()+soutputs.values()+titles for s in ss)
- field_size = max(len(s[1]) for ss in sinputs.values()+soutputs.values()+titles for s in ss)
- discr_size = max(len(s[2]) for ss in sinputs.values()+soutputs.values()+titles for s in ss)
- ghosts_size = max(len(s[3]) for ss in sinputs.values()+soutputs.values()+titles for s in ss)
- order_size = max(len(s[4]) for ss in sinputs.values()+soutputs.values()+titles for s in ss)
- cansplit_size = max(len(s[5]) for ss in sinputs.values() +
- soutputs.values()+titles for s in ss)
- tstates_size = max(len(s[6]) for ss in sinputs.values() +
- soutputs.values()+titles for s in ss)
+ vals = tuple(sinputs.values()) + tuple(soutputs.values()) + tuple(titles)
+ name_size = max(len(s[0]) for ss in vals for s in ss)
+ field_size = max(len(s[1]) for ss in vals for s in ss)
+ discr_size = max(len(s[2]) for ss in vals for s in ss)
+ ghosts_size = max(len(s[3]) for ss in vals for s in ss)
+ order_size = max(len(s[4]) for ss in vals for s in ss)
+ cansplit_size = max(len(s[5]) for ss in vals for s in ss)
+ tstates_size = max(len(s[6]) for ss in vals for s in ss)
template = '\n {:<{name_size}} {:^{field_size}} {:^{discr_size}} {:^{ghosts_size}} {:^{order_size}} {:^{cansplit_size}} {:^{tstates_size}}'
@@ -370,7 +369,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
field_topologies.setdefault(topo, []).append(node)
for topo in sorted(field_topologies.keys(), key=lambda x: x.tag):
pnames = set(node.pretty_name for node in field_topologies[topo])
- pnames = sorted(pnames)
+ pnames = tuple(sorted(pnames))
nbyline = 4
nentries = len(pnames)//nbyline
n0 = len(str(topo.backend.kind).lower())
@@ -393,8 +392,9 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
topologies.setdefault(field, []).append(entries)
titles = [[('BACKEND', 'TOPOLOGY', 'OPERATORS')]]
- backend_size = max(len(s[0]) for ss in topologies.values()+titles for s in ss)
- topo_size = max(len(s[1]) for ss in topologies.values()+titles for s in ss)
+ vals = tuple(topologies.values()) + tuple(titles)
+ backend_size = max(len(s[0]) for ss in vals for s in ss)
+ topo_size = max(len(s[1]) for ss in vals for s in ss)
template = '\n {:<{backend_size}} {:<{topo_size}} {}'
sizes = {'backend_size': backend_size,
'topo_size': topo_size}
diff --git a/hysop/core/graph/computational_node.py b/hysop/core/graph/computational_node.py
index 3ef5a57c7..5222ab09c 100644
--- a/hysop/core/graph/computational_node.py
+++ b/hysop/core/graph/computational_node.py
@@ -556,7 +556,7 @@ class ComputationalGraphNode(OperatorBase, metaclass=ABCMeta):
if fills the 'None' domain.
"""
domains = {}
- for field in set(self.input_fields.keys()+self.output_fields.keys()):
+ for field in set(self.input_fields.keys()).union(self.output_fields.keys()):
domains.setdefault(field.domain, set()).add(self)
if self.is_domainless:
domains.setdefault(None, set()).add(self)
@@ -696,7 +696,7 @@ class ComputationalGraphNode(OperatorBase, metaclass=ABCMeta):
def get_topo_descriptor(cls, variables, field):
if (field in variables):
return variables[field]
- tfields = filter(lambda x: x.is_tensor, variables.keys())
+ tfields = tuple(filter(lambda x: x.is_tensor, variables.keys()))
for tfield in tfields:
if field in tfield:
return variables[tfield]
diff --git a/hysop/core/graph/graph_builder.py b/hysop/core/graph/graph_builder.py
index 2a1a7bfbf..d8ea7e0a9 100644
--- a/hysop/core/graph/graph_builder.py
+++ b/hysop/core/graph/graph_builder.py
@@ -374,7 +374,7 @@ class GraphBuilder(object):
for (fields, io_params, op_kwds) in target_node._output_fields_to_dump:
if not fields:
fields = self.output_fields.keys()
- fields = sorted(fields, key=lambda x: x.name)
+ fields = tuple(sorted(fields, key=lambda x: x.name))
for field in fields:
msg='{} is not an output field.'.format(field.name)
assert field in self.output_fields, msg
@@ -668,7 +668,7 @@ class GraphBuilder(object):
if not write_nodes:
return
- src_topos = write_nodes.keys()
+ src_topos = tuple(write_nodes.keys())
if (src_topo is not None):
assert src_topo in src_topos
src_topos = (src_topo,)
@@ -892,7 +892,7 @@ class GraphBuilder(object):
if (target_topo.backend.kind is Backend.HOST) and write_nodes:
# give source topo priority according to topology_affinity
src_topos = write_nodes.keys()
- src_topos = sorted(src_topos, key=topology_affinity, reverse=True)
+ src_topos = tuple(sorted(src_topos, key=topology_affinity, reverse=True))
src_topo = src_topos[0]
if (src_topo is not target_topo):
msg=' >Redistributing field {} from up to date topologies {} '
@@ -907,7 +907,7 @@ class GraphBuilder(object):
elif (target_topo.backend.kind is Backend.OPENCL) and write_nodes:
# give source topo priority according to topology_affinity
src_topos = write_nodes.keys()
- src_topos = sorted(src_topos, key=topology_affinity, reverse=True)
+ src_topos = tuple(sorted(src_topos, key=topology_affinity, reverse=True))
src_topo = src_topos[0]
if (src_topo is not target_topo):
msg=' >Redistributing field {} from up to date topologies {} '
diff --git a/hysop/core/graph/node_requirements.py b/hysop/core/graph/node_requirements.py
index 243ec3217..273c087ec 100644
--- a/hysop/core/graph/node_requirements.py
+++ b/hysop/core/graph/node_requirements.py
@@ -21,12 +21,12 @@ class NodeRequirements(object):
class OperatorRequirements(NodeRequirements):
- __slots__ = ('_enforce_unique_transposition_state',
+ __slots__ = ('_enforce_unique_transposition_state',
'_enforce_unique_topology_shape',
'_enforce_unique_memory_order',
'_enforce_unique_ghosts')
- def __init__(self, operator,
+ def __init__(self, operator,
enforce_unique_transposition_state=None,
enforce_unique_topology_shape=None,
enforce_unique_memory_order=None,
@@ -85,7 +85,7 @@ class OperatorRequirements(NodeRequirements):
return self._enforce_unique_ghosts
enforce_unique_ghosts = property(_get_enforce_unique_ghosts,
_set_enforce_unique_ghosts)
-
+
def check_and_update_reqs(self, field_requirements):
"""Check and possibly update field requirements against global node requirements."""
if (field_requirements is None):
@@ -93,7 +93,7 @@ class OperatorRequirements(NodeRequirements):
axes = set()
memory_order, can_split, min_ghosts, max_ghosts = None, None, None, None
field_names = ''
- for (is_input, freqs) in field_requirements.iter_requirements():
+ for (is_input, freqs) in field_requirements.iter_requirements():
if (freqs is None):
continue
(field, td, req) = freqs
@@ -103,8 +103,8 @@ class OperatorRequirements(NodeRequirements):
msg ='::GLOBAL OPERATOR REQUIREMENTS ERROR::\n'
msg+='Previous axes: \n {} required by fields {}\nare incompatible '
msg+='with axes requirements \n {} enforced by {} field {}.\n'
- msg=msg.format(tuple(axes), field_names,
- tuple(req.axes),
+ msg=msg.format(tuple(axes), field_names,
+ tuple(req.axes),
'input' if is_input else 'output',
field.name)
raise RuntimeError(msg)
@@ -119,8 +119,8 @@ class OperatorRequirements(NodeRequirements):
msg ='::GLOBAL OPERATOR REQUIREMENTS ERROR::\n'
msg+='Previous memory order: \n {} required by fields {}\nare incompatible '
msg+='with memory order requirements \n {} enforced by {} field {}.\n'
- msg=msg.format(memory_order, field_names,
- req.memory_order,
+ msg=msg.format(memory_order, field_names,
+ req.memory_order,
'input' if is_input else 'output',
field.name)
raise RuntimeError(msg)
@@ -136,8 +136,8 @@ class OperatorRequirements(NodeRequirements):
msg ='::GLOBAL OPERATOR REQUIREMENTS ERROR::\n'
msg+='Previous cartesian split directions: \n {} required by fields {}\nare incompatible '
msg+='with cartesian split directions requirements \n {} enforced by {} field {}.'
- msg=msg.format(can_split, field_names,
- req.can_split,
+ msg=msg.format(can_split, field_names,
+ req.can_split,
'input' if is_input else 'output',
field.name)
msg+='\nDomain cannot be splitted accross multiple processes.\n'
@@ -154,14 +154,14 @@ class OperatorRequirements(NodeRequirements):
if any(maxg<min_ghosts):
msg+='Previous cartesian min_ghosts: \n {} required by fields {}\nare incompatible '
msg+='with cartesian max_ghosts requirements \n {} enforced by {} field {}.\n'
- msg=msg.format(min_ghosts, field_names,
+ msg=msg.format(min_ghosts, field_names,
maxg, 'input' if is_input else 'output',
field.name)
raise RuntimeError(msg)
elif any(ming>max_ghosts):
msg+='Previous cartesian max_ghosts: \n {} required by fields {}\nare incompatible '
msg+='with cartesian min_ghosts requirements \n {} enforced by {} field {}.\n'
- msg=msg.format(max_ghosts, field_names,
+ msg=msg.format(max_ghosts, field_names,
ming, 'input' if is_input else 'output',
field.name)
raise RuntimeError(msg)
@@ -175,19 +175,18 @@ class OperatorRequirements(NodeRequirements):
field_names += field.name + ', '
axes = tuple(axes)
-
+
has_single_input = (len(field_requirements._input_field_requirements)<=1)
-
+
# enforce global operator requirements onto field requirements
- for (is_input, freqs) in field_requirements.iter_requirements():
+ for (is_input, freqs) in field_requirements.iter_requirements():
if (freqs is None):
continue
(field, td, req) = freqs
-
+
# enforce transposition axes
if self.enforce_unique_transposition_state:
if axes:
- #axes = sorted(axes, key=lambda x: sum((xi-i)**2 for (i,xi) in zip(range(len(x)),x)))
req.axes = (axes[0],)
elif not has_single_input:
req.axes = (TranspositionState[field.dim].default_axes(),)
@@ -198,7 +197,7 @@ class OperatorRequirements(NodeRequirements):
req.memory_order = memory_order
elif not has_single_input:
req.memory_order = MemoryOrdering.C_CONTIGUOUS
-
+
# enforce topology shape (indirectly by enforcing split directions)
if self.enforce_unique_topology_shape:
assert (can_split is not None)
@@ -213,4 +212,4 @@ class OperatorRequirements(NodeRequirements):
if self.enforce_unique_ghosts:
req.min_ghosts = min_ghosts
req.max_ghosts = min_ghosts
-
+
diff --git a/hysop/core/memory/memory_request.py b/hysop/core/memory/memory_request.py
index 9b80a06a9..98387c3d6 100644
--- a/hysop/core/memory/memory_request.py
+++ b/hysop/core/memory/memory_request.py
@@ -300,7 +300,7 @@ class MultipleOperatorMemoryRequests(object):
def operators(self):
ops = []
for requests in self._all_requests_per_backend.values():
- ops += requests.keys()
+ ops += list(requests.keys())
return ops
def __iadd__(self, other):
diff --git a/hysop/core/mpi/topo_tools.py b/hysop/core/mpi/topo_tools.py
index a109623b1..07cec6a77 100644
--- a/hysop/core/mpi/topo_tools.py
+++ b/hysop/core/mpi/topo_tools.py
@@ -156,7 +156,6 @@ class TopoTools(object):
# Get the list of processes
assert child is not None
assert parent is not None
- #child_ranks = [i for i in range(child.Get_size())]
child_group = child.Get_group()
parent_group = parent.Get_group()
inter_group = MPI.Group.Intersect(child_group, parent_group)
diff --git a/hysop/fields/continuous_field.py b/hysop/fields/continuous_field.py
index c378e015b..a6339c78a 100644
--- a/hysop/fields/continuous_field.py
+++ b/hysop/fields/continuous_field.py
@@ -372,7 +372,7 @@ class FieldContainerI(TaggedObject):
return False
return True
if isinstance(a, dict):
- for k in set(a.keys()+b.keys()):
+ for k in set(a.keys()).union(b.keys()):
if (k not in a) or (k not in b):
return False
ak, bk = a[k], b[k]
diff --git a/hysop/fields/discrete_field.py b/hysop/fields/discrete_field.py
index de291ea94..c979bfd87 100644
--- a/hysop/fields/discrete_field.py
+++ b/hysop/fields/discrete_field.py
@@ -286,7 +286,7 @@ class DiscreteScalarFieldViewContainerI(object, metaclass=ABCMeta):
return False
return True
if isinstance(a, dict):
- for k in set(a.keys()+b.keys()):
+ for k in set(a.keys()).union(b.keys()):
if (k not in a) or (k not in b):
return False
ak, bk = a[k], b[k]
diff --git a/hysop/fields/ghost_exchangers.py b/hysop/fields/ghost_exchangers.py
index 1866d6325..99bcbfa87 100644
--- a/hysop/fields/ghost_exchangers.py
+++ b/hysop/fields/ghost_exchangers.py
@@ -27,7 +27,7 @@ def gprint_buffer(msg, buf, *args, **kwds):
else:
mpi_type=None
gprint('{}: mpi_type={}, shape={}, dtype={}, c_contiguous={}, f_contiguous={}'.format(msg,
- mpi_type, buf.shape, buf.dtype, buf.flags['C_CONTIGUOUS'], buf.flags['F_CONTIGUOUS']))
+ mpi_type, buf.shape, buf.dtype, buf.flags.c_contiguous, buf.flags.f_contiguous))
if no_data:
return
gprint(' ' + '\n '.join(str(buf).split('\n')))
diff --git a/hysop/fields/tests/test_cartesian.py b/hysop/fields/tests/test_cartesian.py
index a5a415458..baacac2e8 100644
--- a/hysop/fields/tests/test_cartesian.py
+++ b/hysop/fields/tests/test_cartesian.py
@@ -511,16 +511,16 @@ def test_mpi_ghost_exchange_periodic(comm=None):
if rank==0:
print(' >DTYPE={}'.format(dtype))
- F0 = Field(domain=domain, name='F0', nb_components=1, dtype=dtype, _register=False)
- F1 = Field(domain=domain, name='F1', nb_components=2, dtype=dtype, _register=False)
- F2 = Field(domain=domain, name='F2', shape=(2,2), dtype=dtype, _register=False)
