Merged master

doc/notebooks/02_tutorial_basic_kernels.ipynb

@@ -207,7 +207,7 @@
        "<div>Subexpressions:</div><table style=\"border:none; width: 100%; \"><tr style=\"border:none\"> <td style=\"border:none\">$$a \\leftarrow {src}_{(0,1)} + {src}_{(-1,0)}$$</td>  </tr> <tr style=\"border:none\"> <td style=\"border:none\">$$b \\leftarrow 2 {src}_{(1,0)} + {src}_{(0,-1)}$$</td>  </tr> <tr style=\"border:none\"> <td style=\"border:none\">$$c \\leftarrow - {src}_{(0,0)} + 2 {src}_{(1,0)} + {src}_{(0,1)} + {src}_{(0,-1)} + {src}_{(-1,0)}$$</td>  </tr> </table><div>Main Assignments:</div><table style=\"border:none; width: 100%; \"><tr style=\"border:none\"> <td style=\"border:none\">$${dst}_{(0,0)} \\leftarrow a + b + c$$</td>  </tr> </table>"
       ],
       "text/plain": [
-       "AssignmentCollection: dst_C, <- f(src_E, src_C, src_N, src_W, src_S)"
+       "AssignmentCollection: dst_C, <- f(src_N, src_E, src_W, src_C, src_S)"
       ]
      },
      "execution_count": 7,
@@ -274,7 +274,7 @@
        "<div>Subexpressions:</div><table style=\"border:none; width: 100%; \"><tr style=\"border:none\"> <td style=\"border:none\">$$a \\leftarrow {src}_{(0,1)} + {src}_{(-1,0)}$$</td>  </tr> <tr style=\"border:none\"> <td style=\"border:none\">$$b \\leftarrow 2 {src}_{(1,0)} + {src}_{(0,-1)}$$</td>  </tr> <tr style=\"border:none\"> <td style=\"border:none\">$$c \\leftarrow - {src}_{(0,0)} + a + b$$</td>  </tr> </table><div>Main Assignments:</div><table style=\"border:none; width: 100%; \"><tr style=\"border:none\"> <td style=\"border:none\">$${dst}_{(0,0)} \\leftarrow a + b + c$$</td>  </tr> </table>"
       ],
       "text/plain": [
-       "AssignmentCollection: dst_C, <- f(src_E, src_C, src_N, src_W, src_S)"
+       "AssignmentCollection: dst_C, <- f(src_N, src_E, src_W, src_C, src_S)"
       ]
      },
      "execution_count": 9,

pystencils/cache.py

 import os
 from collections.abc import Hashable
-from functools import partial, lru_cache
+from functools import partial, wraps, lru_cache
 from itertools import chain
 
 from joblib import Memory
@@ -27,6 +27,36 @@ def memorycache_if_hashable(maxsize=128, typed=False):
 
     return wrapper
 
+
+def sharedmethodcache(cache_id: str):
+    """Decorator for memoization of instance methods, allowing multiple methods to use the same cache.
+
+    This decorator caches results of instance methods per instantiated object of the surrounding class.
+    It allows multiple methods to use the same cache, by passing them the same `cache_id` string.
+    Cached values are stored in a dictionary, which is added as a member `self.<cache_id>` to the 
+    `self` object instance. Make sure that this doesn't cause any naming conflicts with other members!
+    Of course, for this to be useful, said methods must have the same signature (up to additional kwargs)
+    and must return the same result when called with the same arguments."""
+    def _decorator(user_method):
+        @wraps(user_method)
+        def _decorated_func(self, *args, **kwargs):
+            objdict = self.__dict__
+            cache = objdict.setdefault(cache_id, dict())
+
+            key = args
+            for item in kwargs.items():
+                key += item
+
+            if key not in cache:
+                result = user_method(self, *args, **kwargs)
+                cache[key] = result
+                return result
+            else:
+                return cache[key]
+        return _decorated_func
+    return _decorator
+
+
 # Disable memory cache:
 # disk_cache = lambda o: o
 # disk_cache_no_fallback = lambda o: o

pystencils/cpu/vectorization.py

@@ -270,7 +270,7 @@ def insert_vector_casts(ast_node, instruction_set, default_float_type='double'):
             new_arg = visit_expr(expr.args[0], default_type)
             base_type = get_type_of_expression(expr.args[0]).base_type if type(expr.args[0]) is VectorMemoryAccess \
                 else get_type_of_expression(expr.args[0])
-            pw = sp.Piecewise((-new_arg, new_arg < base_type.numpy_dtype.type(0)),
+            pw = sp.Piecewise((-new_arg, new_arg < cast_func(0, base_type.numpy_dtype)),
                               (new_arg, True))
             return visit_expr(pw, default_type)
         elif expr.func in handled_functions or isinstance(expr, sp.Rel) or isinstance(expr, BooleanFunction):

pystencils/simp/assignment_collection.py

@@ -311,7 +311,7 @@ class AssignmentCollection:
             if eq.lhs in symbols_to_extract:
                 new_assignments.append(eq)
 
