Commit 607aafa8 authored by Michael Kuron's avatar Michael Kuron
Browse files

fix more tests on Ubuntu

parent 01a56d31
......@@ -291,7 +291,10 @@ class Block(Node):
self._nodes = nodes
self.parent = None
for n in self._nodes:
n.parent = self
try:
n.parent = self
except AttributeError:
pass
@property
def args(self):
......
......@@ -386,6 +386,13 @@ class CustomSympyPrinter(CCodePrinter):
return self._print(expr.args[0])
elif isinstance(expr, fast_inv_sqrt):
return "({})".format(self._print(1 / sp.sqrt(expr.args[0])))
elif isinstance(expr, sp.Abs):
return "abs({})".format(self._print(expr.args[0]))
elif isinstance(expr, sp.Mod):
if expr.is_integer:
return "({} % {})".format(self._print(expr.args[0]), self._print(expr.args[1]))
else:
return "fmod({}, {})".format(self._print(expr.args[0]), self._print(expr.args[1]))
elif expr.func in infix_functions:
return "(%s %s %s)" % (self._print(expr.args[0]), infix_functions[expr.func], self._print(expr.args[1]))
elif expr.func == int_power_of_2:
......
......@@ -3,6 +3,8 @@ from tempfile import TemporaryDirectory
import numpy as np
import pytest
from pystencils import Assignment, create_kernel
from pystencils.boundaries import BoundaryHandling, Neumann, add_neumann_boundary
from pystencils.datahandling import SerialDataHandling
......@@ -83,5 +85,6 @@ def test_kernel_vs_copy_boundary():
np.testing.assert_almost_equal(python_copy_result, handling_result)
with TemporaryDirectory() as tmp_dir:
pytest.importorskip('pyevtk')
boundary_handling.geometry_to_vtk(file_name=os.path.join(tmp_dir, 'test_output1'), ghost_layers=False)
boundary_handling.geometry_to_vtk(file_name=os.path.join(tmp_dir, 'test_output2'), ghost_layers=True)
......@@ -22,6 +22,7 @@ FIELD_SIZES = [(4, 3), (9, 3, 7)]
def _generate_fields(dt=np.uint8, stencil_directions=1, layout='numpy'):
pytest.importorskip('pycuda')
field_sizes = FIELD_SIZES
if stencil_directions > 1:
field_sizes = [s + (stencil_directions,) for s in field_sizes]
......@@ -44,7 +45,6 @@ def _generate_fields(dt=np.uint8, stencil_directions=1, layout='numpy'):
return fields
@pytest.mark.gpu
def test_full_scalar_field():
"""Tests fully (un)packing a scalar field (from)to a GPU buffer."""
fields = _generate_fields()
......@@ -73,7 +73,6 @@ def test_full_scalar_field():
np.testing.assert_equal(src_arr, dst_arr)
@pytest.mark.gpu
def test_field_slice():
"""Tests (un)packing slices of a scalar field (from)to a buffer."""
fields = _generate_fields()
......@@ -109,7 +108,6 @@ def test_field_slice():
np.testing.assert_equal(src_arr[pack_slice], dst_arr[unpack_slice])
@pytest.mark.gpu
def test_all_cell_values():
"""Tests (un)packing all cell values of the a field (from)to a buffer."""
num_cell_values = 7
......@@ -148,7 +146,6 @@ def test_all_cell_values():
np.testing.assert_equal(src_arr, dst_arr)
@pytest.mark.gpu
def test_subset_cell_values():
"""Tests (un)packing a subset of cell values of the a field (from)to a buffer."""
num_cell_values = 7
......@@ -190,7 +187,6 @@ def test_subset_cell_values():
np.testing.assert_equal(dst_arr, mask_arr.filled(int(0)))
@pytest.mark.gpu
def test_field_layouts():
num_cell_values = 7
for layout_str in ['numpy', 'fzyx', 'zyxf', 'reverse_numpy']:
......
......@@ -57,6 +57,9 @@ def test_complex_numbers(assignment, scalar_dtypes, target):
print(code)
assert "Not supported" not in code
if target == 'gpu':
pytest.importorskip('pycuda')
kernel = ast.compile()
assert kernel is not None
......@@ -100,6 +103,9 @@ def test_complex_numbers_64(assignment, target):
print(code)
assert "Not supported" not in code
if target == 'gpu':
pytest.importorskip('pycuda')
kernel = ast.compile()
assert kernel is not None
......@@ -125,6 +131,7 @@ def test_complex_execution(dtype, target, with_complex_argument):
})
if target == 'gpu':
pytest.importorskip('pycuda')
from pycuda.gpuarray import zeros
x_arr = zeros((20, 30), complex_dtype)
y_arr = zeros((20, 30), complex_dtype)
......
import sympy
import pytest
import pystencils
from pystencils.astnodes import get_dummy_symbol
from pystencils.backends.cuda_backend import CudaSympyPrinter
......@@ -19,6 +21,7 @@ def test_cuda_known_functions():
ast = pystencils.create_kernel(assignments, 'gpu')
print(pystencils.show_code(ast))
pytest.importorskip('pycuda')
kernel = ast.compile()
assert(kernel is not None)
......