+ F0 = Field(domain=domain, name='F0', nb_components=1, dtype=dtype)
+ F1 = Field(domain=domain, name='F1', nb_components=2, dtype=dtype)
+ F2 = Field(domain=domain, name='F2', shape=(2,2), dtype=dtype)
for (backend, cl_env) in iter_backends():
if rank==0:
print(' >BACKEND.{}{}'.format(backend,
'' if (cl_env is None) else '::{}.{}'.format(
cl_env.platform.name.strip(), cl_env.device.name.strip())))
- for shape in it.product(range(0,size+1), repeat=dim):
+ for shape in it.product(range(0, size+1), repeat=dim):
if np.prod(shape, dtype=np.uint32)!=size:
continue
if rank==0:
@@ -610,14 +610,14 @@ def test_mpi_ghost_exchange_runtime(comm=None):
print('*'*len(msg))
print('test_mpi_ghost_exchange_runtime()'.format(size))
- for dim in range(1,3+__ENABLE_LONG_TESTS__):
+ for dim in range(1, 3+__ENABLE_LONG_TESTS__):
if rank==0:
sys.stdout.write('>DIM={}\n'.format(dim))
npts = (17,16,19)[:dim]
nghosts = (2,1,3)[:dim]
- for shape in it.product(range(0,size+1), repeat=dim):
+ for shape in it.product(range(0, size+1), repeat=dim):
if np.prod(shape, dtype=np.uint32)!=size:
continue
if rank==0:
@@ -638,11 +638,9 @@ def test_mpi_ghost_exchange_runtime(comm=None):
brk = False
try:
for (lbd, rbd) in domain_boundary_iterator(dim):
- domain = Box(dim=dim, lboundaries=lbd,
- rboundaries=rbd)
+ domain = Box(dim=dim, lboundaries=lbd, rboundaries=rbd)
- F = Field(domain=domain, name='F', nb_components=1,
- dtype=dtype, _register=False)
+ F = Field(domain=domain, name='F', nb_components=1, dtype=dtype)
discretization = CartesianDiscretization(npts, nghosts,
lboundaries=F.lboundaries,
@@ -708,9 +706,9 @@ def test_mpi_ghost_accumulate_periodic(comm=None):
if rank==0:
print(' >DTYPE={}'.format(dtype))
- F0 = Field(domain=domain, name='F0', nb_components=1, dtype=dtype, _register=False)
- F1 = Field(domain=domain, name='F1', nb_components=2, dtype=dtype, _register=False)
- F2 = Field(domain=domain, name='F2', shape=(2,2), dtype=dtype, _register=False)
+ F0 = Field(domain=domain, name='F0', nb_components=1, dtype=dtype)
+ F1 = Field(domain=domain, name='F1', nb_components=2, dtype=dtype)
+ F2 = Field(domain=domain, name='F2', shape=(2,2), dtype=dtype)
for (backend, cl_env) in iter_backends():
if rank==0:
@@ -756,7 +754,7 @@ def test_mpi_ghost_accumulate_periodic(comm=None):
ExchangeMethod.NEIGHBOR_ALL_TO_ALL_V,
ExchangeMethod.NEIGHBOR_ALL_TO_ALL_W,):
if rank==0:
- print(' ExchangeMethod.{:<25} |'.format(exchange_method), end=' ')
+ print(' ExchangeMethod.{:<25} |'.format(str(exchange_method)), end=' ')
sys.stdout.flush()
# test one direction at a time
@@ -804,6 +802,7 @@ def test_mpi_ghost_accumulate_periodic(comm=None):
overlaping_neighbours = set(tuple((np.asarray(mask, dtype=np.int32)*displacements).tolist()) for mask in masks)
overlaping_neighbours = filter(lambda x: 0<sum(_!=0 for _ in x)<=max_displacements, overlaping_neighbours) #diagonals
+ overlaping_neighbours = tuple(overlaping_neighbours)
expected_values = (rank+1)*(i+1)
for disp in overlaping_neighbours:
diff --git a/hysop/mesh/cartesian_mesh.py b/hysop/mesh/cartesian_mesh.py
index 9249db90e..8053befc8 100644
--- a/hysop/mesh/cartesian_mesh.py
+++ b/hysop/mesh/cartesian_mesh.py
@@ -703,7 +703,7 @@ class CartesianMeshView(MeshView):
def __init__(self, dim, ghosts, compute_resolution, local_compute_indices):
iter_shape = tuple(compute_resolution[:axes])
gI = np.ix_(*local_compute_indices[axes:])
- I = tuple(gI[i]-ghosts[j] for i,j in enumerate(range(axes, dim)))
+ I = tuple(gI[i]-ghosts[j] for i,j in enumerate(range(axes, dim)))
self._iter_shape = iter_shape
self._data = (dim, ghosts, I, gI)
diff --git a/hysop/numerics/fft/gpyfft_fft.py b/hysop/numerics/fft/gpyfft_fft.py
index e5de67e09..abf665291 100644
--- a/hysop/numerics/fft/gpyfft_fft.py
+++ b/hysop/numerics/fft/gpyfft_fft.py
@@ -563,7 +563,7 @@ Post callback source code:
else:
oip += ('if (b>={}) {{ return; }};'.format(fake_batchsize, fp),)
oip += ('{K} -= {b}*{D};'.format(K=K, b=b, D=D),)
- for i in range(ndim-1,-1,-1):
+ for i in range(ndim-1, -1, -1):
Ki = idx.format('xyz'[i])
Si = S[i]
oip += ('const uint {Ki} = {K}/{Si};'.format(Ki=Ki, K=K, Si=Si),)
@@ -582,7 +582,7 @@ Post callback source code:
real_offset = ('{base_offset}uL'.format(base_offset=base_offset),)
if (fake_batchsize > 1):
real_offset += ('{b}*{D}'.format(b=b, D=real_distance),)
- for i in range(ndim-1,0,-1):
+ for i in range(ndim-1, 0, -1):
Ki = idx.format('xyz'[i])
Si = real_strides[i]
real_offset += ('{Ki}*{Si}'.format(Ki, Si),)
diff --git a/hysop/numerics/fft/host_fft.py b/hysop/numerics/fft/host_fft.py
index ceb5c70e6..2e19a8e31 100644
--- a/hysop/numerics/fft/host_fft.py
+++ b/hysop/numerics/fft/host_fft.py
@@ -70,9 +70,9 @@ class HostFFTI(FFTI):
super(HostFFTI, self).__init__(backend=backend, **kwds)
@classmethod
- def default_interface(cls, threads=None,
+ def default_interface(cls, threads=None,
backend=None, allocator=None,
- planner_effort=None,
+ planner_effort=None,
planning_timelimit=None,
destroy_input=False,
warn_on_allocation=True,
@@ -96,8 +96,8 @@ class HostFFTI(FFTI):
threads = first_not_None(threads, __FFTW_NUM_THREADS__)
planner_effort = first_not_None(planner_effort, __FFTW_PLANNER_EFFORT__)
planning_timelimit = first_not_None(planning_timelimit, __FFTW_PLANNER_TIMELIMIT__)
- return FftwFFT(threads=threads,
- planner_effort=planner_effort,
+ return FftwFFT(threads=threads,
+ planner_effort=planner_effort,
planning_timelimit=planning_timelimit,
backend=backend, allocator=allocator,
destroy_input=destroy_input,
@@ -105,19 +105,19 @@ class HostFFTI(FFTI):
warn_on_misalignment=warn_on_misalignment,
error_on_allocation=error_on_allocation,
**kwds)
-
+
def new_queue(self, tg, name):
return HostFFTQueue(name=name)
-
+
def plan_copy(self, tg, src, dst):
src = self.ensure_callable(src)
dst = self.ensure_callable(dst)
-
+
@static_vars(numba_copy=None)
def exec_copy(src=src, dst=dst):
src, dst = src(), dst()
if can_exec_hptt(src, dst):
- hptt.tensorTransposeAndUpdate(perm=range(src.ndim),
+ hptt.tensorTransposeAndUpdate(perm=tuple(range(src.ndim)),
alpha=1.0, A=src, beta=0.0, B=dst)
elif HAS_NUMBA:
if (exec_copy.numba_copy is None):
@@ -126,11 +126,11 @@ class HostFFTI(FFTI):
else:
dst[...] = src
return exec_copy
-
+
def plan_accumulate(self, tg, src, dst):
src = self.ensure_callable(src)
dst = self.ensure_callable(dst)
-
+
@static_vars(numba_accumulate=None)
def exec_accumulate(src=src, dst=dst):
src, dst = src(), dst()
@@ -162,7 +162,7 @@ class HostFFTI(FFTI):
else:
dst[...] = np.transpose(a=src, axes=axes)
return exec_transpose
-
+
def plan_fill_zeros(self, tg, a, slices):
assert slices
a = self.ensure_callable(a)
@@ -171,21 +171,21 @@ class HostFFTI(FFTI):
for slc in slices:
buf[slc] = 0
return exec_fill_zeros
-
- def plan_compute_energy(self, tg, fshape, src, dst, transforms,
+
+ def plan_compute_energy(self, tg, fshape, src, dst, transforms,
method='round', target=None, **kwds):
"""
- Plan to compute energy from src array to dst array using given transforms,
+ Plan to compute energy from src array to dst array using given transforms,
method (round or weighted) and numba target.
"""
(N, NS2, C2C, R2C, S) = super(HostFFTI, self).plan_compute_energy(tg, fshape, src, dst, transforms, **kwds)
dim = src.ndim
-
+
# We do not forget the hermitian symmetry:
- # normally: E = 1/2 |Fi|**2
+ # normally: E = 1/2 |Fi|**2
# but for a R2C transform: E = 1/2 |Fi|**2 + 1/2 |Fi*|**2 = 1 |Fi|**2
C = 2**(R2C-1)
-
+
target = first_not_None(target, __DEFAULT_NUMBA_TARGET__)
args = (src,)+N+NS2+C2C+(C, S, dst)
signature, layout = make_numba_signature(*args)
diff --git a/hysop/numerics/interpolation/polynomial.py b/hysop/numerics/interpolation/polynomial.py
index c1e2e6277..3f2d446ff 100644
--- a/hysop/numerics/interpolation/polynomial.py
+++ b/hysop/numerics/interpolation/polynomial.py
@@ -74,7 +74,7 @@ class PolynomialInterpolator(object):
else:
msg='Unknown PolynomialInterpolation value {}.'.format(pi)
raise NotImplementedError(msg)
- for i in range(1,5):
+ for i in range(1, 5):
if spi.endswith(str(2*i)):
fd=2*i
break
@@ -321,7 +321,7 @@ class PolynomialInterpolator(object):
warnings.warn(msg, HysopCacheWarning)
P0 = 0
- for idx in it.product(*tuple(range(0,pi) for pi in p)):
+ for idx in it.product(*tuple(range(0, pi) for pi in p)):
P0 += pvals[idx] * np.prod(np.power(xvals, idx))
self.P0 = P0
@@ -341,7 +341,7 @@ class PolynomialInterpolator(object):
print('\nBuilding system...')
eqs = []
- for dvec in it.product(*tuple(range(0,ki+1) for ki in k)):
+ for dvec in it.product(*tuple(range(0, ki+1) for ki in k)):
if verbose:
print(' => derivative {}'.format(dvec))
@@ -354,7 +354,7 @@ class PolynomialInterpolator(object):
print(' stencil:')
print(stencil)
- for idx in it.product(*tuple(range(gi,gi+2) for gi in ghosts)):
+ for idx in it.product(*tuple(range(gi, gi+2) for gi in ghosts)):
if verbose:
print(' -> point {}'.format(idx))
@@ -571,15 +571,15 @@ class PolynomialSubgridInterpolator(object):
msg='Failed to load data from cache because:\n{}'.format(e)
warnings.warn(msg, HysopCacheWarning)
- X = tuple(np.asarray(tuple(sm.Rational(j,gr) for j in range(0,si)))
+ X = tuple(np.asarray(tuple(sm.Rational(j,gr) for j in range(0, si)))
for i,(gr,si) in enumerate(zip(gr, s)))
V = np.vander(X[0], N=p[0], increasing=True)
for i in range(1, dim):
Vi = np.vander(X[i], N=p[i], increasing=True)
V = np.multiply.outer(V,Vi)
- even_axes = range(0,V.ndim,2)
- odd_axes = range(1,V.ndim,2)
+ even_axes = tuple(range(0, V.ndim,2))
+ odd_axes = tuple(range(1, V.ndim,2))
axes = even_axes + odd_axes
V = np.transpose(V, axes=axes).copy()
diff --git a/hysop/numerics/odesolvers/runge_kutta.py b/hysop/numerics/odesolvers/runge_kutta.py
index 52c3d3fcb..ca555e42b 100644
--- a/hysop/numerics/odesolvers/runge_kutta.py
+++ b/hysop/numerics/odesolvers/runge_kutta.py
@@ -56,10 +56,10 @@ class ExplicitRungeKutta(RungeKutta):
"""Buffers = dict of (nb_stages+1) np.ndarray of size compatible with Xin"""
check_instance(Xin, dict, keys=str, values=np.ndarray)
varnames = Xin.keys()
- views = first_not_None(views, { k:Ellipsis for (k,v) in Xin.items() })
- Xout = first_not_None(Xout, { k:np.empty_like(v[views[k]])
+ views = first_not_None(views, { k: Ellipsis for (k,v) in Xin.items() })
+ Xout = first_not_None(Xout, { k: np.empty_like(v[views[k]])
for (k,v) in Xin.items() })
- buffers = first_not_None(buffers, { k:tuple(np.empty_like(v)
+ buffers = first_not_None(buffers, { k: tuple(np.empty_like(v)
for i in range(self.stages+1))
for (k,v) in Xin.items()})
check_instance(views, dict, keys=str, values=(type(Ellipsis),slice,tuple))
@@ -67,7 +67,7 @@ class ExplicitRungeKutta(RungeKutta):
check_instance(buffers, dict, keys=str, values=tuple)
assert callable(RHS), type(RHS)
if __debug__:
- compute_shape = Xout.values()[0].shape
+ compute_shape = next(iter(Xout.values())).shape
assert varnames == Xout.keys()
assert varnames == views.keys()
assert varnames == buffers.keys()
diff --git a/hysop/numerics/remesh/kernel_generator.py b/hysop/numerics/remesh/kernel_generator.py
index 3711b9042..1fd7be909 100644
--- a/hysop/numerics/remesh/kernel_generator.py
+++ b/hysop/numerics/remesh/kernel_generator.py
@@ -76,7 +76,7 @@ class Kernel(object):
print()
#split polynomials
- X = np.arange(-Ms,+Ms+1)
+ X = np.arange(-Ms, +Ms+1)
if split_polys:
Pt_l = []
Pt_r = []
@@ -335,10 +335,6 @@ class SymmetricKernelGenerator(object):
Pp.append(sm.polys.polytools.poly(pexpr,x))
Pm.append(sm.polys.polytools.poly(mexpr,x))
P = Pm[::-1] + Pp
- Pbeg = -Ms
- Pend = +Ms-1
- Prange = lambda: range(-Ms,+Ms)
- Penum = lambda: enumerate(P,start=Pbeg)
#precompute the r first polynomial derivatives
dPs = []
@@ -354,7 +350,7 @@ class SymmetricKernelGenerator(object):
### Continuity equations (Gamma is Cr continuous)
# Parity in x=0 -- Gamma is EVEN -> (r+1)//2 eqs
- for d in range(1,r+1,2):
+ for d in range(1, r+1,2):
eq = coeffs[0][d] # =0
eqs.append(eq)
# Right-most point, zero derivatives -> (r+1) eqs
@@ -374,9 +370,9 @@ class SymmetricKernelGenerator(object):
### Discrete moments
s = sm.symbols('s')
- for m in range(0,n+1):
+ for m in range(0, n+1):
expr = f2q(0)
- for l in range(-Ms+1,Ms+1):
+ for l in range(-Ms+1, Ms+1):
if m>0 and l==0: continue
i = Ms-l
e = P[i].xreplace({x:s-f2q(l)}).as_expr()
@@ -422,7 +418,7 @@ if __name__=='__main__':
sg = StencilGenerator()
sg.configure(dim=1, derivative=2)
- for i in range(1,5):
+ for i in range(1, 5):
p = 2*i
H = sg.generate_exact_stencil(order=p-1, origin=i)
print(H.coeffs)
diff --git a/hysop/numerics/stencil/stencil.py b/hysop/numerics/stencil/stencil.py
index 7135ac813..85dd6c1a6 100644
--- a/hysop/numerics/stencil/stencil.py
+++ b/hysop/numerics/stencil/stencil.py
@@ -140,7 +140,7 @@ class Stencil(object):
assert sdim<=adim, 'Stencil dimension greater than array dimension.'