-        new_sub_expr = [eq for eq in self.subexpressions
+        new_sub_expr = [eq for eq in self.all_assignments
                         if eq.lhs in dependent_symbols and eq.lhs not in symbols_to_extract]
         return self.copy(new_assignments, new_sub_expr)
 

pystencils/sympyextensions.py

@@ -235,6 +235,9 @@ def subs_additive(expr: sp.Expr, replacement: sp.Expr, subexpression: sp.Expr,
 
     normalized_replacement_match = normalize_match_parameter(required_match_replacement, len(subexpression.args))
 
+    if isinstance(subexpression, sp.Number):
+        return expr.subs({replacement: subexpression})
+
     def visit(current_expr):
         if current_expr.is_Add:
             expr_max_length = max(len(current_expr.args), len(subexpression.args))
@@ -263,7 +266,7 @@ def subs_additive(expr: sp.Expr, replacement: sp.Expr, subexpression: sp.Expr,
             return current_expr
         else:
             if current_expr.func == sp.Mul and Zero() in param_list:
-                return Zero()
+                return sp.simplify(current_expr)
             else:
                 return current_expr.func(*param_list, evaluate=False)
 
@@ -359,7 +362,7 @@ def remove_higher_order_terms(expr: sp.Expr, symbols: Sequence[sp.Symbol], order
         if velocity_factors_in_product(expr) <= order:
             return expr
         else:
-            return sp.Rational(0, 1)
+            return Zero()
 
     if type(expr) != Add:
         return expr
@@ -453,6 +456,72 @@ def recursive_collect(expr, symbols, order_by_occurences=False):
     return rec_sum
 
 
+def summands(expr):
+    return set(expr.args) if isinstance(expr, sp.Add) else {expr}
+
+
+def simplify_by_equality(expr, a, b, c):
+    """
+    Uses the equality a = b + c, where a and b must be symbols, to simplify expr 
+    by attempting to express additive combinations of two quantities by the third.
+
+    This works on expressions that are reducible to the form 
+    :math:`a * (...) + b * (...) + c * (...)`,
+    without any mixed terms of a, b and c.
+    """
+    if not isinstance(a, sp.Symbol) or not isinstance(b, sp.Symbol):
+        raise ValueError("a and b must be symbols.")
+
+    c = sp.sympify(c)
+
+    if not (isinstance(c, sp.Symbol) or is_constant(c)):
+        raise ValueError("c must be either a symbol or a constant!")
+
+    expr = sp.sympify(expr)
+
+    expr_expanded = sp.expand(expr)
+    a_coeff = expr_expanded.coeff(a, 1)
+    expr_expanded -= (a * a_coeff).expand()
+    b_coeff = expr_expanded.coeff(b, 1)
+    expr_expanded -= (b * b_coeff).expand()
+    if isinstance(c, sp.Symbol):
+        c_coeff = expr_expanded.coeff(c, 1)
+        rest = expr_expanded - (c * c_coeff).expand()
+    else:
+        c_coeff = expr_expanded / c
+        rest = 0
+
+    a_summands = summands(a_coeff)
+    b_summands = summands(b_coeff)
+    c_summands = summands(c_coeff)
+
+    # replace b + c by a
+    b_plus_c_coeffs = b_summands & c_summands
+    for coeff in b_plus_c_coeffs:
+        rest += a * coeff
+    b_summands -= b_plus_c_coeffs
+    c_summands -= b_plus_c_coeffs
+
+    # replace a - b by c
+    neg_b_summands = {-x for x in b_summands}
+    a_minus_b_coeffs = a_summands & neg_b_summands
+    for coeff in a_minus_b_coeffs:
+        rest += c * coeff
+    a_summands -= a_minus_b_coeffs
+    b_summands -= {-x for x in a_minus_b_coeffs}
+
+    # replace a - c by b
+    neg_c_summands = {-x for x in c_summands}
+    a_minus_c_coeffs = a_summands & neg_c_summands
+    for coeff in a_minus_c_coeffs:
+        rest += b * coeff
+    a_summands -= a_minus_c_coeffs
+    c_summands -= {-x for x in a_minus_c_coeffs}
+
+    # put it back together
+    return (rest + a * sum(a_summands) + b * sum(b_summands) + c * sum(c_summands)).expand()
+
+
 def count_operations(term: Union[sp.Expr, List[sp.Expr], List[Assignment]],
                      only_type: Optional[str] = 'real') -> Dict[str, int]:
     """Counts the number of additions, multiplications and division.