assert set(symbols.keys())==self.variables(), 'Missing symbols {}.'.format(self.variables()-set(symbols.keys()))
out = first_not_None(out, np.empty_like(a[iview]))
- axis = first_not_None(to_tuple(axis), range(adim)[-sdim:])
+ axis = first_not_None(to_tuple(axis), tuple(range(adim))[-sdim:])
assert len(axis) == sdim
assert out.ndim == a.ndim
assert out.shape == a[iview].shape
diff --git a/hysop/numerics/stencil/stencil_generator.py b/hysop/numerics/stencil/stencil_generator.py
index 7c8fe7391..2d78ac6dd 100644
--- a/hysop/numerics/stencil/stencil_generator.py
+++ b/hysop/numerics/stencil/stencil_generator.py
@@ -458,7 +458,7 @@ class StencilGenerator(object):
def preficate(it):
return (it<=N).all() and sum(it)==n
- nn = range(n+1)
+ nn = range(n+1)
itd = it.product(nn, repeat=dim)
itd = filter(preficate, itd)
expr = 0
diff --git a/hysop/numerics/tests/bench_fft.py b/hysop/numerics/tests/bench_fft.py
index 7b625c1bb..ee6d45fc0 100644
--- a/hysop/numerics/tests/bench_fft.py
+++ b/hysop/numerics/tests/bench_fft.py
@@ -141,7 +141,7 @@ class BenchFFT(object):
def iter_shapes(self, offset=0):
minj=12
maxj=27
- for j in range(minj,maxj):
+ for j in range(minj, maxj):
shape = (2**j+offset,)
cshape = list(shape)
cshape[-1] = cshape[-1]//2 + 1
diff --git a/hysop/numerics/tests/test_fft.py b/hysop/numerics/tests/test_fft.py
index ca4dc8b83..d4923c894 100644
--- a/hysop/numerics/tests/test_fft.py
+++ b/hysop/numerics/tests/test_fft.py
@@ -636,7 +636,7 @@ class TestFFT(object):
base = 2+i
print(' '+msg[i])
for ghosts in ((0,0,0),): #(2,0,0),(0,1,0),(0,0,3)):
- for j1 in range(minj[i],maxj[i]):
+ for j1 in range(minj[i], maxj[i]):
shape = (3,2,base**j1,)
cshape = list(shape)
cshape[-1] = cshape[-1]//2 + 1
diff --git a/hysop/operator/analytic.py b/hysop/operator/analytic.py
index 7d243477d..8f6da9093 100644
--- a/hysop/operator/analytic.py
+++ b/hysop/operator/analytic.py
@@ -21,7 +21,7 @@ class AnalyticField(ComputationalGraphNodeGenerator):
"""
AnalyticField operator frontend.
- Apply a user-defined formula onto a field, possibly
+ Apply a user-defined formula onto a field, possibly
dependent on space variables and external fields/parameters.
Parameters
@@ -50,23 +50,23 @@ class AnalyticField(ComputationalGraphNodeGenerator):
check_instance(variables, dict, keys=Field, values=CartesianTopologyDescriptors)
extra_input_kwds = first_not_None(extra_input_kwds, {})
base_kwds = first_not_None(base_kwds, {})
-
+
assert 'extra_input_kwds' not in kwds
assert 'component' not in kwds
assert 'coords' not in kwds
if (implementation is Implementation.PYTHON) and (extra_input_kwds is not None):
- candidate_input_tensors = filter(lambda f: isinstance(f, Field), extra_input_kwds.values())
+ candidate_input_tensors = tuple(filter(lambda f: isinstance(f, Field), extra_input_kwds.values()))
else:
extra_input_kwds = {}
- candidate_input_tensors = ()
+ candidate_input_tensors = tuple()
candidate_output_tensors = (field,)
-
+
formula = to_tuple(formula)
if len(formula) == 1:
formula = formula*field.nb_components
check_instance(formula, tuple, size=field.nb_components)
-
+
super(AnalyticField, self).__init__(
candidate_input_tensors=candidate_input_tensors,
candidate_output_tensors=candidate_output_tensors,
@@ -78,7 +78,7 @@ class AnalyticField(ComputationalGraphNodeGenerator):
self._extra_input_kwds = extra_input_kwds
self._implementation = implementation
self._kwds = kwds
-
+
@debug
def _generate(self):
nodes = []
@@ -95,7 +95,7 @@ class AnalyticField(ComputationalGraphNodeGenerator):
field=field,
formula=formula,
variables=variables,
- implementation=impl,
+ implementation=impl,
extra_input_kwds=extra_input_kwds,
**kwds)
nodes.append(node)
@@ -118,7 +118,7 @@ class AnalyticScalarField(ComputationalGraphNodeFrontend):
Implementation.OPENCL: OpenClAnalyticField
}
return __implementations
-
+
@classmethod
def default_implementation(cls):
return Implementation.PYTHON
@@ -129,7 +129,7 @@ class AnalyticScalarField(ComputationalGraphNodeFrontend):
"""
AnalyticField operator frontend.
- Apply a user-defined formula onto a field, possibly
+ Apply a user-defined formula onto a field, possibly
dependent on space variables and external fields/parameters.
Parameters
@@ -158,6 +158,6 @@ class AnalyticScalarField(ComputationalGraphNodeFrontend):
if (implementation is Implementation.PYTHON):
kwds['extra_input_kwds'] = extra_input_kwds
- super(AnalyticScalarField, self).__init__(field=field, formula=formula,
- variables=variables, implementation=implementation,
+ super(AnalyticScalarField, self).__init__(field=field, formula=formula,
+ variables=variables, implementation=implementation,
base_kwds=base_kwds, **kwds)
diff --git a/hysop/operator/base/convergence.py b/hysop/operator/base/convergence.py
index eeca70420..7d3cfcdbc 100644
--- a/hysop/operator/base/convergence.py
+++ b/hysop/operator/base/convergence.py
@@ -49,7 +49,7 @@ class ConvergenceBase(object):
check_instance(convergence, TensorParameter, allow_none=True)
check_instance(variables, dict, keys=Field, values=CartesianTopologyDescriptors)
- field = variables.keys()[0]
+ field = next(iter(variables))
if convergence is None:
convergence = TensorParameter(name="|residual|", dtype=field.dtype,
shape=(field.nb_components, ),
diff --git a/hysop/operator/base/curl.py b/hysop/operator/base/curl.py
index f6651ca53..e586e32fb 100644
--- a/hysop/operator/base/curl.py
+++ b/hysop/operator/base/curl.py
@@ -19,14 +19,19 @@ class CurlOperatorBase(SpectralOperatorBase):
"""
Compute the curl using a specific implementation.
"""
-
+
+ @debug
+ def __new__(cls, Fin, Fout, variables, **kwds):
+ return super(CurlOperatorBase, cls).__new__(cls,
+ input_fields=None, output_fields=None, **kwds)
+
@debug
def __init__(self, Fin, Fout, variables, **kwds):
"""
Create an operator that computes the curl of an input field Fin.
Given Fin, a 2D ScalarField, a 2D VectorField or a 3D VectorField, compute Fout = curl(Fin).
-
+
Only the following configurations are supported:
dim nb_components | dim nb_components
Input: 2 (1,2) | 3 3
@@ -45,7 +50,7 @@ class CurlOperatorBase(SpectralOperatorBase):
kwds: dict, optional
Extra parameters passed towards base class (MultiSpaceDerivatives).
"""
-
+
check_instance(Fin, Field)
check_instance(Fout, Field)
check_instance(variables, dict, keys=Field, values=CartesianTopologyDescriptors)
@@ -83,18 +88,18 @@ class CurlOperatorBase(SpectralOperatorBase):
else:
msg='Unsupported dimension {}.'.format(dim)
raise RuntimeError(msg)
-
+
# input and output fields
input_fields = { Fin: variables[Fin] }
output_fields = { Fout: variables[Fout] }
- super(CurlOperatorBase, self).__init__(input_fields=input_fields,
+ super(CurlOperatorBase, self).__init__(input_fields=input_fields,
output_fields=output_fields, **kwds)
self.Fin = Fin
self.Fout = Fout
self.dim = dim
-
+
@debug
def discretize(self):
if self.discretized:
@@ -109,19 +114,22 @@ class SpectralCurlOperatorBase(CurlOperatorBase):
"""
Compute the curl using a specific spectral implementation.
"""
+ def __new__(cls, **kwds):
+ return super(SpectralCurlOperatorBase, cls).__new__(cls, **kwds)
+
def __init__(self, **kwds):
super(SpectralCurlOperatorBase, self).__init__(**kwds)
-
+
dim = self.dim
Fin, Fout = self.Fin, self.Fout
assert Fin is not Fout, 'Cannot compute curl inplace!'
-
+
if (dim==2):
tg0 = self.new_transform_group()
tg1 = self.new_transform_group()
if (Fin.nb_components==1):
assert (Fout.nb_components==2)
- F0 = tg0.require_forward_transform(Fin, axes=0,
+ F0 = tg0.require_forward_transform(Fin, axes=0,
custom_output_buffer='auto')
B0 = tg0.require_backward_transform(Fout[0], axes=0,
custom_input_buffer='auto', matching_forward_transform=F0)
@@ -130,7 +138,7 @@ class SpectralCurlOperatorBase(CurlOperatorBase):
custom_output_buffer='auto')
B1 = tg1.require_backward_transform(Fout[1], axes=1,
custom_input_buffer='auto', matching_forward_transform=F1)
-
+
expr0 = Assignment(B0.s, +F0.s.diff(F0.s.frame.coords[1]))
expr1 = Assignment(B1.s, -F1.s.diff(F1.s.frame.coords[0]))
elif (Fin.nb_components==2):
@@ -141,10 +149,10 @@ class SpectralCurlOperatorBase(CurlOperatorBase):
F1 = tg1.require_forward_transform(Fin[0], axes=0,
custom_output_buffer='auto')
- B1 = tg1.require_backward_transform(Fout, axes=0,
+ B1 = tg1.require_backward_transform(Fout, axes=0,
custom_input_buffer='auto', matching_forward_transform=F1,
action=SpectralTransformAction.ACCUMULATE)
-
+
expr0 = Assignment(B0.s, +F0.s.diff(F0.s.frame.coords[0]))
expr1 = Assignment(B1.s, -F1.s.diff(F1.s.frame.coords[1]))
else:
@@ -212,11 +220,11 @@ class SpectralCurlOperatorBase(CurlOperatorBase):
backward_transforms = (B0, B1, B2, B3, B4, B5)
else:
raise NotImplementedError
-
+
self.forward_transforms = forward_transforms
self.backward_transforms = backward_transforms
self.K = K
-
+
@debug
def discretize(self):
if self.discretized:
@@ -224,13 +232,13 @@ class SpectralCurlOperatorBase(CurlOperatorBase):
super(SpectralCurlOperatorBase, self).discretize()
dFin, dFout = self.dFin, self.dFout
K = self.K
-
+
dK = ()
for (tg,Ki) in K:
_, dKi, _ = tg.discrete_wave_numbers[Ki]
dK += (dKi,)
self.dK = dK
-
+
def setup(self, work):
super(SpectralCurlOperatorBase, self).setup(work)
diff --git a/hysop/operator/base/custom_symbolic_operator.py b/hysop/operator/base/custom_symbolic_operator.py
index f83231f7c..3a3df48c8 100644
--- a/hysop/operator/base/custom_symbolic_operator.py
+++ b/hysop/operator/base/custom_symbolic_operator.py
@@ -351,7 +351,7 @@ class SymbolicExpressionInfo(object):
if ((k in self.input_dfields) and (self.input_dfields[k].dfield is v.dfield))}
self.stencils = SortedDict()
- dfields = tuple(input_dfields.values()) + tuple(output_dfields.values())
+ dfields = tuple(input_dfields.values()) + tuple(output_dfields.values())
if (force_symbolic_axes is not None):
if isinstance(force_symbolic_axes, tuple):
axes = force_symbolic_axes
@@ -393,7 +393,7 @@ class SymbolicExpressionInfo(object):
def check_arrays(self):
compute_resolution = self.compute_resolution
- arrays = set(a for a in (self.input_arrays.values() + self.output_arrays.values()))
+ arrays = set(self.input_arrays.values()).union(self.output_arrays.values())
for a in arrays:
if not a.is_bound:
msg='FATAL ERROR: {}::{} has not been bound to any memory '
@@ -419,7 +419,7 @@ class SymbolicExpressionInfo(object):
self.compute_resolution = tuple(compute_resolution)
def check_buffers(self):
- buffers = set(b for b in (self.input_buffers.values() + self.output_buffers.values()))
+ buffers = set(self.input_buffers.values()).union(self.output_buffers.values())
for b in buffers:
if not b.is_bound:
msg='FATAL ERROR: {}::{} has not been bound to any memory '
@@ -531,7 +531,7 @@ class SymbolicExpressionParser(object):
kind = None
fields = SortedDict()
arrays = SortedDict()
- exprs = filter(lambda e: isinstance(e, ValidExpressions), cls.extract_expressions(exprs))
+ exprs = tuple(filter(lambda e: isinstance(e, ValidExpressions), cls.extract_expressions(exprs)))
for expr in exprs:
check_instance(expr, ValidExpressions)
lhs = expr.args[0]
diff --git a/hysop/operator/base/diffusion.py b/hysop/operator/base/diffusion.py
index 227a43257..817562ead 100644
--- a/hysop/operator/base/diffusion.py
+++ b/hysop/operator/base/diffusion.py
@@ -13,9 +13,17 @@ class DiffusionOperatorBase(PoissonOperatorBase):
Common base for spectral diffusion operator.
"""
+ @debug
+ def __new__(cls, Fin, Fout, variables,
+ nu, dt, name=None, pretty_name=None, **kwds):
+ return super(DiffusionOperatorBase, cls).__new__(cls,
+ Fin=Fin, Fout=Fout, variables=variables,
+ name=name, pretty_name=pretty_name,
+ input_params=None, **kwds)
+
@debug
def __init__(self, Fin, Fout, variables,
- nu, dt,
+ nu, dt,
name=None, pretty_name=None,
**kwds):
"""
@@ -41,7 +49,7 @@ class DiffusionOperatorBase(PoissonOperatorBase):
dF/dt = nu*Laplacian(F)
in = Win
out = Wout
-
+
*Implicit resolution in spectral space:
F_hat(tn+1) = 1/(1-nu*dt*sum(Ki**2)) * F_hat(tn)
"""
@@ -50,7 +58,7 @@ class DiffusionOperatorBase(PoissonOperatorBase):
input_params = { dt.name: dt,
nu.name: nu }
-
+
default_name = 'Diffusion_{}_{}'.format(Fin.name, Fout.name)
default_pretty_name = 'Diffusion_{}_{}'.format(Fin.pretty_name, Fout.pretty_name)
name = first_not_None(name, default_name)
diff --git a/hysop/operator/base/memory_reordering.py b/hysop/operator/base/memory_reordering.py
index 66ec7b3dd..85813c916 100644
--- a/hysop/operator/base/memory_reordering.py
+++ b/hysop/operator/base/memory_reordering.py
@@ -98,7 +98,7 @@ class MemoryReorderingBase(object, metaclass=ABCMeta):
output_field=output_field,
input_topology_states=input_topology_states)
assert len(input_topology_states)==1
- istate = input_topology_states.values()[0]
+ istate = next(iter(input_topology_states.values()))
ostate.memory_order = self.target_memory_order
return ostate
diff --git a/hysop/operator/base/poisson.py b/hysop/operator/base/poisson.py
index 99c3380b1..7940f6ef6 100644
--- a/hysop/operator/base/poisson.py
+++ b/hysop/operator/base/poisson.py
@@ -13,6 +13,16 @@ class PoissonOperatorBase(SpectralOperatorBase):
Solves the poisson equation using a specific implementation.
"""
+ @debug
+ def __new__(cls, Fin, Fout, variables,
+ name=None, pretty_name=None,
+ dump_energy=None, dump_input_energy=None, dump_output_energy=None,
+ plot_energy=None, plot_input_energy=None, plot_output_energy=None, plot_inout_energy=None,
+ **kwds):
+ return super(PoissonOperatorBase, cls).__new__(cls,
+ name=name, pretty_name=pretty_name,
+ input_fields=None, output_fields=None, **kwds)
+
@debug
def __init__(self, Fin, Fout, variables,
name=None, pretty_name=None,
diff --git a/hysop/operator/base/poisson_curl.py b/hysop/operator/base/poisson_curl.py
index c7c6e4e2c..ee049b87a 100644
--- a/hysop/operator/base/poisson_curl.py
+++ b/hysop/operator/base/poisson_curl.py
@@ -21,6 +21,19 @@ class PoissonCurlOperatorBase(object):
Solves the poisson-rotational equation using a specific implementation.
"""
+ @debug
+ def __new__(cls, vorticity, velocity, variables,
+ diffusion=None, dt=None, projection=None,
+ dump_energy=None, dump_velocity_energy=None,
+ dump_input_vorticity_energy=None, dump_output_vorticity_energy=None,
+ plot_energy=None, plot_velocity_energy=None,
+ plot_input_vorticity_energy=None, plot_output_vorticity_energy=None, plot_inout_vorticity_energy=None,
+ **kwds):
+ return super(PoissonCurlOperatorBase, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ input_params=None, output_params=None, **kwds)
+
+
@debug
def __init__(self, vorticity, velocity, variables,
diffusion=None, dt=None, projection=None,
@@ -218,6 +231,14 @@ class PoissonCurlOperatorBase(object):
class SpectralPoissonCurlOperatorBase(PoissonCurlOperatorBase, SpectralOperatorBase):
+
+ @debug
+ def __new__(cls, vorticity, velocity, variables,
+ diffusion=None, dt=None, projection=None, **kwds):
+ return super(SpectralPoissonCurlOperatorBase, cls).__new__(cls,
+ vorticity=vorticity, velocity=velocity, variables=variables,
+ diffusion=diffusion, dt=dt, projection=projection, **kwds)
+
@debug
def __init__(self, vorticity, velocity, variables,
diffusion=None, dt=None, projection=None, **kwds):
@@ -256,14 +277,14 @@ class SpectralPoissonCurlOperatorBase(PoissonCurlOperatorBase, SpectralOperatorB
kd1s = ()
for Wi in W_Fts:
expr1 = grad(Wi, Wi.frame)
- kd1 = sorted(tg.push_expressions(*to_tuple(expr1)), key=lambda k: k.axis)
+ kd1 = tuple(sorted(tg.push_expressions(*to_tuple(expr1)), key=lambda k: k.axis))
kd1s += (kd1,)
# laplacian
kd2s = ()
for Wi in W_Fts:
expr2 = laplacian(Wi, Wi.frame)
- kd2 = sorted(tg.push_expressions(*to_tuple(expr2)), key=lambda k: k.axis)
+ kd2 = tuple(sorted(tg.push_expressions(*to_tuple(expr2)), key=lambda k: k.axis))
kd2s += (kd2,)
# curl
diff --git a/hysop/operator/base/solenoidal_projection.py b/hysop/operator/base/solenoidal_projection.py
index 1e6880b88..8181ea633 100644
--- a/hysop/operator/base/solenoidal_projection.py
+++ b/hysop/operator/base/solenoidal_projection.py
@@ -15,14 +15,20 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
"""
Solves solenoidal projection (project a 3d field F such that div(F)=0)
"""
-
+
+ @debug
+ def __new__(cls, input_field, output_field, variables,
+ input_field_div=None, output_field_div=None, **kwds):
+ return super(SolenoidalProjectionOperatorBase, cls).__new__(cls,
+ input_fields=input_field, output_fields=output_field, **kwds)
+
@debug
- def __init__(self, input_field, output_field, variables,
- input_field_div=None, output_field_div=None, **kwds):
+ def __init__(self, input_field, output_field, variables,
+ input_field_div=None, output_field_div=None, **kwds):
"""
- SolenoidalProjection projects a 3D vector field
+ SolenoidalProjection projects a 3D vector field
onto the space of divergence free fields.
-
+
Parameters
----------
input_field: :class:`~hysop.fields.continuous_field.Field`
@@ -35,10 +41,10 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
Optionally compute output field divergence.
variables: dict
dictionary of fields as keys and topologies as values.
- kwds :
+ kwds :
base class parameters.
"""
-
+
check_instance(output_field, Field)
check_instance(input_field, Field)
check_instance(input_field_div, Field, allow_none=True)
@@ -56,11 +62,11 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
output_fields[input_field_div] = variables[input_field_div]
if (output_field_div is not None):
output_fields[output_field_div] = variables[output_field_div]
-
+
dim = input_field.domain.dim
icomp = input_field.nb_components
ocomp = output_field.nb_components
-
+
if (input_field.domain != output_field.domain):
msg = 'input_field and output_field do not share the same domain.'
raise ValueError(msg)
@@ -81,10 +87,10 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
msg='input_field_div component mistmach, got {} components but expected 1.'
msg=msg.format(output_field_div.nb_components)
raise RuntimeError(msg)
-
- super(SolenoidalProjectionOperatorBase, self).__init__(input_fields=input_fields,
+
+ super(SolenoidalProjectionOperatorBase, self).__init__(input_fields=input_fields,
output_fields=output_fields, **kwds)
-
+
Fin = input_field
Fout = output_field
compute_divFin = (input_field_div is not None)
@@ -100,9 +106,9 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
kd1s, kd2s = (), ()
for Wi in Fts:
expr = grad(Wi, Wi.frame)
- kd1 = sorted(tg.push_expressions(*to_tuple(expr)), key=lambda k: k.axis)
+ kd1 = tuple(sorted(tg.push_expressions(*to_tuple(expr)), key=lambda k: k.axis))
expr = laplacian(Wi, Wi.frame)
- kd2 = sorted(tg.push_expressions(expr), key=lambda k: k.axis)
+ kd2 = tuple(sorted(tg.push_expressions(expr), key=lambda k: k.axis))
kd1s += (kd1,)
kd2s += (kd2,)
@@ -122,16 +128,16 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
self.Fout = output_field
self.divFin = input_field_div
self.divFout = output_field_div
-
+
self.compute_divFin = compute_divFout
self.compute_divFout = compute_divFout
-
+
self.tg = tg
self.forward_transforms = forward_transforms
self.backward_transforms = backward_transforms
self.backward_divFin_transform = backward_divFin_transform
self.backward_divFout_transform = backward_divFout_transform
-
+
self.Bts = Bts
self.Fts = Fts
self.kd1s = kd1s
@@ -144,17 +150,17 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
super(SolenoidalProjectionOperatorBase, self).discretize()
dFin = self.get_input_discrete_field(self.Fin)
dFout = self.get_output_discrete_field(self.Fout)
-
+
if self.compute_divFin:
ddivFin = self.output_discrete_fields[self.divFin]
else:
ddivFin = None
-
+
if self.compute_divFout:
ddivFout = self.output_discrete_fields[self.divFout]
else:
ddivFout = None
-
+
kd1s, kd2s = self.kd1s, self.kd2s
dkd1s = ()
for kd1 in kd1s:
@@ -163,7 +169,7 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
idx, dwi, _ = self.tg.discrete_wave_numbers[wi]
dkd1[idx] = dwi
dkd1s += (tuple(dkd1),)
-
+
dkd2s = ()
for kd2 in kd2s:
dkd2 = [None,]*len(kd1)
@@ -171,7 +177,7 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
idx, dwi, _ = self.tg.discrete_wave_numbers[wi]
dkd2[idx] = dwi
dkd2s += (tuple(dkd2),)
-
+
self.dFin = dFin
self.dFout = dFout
self.ddivFin = ddivFin
@@ -179,17 +185,17 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
self.dkd1s = tuple(dkd1s)
self.dkd2s = tuple(dkd2s)
-
+
def get_work_properties(self):
requests = super(SolenoidalProjectionOperatorBase, self).get_work_properties()
- for (i,(Ft,Bt)) in enumerate(zip(self.forward_transforms,
+ for (i,(Ft,Bt)) in enumerate(zip(self.forward_transforms,
self.backward_transforms)):
assert (Ft.backend == Bt.backend)
assert (Ft.output_dtype == Bt.input_dtype), (Ft.output_dtype, Bt.input_dtype)
assert (Ft.output_shape == Bt.input_shape), (Ft.output_shape, Bt.input_shape)
shape = Ft.output_shape
dtype = Ft.output_dtype
- request = MemoryRequest(backend=self.tg.backend, dtype=dtype,
+ request = MemoryRequest(backend=self.tg.backend, dtype=dtype,
shape=shape, nb_components=1,
alignment=self.min_fft_alignment)
requests.push_mem_request('fft_buffer_{}'.format(i), request)
@@ -197,7 +203,7 @@ class SolenoidalProjectionOperatorBase(SpectralOperatorBase):
def setup(self, work):
dkd1s, dkd2s = self.dkd1s, self.dkd2s
-
+
output_axes = self.forward_transforms[0].output_axes
for (i,(Ft,Bt)) in enumerate(zip(self.forward_transforms, self.backward_transforms)):
dtmp, = work.get_buffer(self, 'fft_buffer_{}'.format(i))
diff --git a/hysop/operator/base/spectral_operator.py b/hysop/operator/base/spectral_operator.py
index e5adba837..700508771 100644
--- a/hysop/operator/base/spectral_operator.py
+++ b/hysop/operator/base/spectral_operator.py
@@ -33,13 +33,17 @@ from hysop.numerics.fft.fft import FFTI, simd_alignment, is_byte_aligned, HysopF
class SpectralComputationalGraphNodeFrontend(ComputationalGraphNodeFrontend):
- def __init__(self, implementation, **kwds):
- impl, extra_kwds = self.get_actual_implementation(implementation=implementation, **kwds)
+ def __new__(cls, implementation, enforce_implementation=True, **kwds):
+ return super(SpectralComputationalGraphNodeFrontend, cls).__new__(cls,
+ implementation=implementation, **kwds)
+
+ def __init__(self, implementation, enforce_implementation=True, **kwds):
+ impl, extra_kwds = self.get_actual_implementation(implementation=implementation,
+ enforce_implementation=enforce_implementation, **kwds)
for k in extra_kwds.keys():
assert k not in kwds
kwds.update(extra_kwds)
- super(SpectralComputationalGraphNodeFrontend, self).__init__(
- implementation=impl, **kwds)
+ super(SpectralComputationalGraphNodeFrontend, self).__init__(implementation=impl, **kwds)
@classmethod
def get_actual_implementation(cls, implementation,
@@ -81,7 +85,7 @@ class SpectralComputationalGraphNodeFrontend(ComputationalGraphNodeFrontend):
"""
implementation = first_not_None(implementation, cls.default_implementation())
assert implementation in cls.implementations()
- extra_kwds = {'enable_opencl_host_buffer_mapping': False}
+ extra_kwds = {}
if (enforce_implementation):
return (implementation, extra_kwds)
if (implementation == Implementation.OPENCL):
@@ -92,7 +96,6 @@ class SpectralComputationalGraphNodeFrontend(ComputationalGraphNodeFrontend):
raise RuntimeError(msg)
from hysop.backend.device.opencl import cl
if (cl_env.device.type == cl.device_type.CPU):
- extra_kwds['enable_opencl_host_buffer_mapping'] = True
if (Implementation.PYTHON in cls.implementations()):
from hysop.backend.host.host_operator import HostOperator, OpenClMappable
op_cls = cls.implementations()[Implementation.PYTHON]
@@ -106,6 +109,7 @@ class SpectralComputationalGraphNodeFrontend(ComputationalGraphNodeFrontend):
raise TypeError(msg)
assert Backend.HOST in op_cls.supported_backends()
assert Backend.OPENCL in op_cls.supported_backends()
+ extra_kwds['enable_opencl_host_buffer_mapping'] = True
return (Implementation.PYTHON, extra_kwds)
return (implementation, extra_kwds)
@@ -118,8 +122,11 @@ class SpectralOperatorBase(object):
min_fft_alignment = simd_alignment # FFTW SIMD.