pystencils_tests/test_aligned_array.py

@@ -59,13 +59,13 @@ def test_alignment_of_different_layouts():
     byte_offset = 8
     for tries in range(16):  # try a few times, since we might get lucky and get randomly a correct alignment
         arr = create_numpy_array_with_layout((3, 4, 5), layout=(0, 1, 2),
-                                             alignment=True, byte_offset=byte_offset)
+                                             alignment=8*4, byte_offset=byte_offset)
         assert is_aligned(arr[offset, ...], 8*4, byte_offset)
 
         arr = create_numpy_array_with_layout((3, 4, 5), layout=(2, 1, 0),
-                                             alignment=True, byte_offset=byte_offset)
+                                             alignment=8*4, byte_offset=byte_offset)
         assert is_aligned(arr[..., offset], 8*4, byte_offset)
 
         arr = create_numpy_array_with_layout((3, 4, 5), layout=(2, 0, 1),
-                                             alignment=True, byte_offset=byte_offset)
+                                             alignment=8*4, byte_offset=byte_offset)
         assert is_aligned(arr[:, 0, :], 8*4, byte_offset)

pystencils_tests/test_field_access_poly.py

@@ -7,7 +7,7 @@
 
 """
 
-
+import pytest
 from pystencils.session import *
 
 from sympy import poly
@@ -22,6 +22,12 @@ def test_field_access_poly():
 
 
 def test_field_access_piecewise():
+    try:
+        a = sp.Piecewise((0, 1 < sp.Max(-0.5, sp.Symbol("test") + 0.5)), (1, True))
+        a.simplify()
+    except Exception as e:
+        pytest.skip(f"Bug in SymPy 1.10: {e}")
+    else:
         dh = ps.create_data_handling((20, 20))
         ρ = dh.add_array('rho')
         pw = sp.Piecewise((0, 1 < sp.Max(-0.5, ρ.center+0.5)), (1, True))

pystencils_tests/test_fvm.py

@@ -317,9 +317,7 @@ def diffusion_reaction(fluctuations: bool):
             fluct = sp.sqrt(2 * dens * D) * sp.sqrt(1 / length) * stencil_factor
             # add fluctuations
             fluct *= 2 * (next(rng_symbol_gen) - 0.5) * sp.sqrt(3)
-            
-            flux.main_assignments[i] = ps.Assignment(flux.main_assignments[i].lhs,
-                                                       flux.main_assignments[i].rhs + fluct)
+            flux.main_assignments[i] = ps.Assignment(flux.main_assignments[i].lhs, flux.main_assignments[i].rhs + fluct)
         
         # Add the folding to the flux, so that the random numbers persist through the ghostlayers.
         fold = {ps.astnodes.LoopOverCoordinate.get_loop_counter_symbol(i):
@@ -419,7 +417,7 @@ advection_diffusion_fluctuations.runners = {}
 @pytest.mark.parametrize("density", [27.0, 56.5])
 @pytest.mark.parametrize("fluctuations", [False, True])
 @pytest.mark.longrun
-def test_diffusion_reaction(velocity, density, fluctuations):
+def test_diffusion_reaction(fluctuations, density, velocity):
     diffusion_reaction.runner = diffusion_reaction(fluctuations)
     diffusion_reaction.runner(density, velocity)
 