@debug
- def __init__(self, fft_interface=None, fft_interface_kwds=None,
- **kwds):
+ def __new__(cls, fft_interface=None, fft_interface_kwds=None, **kwds):
+ return super(SpectralOperatorBase, cls).__new__(cls, **kwds)
+
+ @debug
+ def __init__(self, fft_interface=None, fft_interface_kwds=None, **kwds):
"""
Initialize a spectral operator base.
kwds: dict
@@ -217,7 +224,7 @@ class SpectralOperatorBase(object):
for tg in self.transform_groups.values():
for (k, v) in tg.get_mem_requests(**kwds).items():
check_instance(k, str) # temporary buffer name
- check_instance(v, int) # nbytes
+ check_instance(v, (int,np.integer)) # nbytes
K = (k, tg.backend)
if K in memory_requests:
memory_requests[K] = max(memory_requests[K], v)
@@ -229,7 +236,7 @@ class SpectralOperatorBase(object):
requests = super(SpectralOperatorBase, self).get_work_properties(**kwds)
for ((k, backend), v) in self.get_mem_requests(**kwds).items():
check_instance(k, str)
- check_instance(v, int)
+ check_instance(v, (int,np.integer))
if (v > 0):
mrequest = MemoryRequest(backend=backend, size=v,
alignment=self.min_fft_alignment)
@@ -262,6 +269,9 @@ class SpectralTransformGroup(object):
"""
DEBUG = False
+ def __new__(cls, op, tag, mem_tag, **kwds):
+ return super(SpectralTransformGroup, cls).__new__(cls, **kwds)
+
def __init__(self, op, tag, mem_tag, **kwds):
"""
Parameters
@@ -288,6 +298,7 @@ class SpectralTransformGroup(object):
All forward_fields and backward_fields have to live on the same domain and
their boundary conditions should comply with given expressions.
"""
+ super(SpectralTransformGroup, self).__init__(**kwds)
mem_tag = first_not_None(mem_tag, 'fft_pool')
check_instance(op, SpectralOperatorBase)
check_instance(tag, str)
@@ -339,11 +350,11 @@ class SpectralTransformGroup(object):
@property
def forward_fields(self):
- return map(lambda x: x[0], self._forward_transforms.keys())
+ return tuple(map(lambda x: x[0], self._forward_transforms.keys()))
@property
def backward_fields(self):
- return map(lambda x: x[0], self._backward_transforms.keys())
+ return tuple(map(lambda x: x[0], self._backward_transforms.keys()))
@property
def forward_transforms(self):
@@ -549,7 +560,7 @@ class SpectralTransformGroup(object):
memory_requests = {}
for fwd in self.forward_transforms.values():
mem_requests = fwd.get_mem_requests(**kwds)
- check_instance(mem_requests, dict, keys=str, values=int)
+ check_instance(mem_requests, dict, keys=str, values=(int,np.integer))
for (k, v) in mem_requests.items():
if k in memory_requests:
memory_requests[k] = max(memory_requests[k], v)
@@ -557,7 +568,7 @@ class SpectralTransformGroup(object):
memory_requests[k] = v
for bwd in self.backward_transforms.values():
mem_requests = bwd.get_mem_requests(**kwds)
- check_instance(mem_requests, dict, keys=str, values=int)
+ check_instance(mem_requests, dict, keys=str, values=(int,np.integer))
for (k, v) in mem_requests.items():
if k in memory_requests:
memory_requests[k] = max(memory_requests[k], v)
@@ -828,7 +839,7 @@ class SpectralTransformGroup(object):
@property
def output_parameters(self):
parameters = set()
- for pt in self._forward_transforms.values() + self._backward_transforms.values():
+ for pt in tuple(self._forward_transforms.values()) + tuple(self._backward_transforms.values()):
parameters.update(pt.output_parameters)
return parameters
@@ -889,10 +900,20 @@ class PlannedSpectralTransform(object):
"""
DEBUG = False
+ def __new__(cls, transform_group, tag, symbolic_transform, action,
+ custom_input_buffer=None, custom_output_buffer=None,
+ matching_forward_transform=None,
+ dump_energy=None, plot_energy=None, compute_energy_frequencies=None,
+ **kwds):
+ return super(PlannedSpectralTransform, cls).__new__(cls, **kwds)
+
def __init__(self, transform_group, tag, symbolic_transform, action,
custom_input_buffer=None, custom_output_buffer=None,
matching_forward_transform=None,
- dump_energy=None, plot_energy=None, compute_energy_frequencies=None):
+ dump_energy=None, plot_energy=None, compute_energy_frequencies=None,
+ **kwds):
+
+ super(PlannedSpectralTransform, self).__init__(**kwds)
check_instance(transform_group, SpectralTransformGroup)
check_instance(transform_group.op, SpectralOperatorBase)
@@ -1707,10 +1728,11 @@ class PlannedSpectralTransform(object):
B1_tag: nbytes,
TMP_tag: tmp_nbytes}
- if (self._energy_nbytes > 0):
- requests[ENERGY_tag] = self._energy_nbytes
- if (self._mutexes_nbytes > 0):
- requests[MUTEXES_tag] = self._mutexes_nbytes
+ if self._do_compute_energy:
+ if (self._energy_nbytes > 0):
+ requests[ENERGY_tag] = self._energy_nbytes
+ if (self._mutexes_nbytes > 0):
+ requests[MUTEXES_tag] = self._mutexes_nbytes
return requests
@@ -1747,7 +1769,7 @@ class PlannedSpectralTransform(object):
except ValueError:
TMP = None
- if (self._energy_nbytes > 0):
+ if (self._energy_nbytes is not None) and (self._energy_nbytes > 0):
ENERGY, = work.get_buffer(op, ENERGY_tag, handle=True)
energy_buffer = ENERGY[:self._energy_nbytes].view(dtype=self.dfield.dtype)
assert energy_buffer.size == self._max_wavenumber+1
@@ -1755,7 +1777,7 @@ class PlannedSpectralTransform(object):
ENERGY = None
energy_buffer = None
- if (self._mutexes_nbytes > 0):
+ if (self._mutexes_nbytes is not None) and (self._mutexes_nbytes > 0):
MUTEXES, = work.get_buffer(op, MUTEXES_tag, handle=True)
mutexes_buffer = MUTEXES[:self._mutexes_nbytes].view(dtype=np.int32)
assert mutexes_buffer.size == self._max_wavenumber+1
diff --git a/hysop/operator/base/stretching_dir.py b/hysop/operator/base/stretching_dir.py
index 9ad570e3a..2939654f0 100644
--- a/hysop/operator/base/stretching_dir.py
+++ b/hysop/operator/base/stretching_dir.py
@@ -38,6 +38,15 @@ class DirectionalStretchingBase(object):
am.update(cls.__available_methods)
return am
+ @debug
+ def __new__(cls, formulation, velocity, vorticity, variables, dt,
+ C=None, A=None, name=None,
+ implementation=None, base_kwds=None, **kwds):
+ return super(DirectionalStretchingBase, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ input_params=None, output_params=None,
+ **kwds)
+
@debug
def __init__(self, formulation, velocity, vorticity, variables, dt,
C=None, A=None, name=None,
@@ -91,8 +100,8 @@ class DirectionalStretchingBase(object):
Should only be given for MIXED_GRAD_UW formulations.
ValueError will be raised on other formulations.
The linear combination coefficients A is a scalar.
- Contained value should be a numerical coefficient, a parameter
- (or a generic symbolic expression) such that C*(A*grad(U).W + (1-A)*grad^T(U).W)
+ Contained value should be a numerical coefficient, a parameter
+ (or a generic symbolic expression) such that C*(A*grad(U).W + (1-A)*grad^T(U).W)
is directionally splittable.
Here * is the classical elementwise multiplication.
Default value is 0.5.
diff --git a/hysop/operator/directional/diffusion_dir.py b/hysop/operator/directional/diffusion_dir.py
index 993dc4ee4..27222c4cb 100644
--- a/hysop/operator/directional/diffusion_dir.py
+++ b/hysop/operator/directional/diffusion_dir.py
@@ -21,6 +21,19 @@ class DirectionalDiffusion(DirectionalSymbolic):
Directional diffusion using the symbolic code generation framework.
"""
+ @debug
+ def __new__(cls, fields, coeffs, variables, dt,
+ laplacian_formulation=True,
+ name=None, implementation=None, base_kwds=None, **kwds):
+ base_kwds = first_not_None(base_kwds, {})
+ return super(DirectionalDiffusion, cls).__new__(cls,
+ name=name, variables=variables, dt=dt,
+ base_kwds=base_kwds, implementation=implementation, exprs=None,
+ candidate_input_tensors=None,
+ candidate_output_tensors=None,
+ **kwds)
+
+
@debug
def __init__(self, fields, coeffs, variables, dt,
laplacian_formulation=True,
diff --git a/hysop/operator/directional/stretching_dir.py b/hysop/operator/directional/stretching_dir.py
index 8a1d84d6a..905b31bb7 100644
--- a/hysop/operator/directional/stretching_dir.py
+++ b/hysop/operator/directional/stretching_dir.py
@@ -22,6 +22,17 @@ class DirectionalStretching(DirectionalSymbolic):
Directional stretching using the symbolic code generation framework.
"""
+ @debug
+ def __new__(cls, formulation, velocity, vorticity, variables, dt,
+ C=None, A=None, name=None, implementation=None, base_kwds=None, **kwds):
+ base_kwds = first_not_None(base_kwds, {})
+ return super(DirectionalStretching, cls).__new__(cls,
+ name=name, variables=variables, dt=dt,
+ candidate_input_tensors=None,
+ candidate_output_tensors=None,
+ base_kwds=base_kwds, implementation=implementation,
+ exprs=None, **kwds)
+
@debug
def __init__(self, formulation, velocity, vorticity, variables, dt,
C=None, A=None, name=None, implementation=None, base_kwds=None, **kwds):
@@ -181,6 +192,7 @@ class DirectionalStretching(DirectionalSymbolic):
return exprs
+
class StaticDirectionalStretching(DirectionalOperatorFrontend):
"""
Directional stretching using the symbolic code generation framework.
@@ -196,6 +208,19 @@ class StaticDirectionalStretching(DirectionalOperatorFrontend):
def default_implementation(cls):
return Implementation.PYTHON
+ @debug
+ def __new__(cls, formulation, velocity, vorticity, variables, dt,
+ C=None, A=None, name=None, implementation=None, base_kwds=None, **kwds):
+ base_kwds = first_not_None(base_kwds, {})
+ return super(StaticDirectionalStretching, cls).__new__(cls,
+ name=name, variables=variables, dt=dt,
+ formulation=formulation,
+ velocity=velocity, vorticity=vorticity,
+ C=C, A=A,
+ candidate_input_tensors=None,
+ candidate_output_tensors=None,
+ base_kwds=base_kwds, implementation=implementation, **kwds)
+
@debug
def __init__(self, formulation, velocity, vorticity, variables, dt,
C=None, A=None, name=None, implementation=None, base_kwds=None, **kwds):
@@ -322,3 +347,4 @@ class StaticDirectionalStretching(DirectionalOperatorFrontend):
candidate_input_tensors=(velocity, vorticity,),
candidate_output_tensors=(vorticity,),
base_kwds=base_kwds, implementation=implementation, **kwds)
+
diff --git a/hysop/operator/hdf_io.py b/hysop/operator/hdf_io.py
index 3cc7e687c..76dcab47f 100755
--- a/hysop/operator/hdf_io.py
+++ b/hysop/operator/hdf_io.py
@@ -41,6 +41,11 @@ class HDF_IO(ComputationalGraphOperator, metaclass=ABCMeta):
"""
return Backend.all
+ def __new__(cls, var_names=None,
+ name_prefix='', name_postfix='',
+ force_backend=None, **kwds):
+ return super(HDF_IO, cls).__new__(cls, **kwds)
+
def __init__(self, var_names=None,
name_prefix='', name_postfix='',
force_backend=None, **kwds):
@@ -184,7 +189,7 @@ class HDF_IO(ComputationalGraphOperator, metaclass=ABCMeta):
def discretize(self):
super(HDF_IO, self).discretize()
- topo = self.input_fields.values()[0]
+ topo = next(iter(self.input_fields.values()))
use_local_hdf5 = (topo.cart_size == 1)
use_local_hdf5 |= (topo.proc_shape[0] == topo.cart_size) and (topo.cart_size <= 16) and (not self.io_params.hdf5_disable_slicing)
# XDMF JOIN do not support more than 16 arguments
@@ -216,7 +221,7 @@ class HDF_IO(ComputationalGraphOperator, metaclass=ABCMeta):
local_compute_slices[field] = mesh.local_compute_slices
global_compute_slices[field] = mesh.global_compute_slices
else:
- local_compute_slices[field] = tuple(slice(0, 0) for _ in range(self.domain.dim))
+ local_compute_slices[field] = tuple(slice(0, 0) for _ in range(self.domain.dim))
global_compute_slices[field] = tuple(slice(0, 0) for _ in range(self.domain.dim))
self._local_compute_slices = local_compute_slices
self._global_compute_slices = global_compute_slices
@@ -294,6 +299,12 @@ class HDF_Writer(HDF_IO):
</Xdmf>
"""
+ def __new__(cls, variables,
+ name=None, pretty_name=None, **kwds):
+ return super(HDF_Writer, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ name=name, pretty_name=pretty_name, **kwds)
+
def __init__(self, variables,
name=None, pretty_name=None, **kwds):
"""
@@ -436,7 +447,7 @@ class HDF_Writer(HDF_IO):
ds_names = self.dataset.keys()
joinrkfiles = None
if self.use_local_hdf5 and (self.topology.cart_size > 1):
- joinrkfiles = range(self.topology.cart_size)
+ joinrkfiles = tuple(range(self.topology.cart_size))
grid_attributes = XMF.prepare_grid_attributes(
ds_names,
resolution, origin, step, joinrkfiles=joinrkfiles)
@@ -593,6 +604,11 @@ class HDF_Reader(HDF_IO):
Parallel reading of hdf/xdmf files to fill some fields in.
"""
+ def __new__(cls, variables, restart=None, name=None, **kwds):
+ return super(HDF_Reader, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ name=name, **kwds)
+
def __init__(self, variables, restart=None, name=None, **kwds):
"""Read some fields data from hdf/xmdf files.
Parallel readings.
diff --git a/hysop/operator/memory_reordering.py b/hysop/operator/memory_reordering.py
index b75230f04..6d9f8dbc2 100644
--- a/hysop/operator/memory_reordering.py
+++ b/hysop/operator/memory_reordering.py
@@ -21,8 +21,8 @@ class MemoryReorderingNotImplementedError(NotImplementedError):
class MemoryReordering(ComputationalGraphNodeGenerator):
"""
Operator generator for inplace and out of place field memory reordering.
-
- Available implementations are:
+
+ Available implementations are:
*python (numpy based memory reordering, n-dimensional)
This is currently used to convert C_CONTIGUOUS fields to F_CONTIGUOUS fields.
@@ -31,10 +31,10 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
graph node generator generates an operator per supplied field,
possibly on different implementation backends.
- See hysop.operator.base.reorder.MemoryReorderingBase for operator backend
+ See hysop.operator.base.reorder.MemoryReorderingBase for operator backend
implementation interface.
"""
-
+
@classmethod
def implementations(cls):
from hysop.backend.host.python.operator.memory_reordering import PythonMemoryReordering
@@ -44,25 +44,25 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
Implementation.OPENCL: OpenClMemoryReordering,
}
return _implementations
-
+
@classmethod
def default_implementation(cls):
msg='MemoryReordering has no default implementation, '
msg+='implementation should match the discrete field topology backend.'
raise RuntimeError(msg)
-
+
@debug
- def __init__(self, fields, variables,
+ def __init__(self, fields, variables,
target_memory_order,
output_fields=None,
- implementation=None,
+ implementation=None,
name=None,
- base_kwds=None,
+ base_kwds=None,
**kwds):
"""
Initialize a MemoryReordering operator generator operating on CartesianTopology topologies.
MemoryReordering is deduced from topology requirements.
-
+
Parameters
----------
fields: Field, list or tuple of Fields
@@ -71,7 +71,7 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
output_fields: Field, list or tuple of Fields, optional
Output continuous fields where the results are stored.
Reordered shapes should match the input shapes.
- By default output_fields are the same as input_fields
+ By default output_fields are the same as input_fields
resulting in inplace memory reordering.
Input and output are matched by order int list/tuple.
variables: dict
@@ -80,10 +80,10 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
Target memory order to achieve.
implementation: Implementation, optional, defaults to None
target implementation, should be contained in available_implementations().
- If implementation is set and topology does not match backend,
+ If implementation is set and topology does not match backend,
RuntimeError will be raised on _generate.
If None, implementation will be set according to topologies backend,
- different implementations may be choosen for different Fields if
+ different implementations may be choosen for different Fields if
defined on different backends.
name: string
prefix for generated operator names
@@ -91,9 +91,9 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
Base class keywords arguments.
If None, an empty dict will be passed.
kwds:
- Keywords arguments that will be passed towards implementation
+ Keywords arguments that will be passed towards implementation
memory reordering operator __init__.
-
+
Notes
-----
Out of place reordering will always be faster to process.
@@ -105,10 +105,10 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
A MemoryReordering operator implementation should support the MemoryReorderingBase
interface (see hysop.operator.base.memory_ordering.MemoryOrdering).
- This ComputationalGraphNodeFrontend will generate a operator for each
+ This ComputationalGraphNodeFrontend will generate a operator for each
input and output ScalarField pair.
- All implementations should raise MemoryReorderingNotImplementedError if the user supplied
+ All implementations should raise MemoryReorderingNotImplementedError if the user supplied
parameters leads to unimplemented or unsupported memory reordering features.
"""
input_fields = to_tuple(fields)
@@ -119,23 +119,23 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
for (ifield,ofield) in zip(input_fields, output_fields) )
else:
output_fields = tuple( ifield for ifield in input_fields )
-
+
check_instance(input_fields, tuple, values=Field)
check_instance(output_fields, tuple, values=Field, size=len(input_fields))
check_instance(target_memory_order, MemoryOrdering)
assert target_memory_order in (MemoryOrdering.C_CONTIGUOUS,
MemoryOrdering.F_CONTIGUOUS)
-
- candidate_input_tensors = filter(lambda x: x.is_tensor, input_fields)
- candidate_output_tensors = filter(lambda x: x.is_tensor, output_fields)
-
+
+ candidate_input_tensors = tuple(filter(lambda x: x.is_tensor, input_fields))
+ candidate_output_tensors = tuple(filter(lambda x: x.is_tensor, output_fields))
+
base_kwds = first_not_None(base_kwds, {})
- super(MemoryReordering, self).__init__(name=name,
+ super(MemoryReordering, self).__init__(name=name,
candidate_input_tensors=candidate_input_tensors,
candidate_output_tensors=candidate_output_tensors,
**base_kwds)
-
+
# expand tensors
ifields, ofields = (), ()
for (ifield, ofield) in zip(input_fields, output_fields):
@@ -143,7 +143,7 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
msg+='and field {} of shape {}.'
if (ifield.is_tensor ^ ofield.is_tensor):
if ifield.is_tensor:
- msg=msg.format(ifield.short_description(), ifield.shape,
+ msg=msg.format(ifield.short_description(), ifield.shape,
ofield.short_description(), '(1,)')
else:
msg=msg.format(ifield.short_description(), '(1,)',
@@ -155,13 +155,13 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
raise RuntimeError(msg)
ifields += ifield.fields
ofields += ofield.fields
-
+
input_fields = ifields
output_fields = ofields
check_instance(input_fields, tuple, values=ScalarField)
check_instance(output_fields, tuple, values=ScalarField, size=len(input_fields))
-
+
check_instance(variables, dict, keys=Field, values=CartesianTopologyDescriptors)
check_instance(base_kwds, dict, keys=str)
@@ -204,14 +204,14 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
msg += 'input_field {} dimension {}.'
msg.format(input_field, idim, input_fields[0].name, dim)
raise ValueError(msg)
-
+
self.input_fields = input_fields
self.output_fields = output_fields
self.variables = variables
self.implementation = implementation
self.target_memory_order = target_memory_order
self.kwds = kwds
-
+
def _get_op_and_check_implementation(self, src_topo, dst_topo):
backend = getattr(src_topo,'backend', None) or getattr(dst_topo, 'backend', None)
@@ -259,23 +259,23 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
raise TypeError(msg)
return op_cls
-
+
@debug
def _generate(self):
nodes = []
for (ifield, ofield) in zip(self.input_fields, self.output_fields):
src_topo = ComputationalGraphNode.get_topo_descriptor(self.variables, ifield)
dst_topo = ComputationalGraphNode.get_topo_descriptor(self.variables, ofield)
-
+
MemoryReorderingOp = self._get_op_and_check_implementation(src_topo, dst_topo)
kwds = self.kwds.copy()
variables = { ifield: src_topo }
variables[ofield] = dst_topo
-
+
# instantiate operator
- node = MemoryReorderingOp(input_field=ifield, output_field=ofield,
- variables=variables,
+ node = MemoryReorderingOp(input_field=ifield, output_field=ofield,
+ variables=variables,
target_memory_order=self.target_memory_order,
**kwds)
nodes.append(node)
@@ -284,4 +284,4 @@ class MemoryReordering(ComputationalGraphNodeGenerator):
raise RuntimeError(msg)
return nodes
-
+
diff --git a/hysop/operator/tests/test_bilevel_advection.py b/hysop/operator/tests/test_bilevel_advection.py
index 516011b9d..3b2f64eec 100644
--- a/hysop/operator/tests/test_bilevel_advection.py
+++ b/hysop/operator/tests/test_bilevel_advection.py
@@ -111,9 +111,8 @@ class TestBilevelAdvectionOperator(object):
dt.value = (0.99 * velocity_cfl) / (max(shape)-1)
ref_impl = Implementation.FORTRAN
- implementations = DirectionalAdvection.implementations().keys()
- implementations += Advection.implementations().keys()
- implementations = list(set(implementations))
+ implementations = set(DirectionalAdvection.implementations().keys()).union(Advection.implementations().keys())
+ implementations = list(implementations)
assert (ref_impl in implementations)
implementations.remove(ref_impl)
implementations = [ref_impl] + implementations
diff --git a/hysop/operator/tests/test_custom_symbolic.py b/hysop/operator/tests/test_custom_symbolic.py
index 2bf80f1aa..935b43d91 100644
--- a/hysop/operator/tests/test_custom_symbolic.py
+++ b/hysop/operator/tests/test_custom_symbolic.py
@@ -186,11 +186,11 @@ class TestCustomSymbolic(object):
for dtype in dtypes:
print(' DTYPE {}'.format(dtype.__name__))
A = Field(domain=domain, name='A', dtype=dtype,
- nb_components=1, register_object=False)
+ nb_components=1)
B = Field(domain=domain, name='B', dtype=dtype,
- nb_components=1, register_object=False)
+ nb_components=1)
C = Field(domain=domain, name='C', dtype=dtype,
- nb_components=3, register_object=False)
+ nb_components=3)
P0 = ScalarParameter('P0', dtype=np.float32, initial_value=1.0)
P1 = ScalarParameter('P1', dtype=np.float64, initial_value=2.0, const=True)
@@ -390,11 +390,11 @@ class TestCustomSymbolic(object):
print(' DISCRETIZATION {}'.format(discretization))
A = Field(domain=domain, name='A', dtype=np.float32,
- nb_components=1, register_object=False)
+ nb_components=1)
B = Field(domain=domain, name='B', dtype=np.float32,
- nb_components=2, register_object=False)
+ nb_components=2)
C = Field(domain=domain, name='C', dtype=np.float64,
- nb_components=3, register_object=False)
+ nb_components=3)
P0 = ScalarParameter('P0', dtype=np.float32, initial_value=3.14)
T0 = TensorParameter('T', shape=(3,), dtype=np.int32, initial_value=[4,3,2])
@@ -518,11 +518,11 @@ class TestCustomSymbolic(object):
print(' DISCRETIZATION {}'.format(discretization))
A = Field(domain=domain, name='A', dtype=np.float32,
- nb_components=1, register_object=False)
+ nb_components=1)
B = Field(domain=domain, name='B', dtype=np.float32,
- nb_components=2, register_object=False)
+ nb_components=2)
C = Field(domain=domain, name='C', dtype=np.float32,
- nb_components=3, register_object=False)
+ nb_components=3)
P0 = ScalarParameter('P0', dtype=np.float32, initial_value=3.14)
T0 = TensorParameter('T', shape=(3,), dtype=np.int32, initial_value=[4,3,2])
diff --git a/hysop/operator/tests/test_diffusion.py b/hysop/operator/tests/test_diffusion.py
index ce25f3ab4..9dad287c7 100644
--- a/hysop/operator/tests/test_diffusion.py
+++ b/hysop/operator/tests/test_diffusion.py
@@ -52,9 +52,9 @@ class TestDiffusionOperator(object):
nu = ScalarParameter('nu', dtype=dtype, initial_value=random.random(), const=True)
nb_components = 5 if (dim==2) else 6
Fin = Field(domain=domain, name='Fin', dtype=dtype,
- nb_components=nb_components, register_object=False)
+ nb_components=nb_components)
Fout = Field(domain=domain, name='Fout', dtype=dtype,
- nb_components=nb_components, register_object=False)
+ nb_components=nb_components)
self._test_one(shape=shape, dim=dim, dtype=dtype,
is_inplace=is_inplace, domain=domain,
Fin=Fin, Fout=Fout, nu=nu)
diff --git a/hysop/operator/tests/test_directional_diffusion.py b/hysop/operator/tests/test_directional_diffusion.py
index ba4c87ef8..e6ae504d6 100644
--- a/hysop/operator/tests/test_directional_diffusion.py
+++ b/hysop/operator/tests/test_directional_diffusion.py
@@ -64,9 +64,9 @@ class TestDirectionalDiffusionOperator(object):
domain = Box(length=(2*npw.pi,)*dim)
for dtype in flt_types:
Fin = Field(domain=domain, name='Fin', dtype=dtype,
- nb_components=3, register_object=False)
+ nb_components=3)
Fout = Field(domain=domain, name='Fout', dtype=dtype,
- nb_components=3, register_object=False)
+ nb_components=3)
coeffs = npw.random.rand(Fin.nb_components, dim).astype(dtype)
for order in orders:
for time_integrator in time_integrators:
@@ -241,7 +241,7 @@ class TestDirectionalDiffusionOperator(object):
csg.configure(dtype=MPQ, dim=1)
D2 = csg.generate_exact_stencil(derivative=2, order=order)
- directions = range(dim) + range(dim)[::-1]
+ directions = tuple(range(dim)) + tuple(range(dim))[::-1]
dt_coeffs = (0.5,)*(2*dim)
Xin = { 'F{}'.format(i): dfin[i] for i in range(len(dfin)) }
views = { 'F{}'.format(i): view for i in range(len(dfin)) }
diff --git a/hysop/operator/tests/test_directional_stretching.py b/hysop/operator/tests/test_directional_stretching.py
index dd795a428..811caabb0 100644
--- a/hysop/operator/tests/test_directional_stretching.py
+++ b/hysop/operator/tests/test_directional_stretching.py
@@ -68,11 +68,11 @@ class TestDirectionalStretchingOperator(object):
domain = Box(length=(2*npw.pi,)*dim)
for dtype in flt_types:
Vin = Field(domain=domain, name='Vin', dtype=dtype,