pystencils_tests/test_sharedmethodcache.py

+from pystencils.cache import sharedmethodcache
+
+
+class Fib:
+
+    def __init__(self):
+        self.fib_rec_called = 0
+        self.fib_iter_called = 0
+
+    @sharedmethodcache("fib_cache")
+    def fib_rec(self, n):
+        self.fib_rec_called += 1
+        return 1 if n <= 1 else self.fib_rec(n-1) + self.fib_rec(n-2)
+
+    @sharedmethodcache("fib_cache")
+    def fib_iter(self, n):
+        self.fib_iter_called += 1
+        f1, f2 = 0, 1
+        for i in range(n):
+            f2 = f1 + f2
+            f1 = f2 - f1
+        return f2
+
+
+def test_fib_memoization_1():
+    fib = Fib()
+
+    assert "fib_cache" not in fib.__dict__
+
+    f13 = fib.fib_rec(13)
+    assert fib.fib_rec_called == 14
+    assert "fib_cache" in fib.__dict__
+    assert fib.fib_cache[(13,)] == f13
+
+    for k in range(14):
+        #   fib_iter should use cached results from fib_rec
+        fib.fib_iter(k)
+    
+    assert fib.fib_iter_called == 0
+
+
+def test_fib_memoization_2():
+    fib = Fib()
+
+    f11 = fib.fib_iter(11)
+    f12 = fib.fib_iter(12)
+
+    assert fib.fib_iter_called == 2
+
+    f13 = fib.fib_rec(13)
+
+    #   recursive calls should be cached
+    assert fib.fib_rec_called == 1
+
+
+class Triad:
+    
+    def __init__(self):
+        self.triad_called = 0
+
+    @sharedmethodcache("triad_cache")
+    def triad(self, a, b, c=0):
+        """Computes the triad a*b+c."""
+        self.triad_called += 1
+        return a * b + c
+
+
+def test_triad_memoization():
+    triad = Triad()
+
+    assert triad.triad.__doc__ == "Computes the triad a*b+c."
+
+    t = triad.triad(12, 4, 15)
+    assert triad.triad_called == 1
+    assert triad.triad_cache[(12, 4, 15)] == t
+
+    t = triad.triad(12, 4, c=15)
+    assert triad.triad_called == 2
+    assert triad.triad_cache[(12, 4, 'c', 15)] == t
+
+    t = triad.triad(12, 4, 15)
+    assert triad.triad_called == 2
+
+    t = triad.triad(12, 4, c=15)
+    assert triad.triad_called == 2

pystencils_tests/test_sympyextensions.py

 import sympy
 import numpy as np
+import sympy as sp
 import pystencils
 
 from pystencils.sympyextensions import replace_second_order_products
 from pystencils.sympyextensions import remove_higher_order_terms
 from pystencils.sympyextensions import complete_the_squares_in_exp
 from pystencils.sympyextensions import extract_most_common_factor
+from pystencils.sympyextensions import simplify_by_equality
 from pystencils.sympyextensions import count_operations
 from pystencils.sympyextensions import common_denominator
 from pystencils.sympyextensions import get_symmetric_part
@@ -176,3 +178,26 @@ def test_get_symmetric_part():
     sym_part = get_symmetric_part(expr, sympy.symbols(f'y z'))
 
     assert sym_part == expected_result
+
+
+def test_simplify_by_equality():
+    x, y, z = sp.symbols('x, y, z')
+    p, q = sp.symbols('p, q')
+
+    #   Let x = y + z
+    expr = x * p - y * p + z * q
+    expr = simplify_by_equality(expr, x, y, z)
+    assert expr == z * p + z * q
+
+    expr = x * (p - 2 * q) + 2 * q * z
+    expr = simplify_by_equality(expr, x, y, z)
+    assert expr == x * p - 2 * q * y
+
+    expr = x * (y + z) - y * z
+    expr = simplify_by_equality(expr, x, y, z)
+    assert expr == x*y + z**2
+
+    #   Let x = y + 2
+    expr = x * p - 2 * p
+    expr = simplify_by_equality(expr, x, y, 2)
+    assert expr == y * p

pystencils_tests/test_timeloop.py

@@ -59,4 +59,6 @@ def test_timeloop():
     timeloop.run_time_span(seconds=seconds)
     end = time.perf_counter()
 
-    np.testing.assert_almost_equal(seconds, end - start, decimal=2)
+    # This test case fails often due to time measurements. It is not a good idea to assert here
+    # np.testing.assert_almost_equal(seconds, end - start, decimal=2)
+    print("timeloop: ", seconds, "  own meassurement: ", end - start)

pytest.ini

@@ -53,7 +53,7 @@ exclude_lines =
        if __name__ == .__main__.:
 
 skip_covered = True
-fail_under = 86
+fail_under = 85
 
 [html]
 directory = coverage_report

setup.py

@@ -90,7 +90,7 @@ setuptools.setup(name='pystencils',
                  author_email='cs10-codegen@fau.de',
                  url='https://i10git.cs.fau.de/pycodegen/pystencils/',
                  packages=['pystencils'] + ['pystencils.' + s for s in setuptools.find_packages('pystencils')],
-                 install_requires=['sympy>=1.6,<=1.9', 'numpy>=1.8.0', 'appdirs', 'joblib'],
+                 install_requires=['sympy>=1.6,<=1.10', 'numpy>=1.8.0', 'appdirs', 'joblib'],
                  package_data={'pystencils': ['include/*.h',
                                               'backends/cuda_known_functions.txt',
                                               'backends/opencl1.1_known_functions.txt',