- nb_components=dim, register_object=False)
+ nb_components=dim)
Win = Field(domain=domain, name='Win', dtype=dtype,
- nb_components=dim, register_object=False)
+ nb_components=dim)
Wout = Field(domain=domain, name='Wout', dtype=dtype,
- nb_components=dim, register_object=False)
+ nb_components=dim)
C = npw.random.rand(dim).astype(dtype)
for A in As:
for order in orders:
@@ -265,7 +265,7 @@ class TestDirectionalStretchingOperator(object):
Vin = tuple(d.get().handle.copy() for d in dvin.data)
Win = tuple(d.get().handle.copy() for d in dwin.data)
- directions = range(dim) + range(dim)[::-1]
+ directions = tuple(range(dim)) + tuple(range(dim))[::-1]
dt_coeffs = (0.5,)*(2*dim)
wis = tuple('W{}'.format(i) for i in range(3))
diff --git a/hysop/operator/tests/test_poisson.py b/hysop/operator/tests/test_poisson.py
index 3de240114..151f0477f 100644
--- a/hysop/operator/tests/test_poisson.py
+++ b/hysop/operator/tests/test_poisson.py
@@ -121,9 +121,9 @@ class TestPoissonOperator(object):
rboundaries=rboundaries)
Psi = Field(domain=domain, name='Psi', dtype=dtype,
- nb_components=nb_components, register_object=False)
+ nb_components=nb_components)
W = Field(domain=domain, name='W', dtype=dtype,
- nb_components=nb_components, register_object=False)
+ nb_components=nb_components)
self._test_one(shape=shape, dim=dim, dtype=dtype,
domain=domain, Psi=Psi, W=W,
diff --git a/hysop/operator/tests/test_solenoidal_projection.py b/hysop/operator/tests/test_solenoidal_projection.py
index 966a8cf56..79ad2fe2d 100644
--- a/hysop/operator/tests/test_solenoidal_projection.py
+++ b/hysop/operator/tests/test_solenoidal_projection.py
@@ -129,9 +129,9 @@ class TestSolenoidalProjectionOperator(object):
U = VelocityField(domain=domain, name='U', dtype=dtype)
U0 = VelocityField(domain=domain, name='U0', dtype=dtype)
U1 = VelocityField(domain=domain, name='U1', dtype=dtype)
- divU = U.div(name='divU', register_object=False)
- divU0 = U0.div(name='divU0', register_object=False)
- divU1 = U1.div(name='divU1', register_object=False)
+ divU = U.div(name='divU')
+ divU0 = U0.div(name='divU0')
+ divU1 = U1.div(name='divU1')
self._test_one(shape=shape, dtype=dtype, polynomial=polynomial,
domain=domain, U=U, U0=U0, U1=U1,
diff --git a/hysop/operator/transpose.py b/hysop/operator/transpose.py
index cf8228cb8..b80b8e825 100644
--- a/hysop/operator/transpose.py
+++ b/hysop/operator/transpose.py
@@ -159,8 +159,8 @@ class Transpose(ComputationalGraphNodeGenerator):
check_instance(input_fields, tuple, values=Field)
check_instance(output_fields, tuple, values=Field, size=len(input_fields))
- candidate_input_tensors = filter(lambda x: x.is_tensor, input_fields)
- candidate_output_tensors = filter(lambda x: x.is_tensor, output_fields)
+ candidate_input_tensors = tuple(filter(lambda x: x.is_tensor, input_fields))
+ candidate_output_tensors = tuple(filter(lambda x: x.is_tensor, output_fields))
base_kwds = {} if (base_kwds is None) else {}
super(Transpose,self).__init__(name=name,
diff --git a/hysop/problem.py b/hysop/problem.py
index 236f2d9cf..b7938075a 100644
--- a/hysop/problem.py
+++ b/hysop/problem.py
@@ -87,7 +87,7 @@ class Problem(ComputationalGraph):
def check_unique_clenv(self):
cl_env, first_op = None, None
for op in self.nodes:
- for topo in set(op.input_fields.values() + op.output_fields.values()):
+ for topo in set(op.input_fields.values()).union(op.output_fields.values()):
if (topo.backend.kind == Backend.OPENCL):
if (cl_env is None):
first_op = op
diff --git a/hysop/symbolic/spectral.py b/hysop/symbolic/spectral.py
index 4813b28cc..8ba27630e 100644
--- a/hysop/symbolic/spectral.py
+++ b/hysop/symbolic/spectral.py
@@ -22,6 +22,9 @@ class WaveNumberIndex(sm.Symbol):
obj._real_index = None
return obj
+ def __init__(self, axis):
+ super(WaveNumberIndex, self).__init__()
+
def bind_axes(self, axes):
assert (self._axes is None) or (axes == self._axes)
dim = len(axes)
@@ -108,6 +111,9 @@ class WaveNumber(Dummy):
return obj
+ def __init__(self, axis, transform, exponent, **kwds):
+ super(WaveNumber, self).__init__(name=None, pretty_name=None, **kwds)
+
@property
def axis(self):
return self._axis
diff --git a/hysop/tools/callback.py b/hysop/tools/callback.py
index 2d51b476b..f5d1f605b 100644
--- a/hysop/tools/callback.py
+++ b/hysop/tools/callback.py
@@ -271,7 +271,7 @@ class CallbackGroup(CallbackTask):
def report(self,offset=0):
s = ''
s += '{}{}'.format(self.offset_str(offset), self.name)
- tasks = sorted(self.tasks, key=lambda x:x.total(), reverse=True)
+ tasks = tuple(sorted(self.tasks, key=lambda x:x.total(), reverse=True))
for task in tasks:
s += '\n'+task.report(offset+1)
s += '\n{}{:15s} {}'.format(self.offset_str(offset+1),'total:',
@@ -432,7 +432,7 @@ class CallbackProfiler(object):
self.groups[groupname] = group
def registered_targets(self):
- return self.groups.keys() + self.tasks.keys()
+ return tuple(self.groups.keys()) + tuple(self.tasks.keys())
def register_callbacks(self,target,tic_callbacks=[],tac_callbacks=[]):
dic = self._check_registered(target)
@@ -466,12 +466,12 @@ class CallbackProfiler(object):
s += '\n'+task.report(1)
elif mode =='recursive':
if self.has_groups():
- groups = sorted(self.groups.values(), key=lambda x:x.total(), reverse=True)
+ groups = tuple(sorted(self.groups.values(), key=lambda x:x.total(), reverse=True))
for group in groups:
s += '\n'+group.report(1)
if self.has_tasks():
individual_tasknames = set(self.tasks.keys()).difference(self._tasks_in_group)
- tasknames = sorted(individual_tasknames, key=lambda x:self.tasks[x].total(), reverse=True)
+ tasknames = tuple(sorted(individual_tasknames, key=lambda x:self.tasks[x].total(), reverse=True))
for taskname in tasknames:
task = self.tasks[taskname]
s += '\n'+task.report(1)
diff --git a/hysop/tools/debug_dumper.py b/hysop/tools/debug_dumper.py
index 3592cf40d..bf94fd838 100644
--- a/hysop/tools/debug_dumper.py
+++ b/hysop/tools/debug_dumper.py
@@ -60,10 +60,10 @@ class DebugDumper(object):
def lformat(cls, id_, iteration, time, tag, min_, max_, mean, variance, dtype, shape, description='', dump_precision=None):
try:
return '{:<4} {:<10} {:<20.{p}f} {:<40} {:<+20.{p}f} {:<+20.{p}f} {:<+20.{p}f} {:<+20.{p}f} {:<20} {:<20} {}'.format(
- id_, iteration, time, tag, min_, max_, mean, variance, dtype, shape, description, p=dump_precision)
+ id_, iteration, time, tag, min_, max_, mean, variance, str(dtype), str(shape), description, p=dump_precision)
except:
return '{:<4} {:<10} {:<20} {:<40} {:<20} {:<20} {:<20} {:<20} {:<20} {:<20} {}'.format(
- id_, iteration, time, tag, min_, max_, mean, variance, dtype, shape, description)
+ id_, iteration, time, tag, min_, max_, mean, variance, str(dtype), str(shape), description)
def print_header(self, with_datetime=False):
now = datetime.datetime.now()
diff --git a/hysop/tools/decorators.py b/hysop/tools/decorators.py
index 6b57a9144..23a859037 100644
--- a/hysop/tools/decorators.py
+++ b/hysop/tools/decorators.py
@@ -179,7 +179,7 @@ def not_implemented(f):
fname = f.__name__
@wraps(f)
def wrapper(*args, **kargs):
- args = list(args) + kargs.values()
+ args = list(args) + list(kargs.values())
if len(args)>0:
arg0 = args[0]
if isinstance(arg0,type): # @classmethod
diff --git a/hysop/tools/enum.py b/hysop/tools/enum.py
index ccf4eb5d1..e5aed8ad1 100644
--- a/hysop/tools/enum.py
+++ b/hysop/tools/enum.py
@@ -206,7 +206,7 @@ class EnumFactory(object):
mcls = type(name+'MetaEnum', (EnumFactory.MetaEnum,), mcls_dic)
class Enum(base_cls, metaclass=mcls):
- def __init__(self, field=sorted(fields.keys())[0]):
+ def __init__(self, field=tuple(sorted(fields.keys()))[0]):
assert isinstance(field, str) and len(field)>0
self._field = field
self._value = self.__class__.dtype(self.__class__._fields[field])
diff --git a/hysop/tools/field_utils.py b/hysop/tools/field_utils.py
index 10090f484..20e335d20 100644
--- a/hysop/tools/field_utils.py
+++ b/hysop/tools/field_utils.py
@@ -411,7 +411,7 @@ if __name__ == '__main__':
print
bxvars, pxvars, vxvars, lxvars = (('x',)*5,)*4
varpows = (1,)*5
- xvars_components = range(5)
+ xvars_components = tuple(range(5))
var_components=(0,4,3,2)
_print(DifferentialStringFormatter.format_pd(bvar, pvar, vvar, lvar,
bxvars, pxvars, vxvars, lxvars,
diff --git a/hysop/tools/hptt_utils.py b/hysop/tools/hptt_utils.py
index ec7af8190..2594ac704 100644
--- a/hysop/tools/hptt_utils.py
+++ b/hysop/tools/hptt_utils.py
@@ -26,11 +26,11 @@ if HAS_HPTT:
return False
if src.dtype not in (np.float32, np.float64, np.complex64, np.complex128):
return False
- if src.flags['C_CONTIGUOUS'] != dst.flags['C_CONTIGUOUS']:
+ if src.flags.c_contiguous != dst.flags.c_contiguous:
return False
- if src.flags['F_CONTIGUOUS'] != dst.flags['F_CONTIGUOUS']:
+ if src.flags.f_contiguous != dst.flags.f_contiguous:
return False
- if not (src.flags['C_CONTIGUOUS'] ^ src.flags['F_CONTIGUOUS']):
+ if not (src.flags.c_contiguous ^ src.flags.f_contiguous):
return False
return not array_share_data(src, dst)
else:
diff --git a/hysop/tools/misc.py b/hysop/tools/misc.py
index 22f3b47b4..98df7fdf7 100644
--- a/hysop/tools/misc.py
+++ b/hysop/tools/misc.py
@@ -122,7 +122,7 @@ class Utils(object):
"""
@staticmethod
def argsort(seq):
- return sorted(range(len(seq)), key=seq.__getitem__)
+ return tuple(sorted(range(len(seq)), key=seq.__getitem__))
@staticmethod
def upper_pow2(x):
diff --git a/hysop/tools/mpi_utils.py b/hysop/tools/mpi_utils.py
index 0fab45c3d..3a211ba67 100644
--- a/hysop/tools/mpi_utils.py
+++ b/hysop/tools/mpi_utils.py
@@ -50,9 +50,9 @@ def dtype_to_mpi_type(dtype):
def order_to_mpi_order(order):
from hysop.constants import MemoryOrdering
- if (order in 'cC') or (order==MemoryOrdering.C_CONTIGUOUS) or (order==MPI.ORDER_C):
+ if (order in 'cC') or (order==MemoryOrdering.C_CONTIGUOUS) or (order==MPI.ORDER_C):
return MPI.ORDER_C
- elif (order in 'fF') or (order==MemoryOrdering.F_CONTIGUOUS) or (order==MPI.ORDER_F):
+ elif (order in 'fF') or (order==MemoryOrdering.F_CONTIGUOUS) or (order==MPI.ORDER_F):
return MPI.ORDER_F
else:
msg='Unknown value of type {}.'.format(type(order))
@@ -65,8 +65,8 @@ def get_mpi_order(data):
is_f_contiguous = data.is_fortran_contiguous
else:
# assume numpy like interface
- is_c_contiguous = data.flags['C_CONTIGUOUS']
- is_f_contiguous = data.flags['F_CONTIGUOUS']
+ is_c_contiguous = data.flags.c_contiguous
+ is_f_contiguous = data.flags.f_contiguous
if is_c_contiguous:
return MPI.ORDER_C
elif is_f_contiguous:
diff --git a/hysop/tools/numba_utils.py b/hysop/tools/numba_utils.py
index 7c5bc6bbb..62ad05cb7 100644
--- a/hysop/tools/numba_utils.py
+++ b/hysop/tools/numba_utils.py
@@ -76,9 +76,9 @@ def make_numba_signature(*args, **kwds):
elif isinstance(a, np.ndarray):
assert a.dtype.type in dtype_to_ntype, a.dtype.type
dtype = dtype_to_ntype[a.dtype.type]
- if a.flags['C_CONTIGUOUS']:
+ if a.flags.c_contiguous:
na = nb.types.Array(dtype=dtype, ndim=a.ndim, layout='C')
- elif a.flags['F_CONTIGUOUS']:
+ elif a.flags.f_contiguous:
na = nb.types.Array(dtype=dtype, ndim=a.ndim, layout='F')
else:
na = nb.types.Array(dtype=dtype, ndim=a.ndim, layout='A')
diff --git a/hysop/tools/profiler.py b/hysop/tools/profiler.py
index dd2330c0f..57d9e49be 100644
--- a/hysop/tools/profiler.py
+++ b/hysop/tools/profiler.py
@@ -123,8 +123,8 @@ class Profiler(object):
summary = self.summary
if len(summary) > 0:
if (self._l>1) and (len(summary) == 1) and \
- isinstance(summary.values()[0], FProfiler):
- s = '>{}::{}'.format(self.get_name(), summary.values()[0])
+ isinstance(next(iter(summary.values())), FProfiler):
+ s = '>{}::{}'.format(self.get_name(), next(iter(summary.values())))
else:
s = '{}[{}]>{}{}'.format(
'\n' if (self._l==1) else '',
diff --git a/hysop/tools/spectral_utils.py b/hysop/tools/spectral_utils.py
index 045b24eec..c7c3dbfec 100644
--- a/hysop/tools/spectral_utils.py
+++ b/hysop/tools/spectral_utils.py
@@ -823,7 +823,7 @@ class EnergyPlotter(object):
if len(energy_parameters)==1:
default_fig_title = 'Energy parameter {}'.format(
- energy_parameters.values()[0].pretty_name)
+ next(iter(energy_parameters.values())).pretty_name)
else:
default_fig_title = 'Energy parameters {}'.format(
' | '.join(p.pretty_name for p in energy_parameters.values()))
diff --git a/hysop/tools/transposition_states.py b/hysop/tools/transposition_states.py
index 79e8c5ab5..a3d9ed47e 100644
--- a/hysop/tools/transposition_states.py
+++ b/hysop/tools/transposition_states.py
@@ -55,7 +55,7 @@ class TranspositionStateType(type):
return it.permutations(range(dim), dim)
def __filter_axes(cls, predicate):
"""Return a filtered iterator on all possible permutations."""
- return filter(predicate, cls.all_axes())
+ return tuple(filter(predicate, cls.all_axes()))
cls_methods['dimension'] = classmethod(__dimension)
cls_methods['default_axes'] = classmethod(__default_axes)
diff --git a/hysop/topology/cartesian_descriptor.py b/hysop/topology/cartesian_descriptor.py
index 7e7ee3482..747109168 100644
--- a/hysop/topology/cartesian_descriptor.py
+++ b/hysop/topology/cartesian_descriptor.py
@@ -178,8 +178,7 @@ class CartesianTopologyDescriptor(TopologyDescriptor):
If None is returned, create_topology will be called instead.
"""
if known_topologies:
- ordered_topologies = sorted(known_topologies,
- key=lambda topo: sum(topo.ghosts))
+ ordered_topologies = tuple(sorted(known_topologies, key=lambda topo: sum(topo.ghosts)))
return ordered_topologies[0]
else:
return None
diff --git a/hysop_examples/example_utils.py b/hysop_examples/example_utils.py
index cf67e6a98..41dc24d53 100644
--- a/hysop_examples/example_utils.py
+++ b/hysop_examples/example_utils.py
@@ -195,6 +195,7 @@ class HysopArgParser(argparse.ArgumentParser):
dump_dirs = map(lambda ddir: os.path.abspath(ddir), dump_dirs)
dump_dirs = filter(lambda ddir: os.path.isdir(ddir) and \
(ddir not in ('/','/home','~',os.path.expanduser('~'))), dump_dirs)
+ dump_dirs = tuple(dump_dirs)
if args.no_interactive:
confirm_deletion = True
else:
@@ -1298,7 +1299,7 @@ class HysopArgParser(argparse.ArgumentParser):
return graphical_io
def _check_graphical_io_args(self, args):
- if (args.visu_rank<0):
+ if (args.visu_rank is not None) and (args.visu_rank<0):
args.visu_rank = None
self._check_default(args, 'visu_rank', int, allow_none=True)
self._check_positive(args, 'visu_rank', strict=False, allow_none=True)
diff --git a/hysop_examples/examples/analytic/analytic.py b/hysop_examples/examples/analytic/analytic.py
index 4c27e7253..011865c2a 100755
--- a/hysop_examples/examples/analytic/analytic.py
+++ b/hysop_examples/examples/analytic/analytic.py
@@ -1,8 +1,6 @@
-#!/usr/bin/env python2
import numpy as np
import sympy as sm
-
def compute(args):
'''
HySoP Analytic Example: Initialize a field with a space and time dependent analytic formula.
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
index 1054d6ace..d0b941991 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
@@ -1,6 +1,6 @@
## See Meiburg 2012 & 2014
## Sediment-laden fresh water above salt water.
-
+
import numpy as np
import scipy as sp
import sympy as sm
@@ -21,7 +21,7 @@ def delta(Ys, l0):
for Yi in Ys:
Y0 = Y0*Yi
return 0.1*l0*(np.random.rand(*Y0.shape)-0.5)
-
+
def init_concentration(data, coords, l0, component):
assert (component==0)
X = coords[0]
@@ -55,7 +55,7 @@ def compute(args):
from hysop.methods import SpaceDiscretization, Remesh, TimeIntegrator, \
ComputeGranularity, Interpolation
-
+
from hysop.symbolic import sm, space_symbols, local_indices_symbols
from hysop.symbolic.base import SymbolicTensor
from hysop.symbolic.field import curl
@@ -82,7 +82,7 @@ def compute(args):
npts=N[::-1]
Xo=Xo[::-1]
Xn=Xn[::-1]
-
+
lboundaries = (BoxBoundaryCondition.PERIODIC,)*(dim-1)+(BoxBoundaryCondition.SYMMETRIC,)
rboundaries = (BoxBoundaryCondition.PERIODIC,)*(dim-1)+(BoxBoundaryCondition.SYMMETRIC,)
@@ -93,7 +93,7 @@ def compute(args):
box = Box(origin=Xo, length=np.subtract(Xn,Xo),
lboundaries=lboundaries, rboundaries=rboundaries)
-
+
# Get default MPI Parameters from domain (even for serial jobs)
mpi_params = MPIParams(comm=box.task_comm,
task_id=box.current_task())
@@ -107,18 +107,18 @@ def compute(args):
elif (impl is Implementation.OPENCL):
# For the OpenCL implementation we need to setup the compute device
# and configure how the code is generated and compiled at runtime.
-
+
# Create an explicit OpenCL context from user parameters
from hysop.backend.device.opencl.opencl_tools import get_or_create_opencl_env, get_device_number
cl_env = get_or_create_opencl_env(
mpi_params=mpi_params,
- platform_id=args.cl_platform_id,
+ platform_id=args.cl_platform_id,
device_id=box.machine_rank%get_device_number() if args.cl_device_id is None else None)
-
+
# Configure OpenCL kernel generation and tuning (already done by HysopArgParser)
from hysop.methods import OpenClKernelConfig
method = { OpenClKernelConfig: args.opencl_kernel_config }
-
+
# Setup opencl specific extra operator keyword arguments
extra_op_kwds['cl_env'] = cl_env
else:
@@ -131,7 +131,7 @@ def compute(args):
vorti = VorticityField(velocity=velo)
C = Field(domain=box, name='C', dtype=args.dtype, lboundaries=C_lboundaries, rboundaries=C_rboundaries)
S = Field(domain=box, name='S', dtype=args.dtype, lboundaries=S_lboundaries, rboundaries=S_rboundaries)
-
+
# Symbolic fields
frame = velo.domain.frame
Us = velo.s(*frame.vars)
@@ -141,43 +141,43 @@ def compute(args):
dts = dt.s
### Build the directional operators
- #> Directional advection
+ #> Directional advection
advec = DirectionalAdvection(implementation=impl,
name='advec',
- velocity = velo,
+ velocity = velo,
advected_fields = (vorti,S),
velocity_cfl = args.cfl,
variables = {velo: npts, vorti: npts, S: npts},
dt=dt, **extra_op_kwds)
-
+
V0 = [0]*dim
VP = [0]*dim
VP[0] = Vp
advec_C = DirectionalAdvection(implementation=impl,
name='advec_C',
- velocity = velo,
+ velocity = velo,
advected_fields = (C,),
relative_velocity = VP,
velocity_cfl = args.cfl,
variables = {velo: npts, C: npts},
dt=dt, **extra_op_kwds)
-
+
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
name='stretch',
pretty_name='stretch',
formulation = args.stretching_formulation,
- velocity = velo,
+ velocity = velo,
vorticity = vorti,
variables = {velo: npts, vorti: npts},
dt=dt, **extra_op_kwds)
elif (dim==2):
- stretch = None
+ stretch = None
else:
msg='Unsupported dimension {}.'.format(dim)
raise RuntimeError(msg)
-
+
#> Diffusion of vorticity, S and C
diffuse_S = Diffusion(implementation=impl,
enforce_implementation=enforce_implementation,
@@ -186,7 +186,7 @@ def compute(args):
nu = nu_S,
Fin = S,
variables = {S: npts},
- dt=dt,
+ dt=dt,
**extra_op_kwds)
diffuse_C = Diffusion(implementation=impl,
enforce_implementation=enforce_implementation,
@@ -204,27 +204,27 @@ def compute(args):
lhs = Ws.diff(frame.time)
rhs = curl(Fext, frame)
exprs = Assignment.assign(lhs, rhs)
- external_force = DirectionalSymbolic(name='Fext',
+ external_force = DirectionalSymbolic(name='Fext',
implementation=impl,
exprs=exprs, dt=dt,
variables={vorti: npts,
S: npts,
C: npts},
**extra_op_kwds)
-
- splitting = StrangSplitting(splitting_dim=dim,
+
+ splitting = StrangSplitting(splitting_dim=dim,
order=args.strang_order)
splitting.push_operators(advec, advec_C, stretch, external_force)
-
+
### Build standard operators
#> Poisson operator to recover the velocity from the vorticity
- poisson = PoissonCurl(name='poisson', velocity=velo, vorticity=vorti,
+ poisson = PoissonCurl(name='poisson', velocity=velo, vorticity=vorti,
variables={velo:npts, vorti: npts},
diffusion=nu_W, dt=dt,
implementation=impl,
enforce_implementation=enforce_implementation,
**extra_op_kwds)
-
+
#> Operator to compute the infinite norm of the velocity
min_max_U = MinMaxFieldStatistics(name='min_max_U', field=velo,
Finf=True, implementation=impl, variables={velo:npts},
@@ -233,14 +233,14 @@ def compute(args):
min_max_W = MinMaxFieldStatistics(field=vorti,
Finf=True, implementation=impl, variables={vorti:npts},
**extra_op_kwds)
-
+
#> Operators to dump all fields
dump_fields = HDF_Writer(name='dump',
io_params=args.io_params.clone(filename='fields'),
force_backend=Backend.OPENCL,
- variables={velo: npts,
+ variables={velo: npts,
vorti: npts,
- C: npts,
+ C: npts,
S: npts},
**extra_op_kwds)
@@ -250,7 +250,7 @@ def compute(args):
view[-1] = (-200.0,+200.0)
view = tuple(view)
io_params = IOParams(filename='horizontally_averaged_profiles', frequency=0)
- compute_mean_fields = ComputeMeanField(name='mean',
+ compute_mean_fields = ComputeMeanField(name='mean',
fields={C: (view, axes), S: (view, axes)},
variables={C: npts, S: npts},
io_params=io_params)
@@ -258,23 +258,23 @@ def compute(args):
### Adaptive timestep operator
adapt_dt = AdaptiveTimeStep(dt, equivalent_CFL=True,
name='merge_dt', pretty_name='dt', )
- dt_cfl = adapt_dt.push_cfl_criteria(cfl=args.cfl,
+ dt_cfl = adapt_dt.push_cfl_criteria(cfl=args.cfl,
Fmin=min_max_U.Fmin,
Fmax=min_max_U.Fmax,
- equivalent_CFL=True,
+ equivalent_CFL=True,
relative_velocities=[V0, VP],
name='dt_cfl', pretty_name='CFL')
dt_advec = adapt_dt.push_advection_criteria(lcfl=args.lcfl, Finf=min_max_W.Finf,
criteria=AdvectionCriteria.W_INF,
name='dt_lcfl', pretty_name='LCFL')
-
- ## Create the problem we want to solve and insert our
+
+ ## Create the problem we want to solve and insert our
# directional splitting subgraph and the standard operators.
# The method dictionnary passed to this graph will be dispatched
# accross all operators contained in the graph.
method.update(
- {
+ {
ComputeGranularity: args.compute_granularity,
SpaceDiscretization: args.fd_order,
TimeIntegrator: args.time_integrator,
@@ -283,42 +283,42 @@ def compute(args):
)
problem = Problem(method=method)
- problem.insert(poisson,
+ problem.insert(poisson,
diffuse_S, diffuse_C,
- splitting,
+ splitting,
dump_fields,
compute_mean_fields,
- min_max_U, min_max_W,
+ min_max_U, min_max_W,
adapt_dt)
problem.build(args)
-
+
# If a visu_rank was provided, and show_graph was set,
# display the graph on the given process rank.
if args.display_graph:
problem.display(args.visu_rank)
-
+
# Create a simulation
# (do not forget to specify the t and dt parameters here)
- simu = Simulation(start=args.tstart, end=args.tend,
+ simu = Simulation(start=args.tstart, end=args.tend,
nb_iter=args.nb_iter,
max_iter=args.max_iter,
dt0=args.dt, times_of_interest=args.times_of_interest,
t=t, dt=dt)
- simu.write_parameters(t, dt_cfl, dt_advec, dt,
+ simu.write_parameters(t, dt_cfl, dt_advec, dt,
min_max_U.Finf, min_max_W.Finf, adapt_dt.equivalent_CFL,
filename='parameters.txt', precision=8)
-
+
# Initialize vorticity, velocity, S and C on all topologies
problem.initialize_field(field=velo, formula=init_velocity)
problem.initialize_field(field=vorti, formula=init_vorticity)
problem.initialize_field(field=C, formula=init_concentration, l0=l0)
problem.initialize_field(field=S, formula=init_salinity, l0=l0)
-
+
# Finally solve the problem
- problem.solve(simu, dry_run=args.dry_run,
+ problem.solve(simu, dry_run=args.dry_run,
debug_dumper=args.debug_dumper,
checkpoint_handler=args.checkpoint_handler)
-
+
# Finalize
problem.finalize()
@@ -329,18 +329,18 @@ if __name__=='__main__':
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
prog_name = 'particle_above_salt_bc'
- default_dump_dir = '{}/hysop_examples/{}'.format(HysopArgParser.tmp_dir(),
+ default_dump_dir = '{}/hysop_examples/{}'.format(HysopArgParser.tmp_dir(),
prog_name)
description=colors.color('HySoP Particles Above Salt Example: ', fg='blue',
style='bold')
description+=colors.color('[Meiburg 2014]', fg='yellow', style='bold')
- description+=colors.color('\nSediment-laden fresh water above salt water.',
+ description+=colors.color('\nSediment-laden fresh water above salt water.',
fg='yellow')
description+='\n'
description+='\nThis example focuses on a validation study for the '
description+='hybrid particle-mesh vortex method in the Boussinesq approximation.'
-
+
super(ParticleAboveSaltArgParser, self).__init__(
prog_name=prog_name,
description=description,
@@ -357,10 +357,10 @@ if __name__=='__main__':
parser = ParticleAboveSaltArgParser()
parser.set_defaults(impl='cl', ndim=2, npts=(64,),
- box_origin=(0.0,), box_length=(1.0,),
- tstart=0.0, tend=500.0,
+ box_origin=(0.0,), box_length=(1.0,),
+ tstart=0.0, tend=500.0,
dt=1e-6, cfl=4.00, lcfl=0.95,
- dump_times=tuple(float(x) for x in range(0,500,10)),
+ dump_times=tuple(float(x) for x in range(0, 500, 10)),
dump_freq=0)
parser.run(compute)
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_periodic.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_periodic.py
index 1e9905192..7965443c5 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_periodic.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_periodic.py
@@ -372,7 +372,7 @@ if __name__=='__main__':
box_origin=(0.0,), box_length=(1.0,),
tstart=0.0, tend=500.0,
dt=1e-6, cfl=0.5, lcfl=0.125,
- dump_times=tuple(float(x) for x in range(0,500,5)),
+ dump_times=tuple(float(x) for x in range(0, 500, 5)),
dump_freq=0)
parser.run(compute)
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
index cf3aa0b13..36e8009be 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
@@ -359,7 +359,7 @@ if __name__=='__main__':
box_origin=(0.0,), box_length=(1.0,),
tstart=0.0, tend=500.0,
dt=1e-6, cfl=0.5, lcfl=0.125,
- dump_times=tuple(float(x) for x in range(0,500,5)),
+ dump_times=tuple(float(x) for x in range(0, 500, 5)),
dump_freq=0)
parser.run(compute)
diff --git a/setup.py.in b/setup.py.in
index da7b1c75a..c00757c87 100644
--- a/setup.py.in
+++ b/setup.py.in
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""setup.py file for @PYPACKAGE_NAME@
--
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