......@@ -3,6 +3,8 @@ from tempfile import TemporaryDirectory
import numpy as np
import pytest
import pystencils as ps
from pystencils import create_data_handling, create_kernel
......@@ -128,6 +130,7 @@ def kernel_execution_jacobi(dh, target):
def vtk_output(dh):
pytest.importorskip('pyevtk')
dh.add_array('scalar_field')
dh.add_array('vector_field', values_per_cell=dh.dim)
dh.add_array('multiple_scalar_field', values_per_cell=9)
......@@ -223,6 +226,7 @@ def test_kernel_param(target):
def test_vtk_output():
pytest.importorskip('pyevtk')
for domain_shape in [(4, 5), (3, 4, 5)]:
dh = create_data_handling(domain_size=domain_shape, periodicity=True)
vtk_output(dh)
......
%% Cell type:code id: tags:
``` python
import pytest
pytest.importorskip('pycuda')
```
%% Cell type:code id: tags:
``` python
from pystencils.session import *
sp.init_printing()
frac = sp.Rational
```
%% Cell type:markdown id: tags:
# Phase-field simulation of dentritic solidification in 3D
This notebook tests the model presented in the dentritic growth tutorial in 3D.
%% Cell type:code id: tags:
``` python
target = 'gpu'
gpu = target == 'gpu'
domain_size = (25, 25, 25) if 'is_test_run' in globals() else (300, 300, 300)
dh = ps.create_data_handling(domain_size=domain_size, periodicity=True, default_target=target)
φ_field = dh.add_array('phi', latex_name='φ')
φ_delta_field = dh.add_array('phidelta', latex_name='φ_D')
t_field = dh.add_array('T')
```
%% Cell type:code id: tags:
``` python
ε, m, δ, j, θzero, α, γ, Teq, κ, τ = sp.symbols("ε m δ j θ_0 α γ T_eq κ τ")
εb = sp.Symbol("\\bar{\\epsilon}")
discretize = ps.fd.Discretization2ndOrder(dx=0.03, dt=1e-5)
φ = φ_field.center
T = t_field.center
d = ps.fd.Diff
def f(φ, m):
return φ**4 / 4 - (frac(1, 2) - m/3) * φ**3 + (frac(1,4)-m/2)*φ**2
bulk_free_energy_density = f(φ, m)
interface_free_energy_density = ε ** 2 / 2 * (d(φ, 0) ** 2 + d(φ, 1) ** 2 + d(φ, 2) ** 2)
```
%% Cell type:markdown id: tags:
Here comes the major change, that has to be made for the 3D model: $\epsilon$ depends on the interface normal, which can not be computed simply as atan() as in the 2D case
%% Cell type:code id: tags:
``` python
n = sp.Matrix([d(φ, i) for i in range(3)])
nLen = sp.sqrt(sum(n_i**2 for n_i in n))
n = n / nLen
nVal = sum(n_i**4 for n_i in n)
σ = δ * nVal
εVal = εb * (1 + σ)
εVal
```
%% Output
$\displaystyle \bar{\epsilon} \left(δ \left(\frac{{\partial_{0} {{φ}_{(0,0,0)}}}^{4}}{\left({\partial_{0} {{φ}_{(0,0,0)}}}^{2} + {\partial_{1} {{φ}_{(0,0,0)}}}^{2} + {\partial_{2} {{φ}_{(0,0,0)}}}^{2}\right)^{2}} + \frac{{\partial_{1} {{φ}_{(0,0,0)}}}^{4}}{\left({\partial_{0} {{φ}_{(0,0,0)}}}^{2} + {\partial_{1} {{φ}_{(0,0,0)}}}^{2} + {\partial_{2} {{φ}_{(0,0,0)}}}^{2}\right)^{2}} + \frac{{\partial_{2} {{φ}_{(0,0,0)}}}^{4}}{\left({\partial_{0} {{φ}_{(0,0,0)}}}^{2} + {\partial_{1} {{φ}_{(0,0,0)}}}^{2} + {\partial_{2} {{φ}_{(0,0,0)}}}^{2}\right)^{2}}\right) + 1\right)$
⎛ ⎛ 4
⎜ ⎜ D(φ[0,0,0])
\bar{\epsilon}⋅⎜δ⋅⎜───────────────────────────────────────────── + ───────────
⎜ ⎜ 2
⎜ ⎜⎛ 2 2 2⎞ ⎛
⎝ ⎝⎝D(φ[0,0,0]) + D(φ[0,0,0]) + D(φ[0,0,0]) ⎠ ⎝D(φ[0,0,0]
4 4
D(φ[0,0,0]) D(φ[0,0,0])
────────────────────────────────── + ─────────────────────────────────────────
2
2 2 2⎞ ⎛ 2 2
) + D(φ[0,0,0]) + D(φ[0,0,0]) ⎠ ⎝D(φ[0,0,0]) + D(φ[0,0,0]) + D(φ[0,0,0]
⎞ ⎞
⎟ ⎟
────⎟ + 1⎟
2⎟ ⎟
2⎞ ⎟ ⎟
) ⎠ ⎠ ⎠
%% Cell type:code id: tags:
``` python
def m_func(temperature):
return (α / sp.pi) * sp.atan(γ * (Teq - temperature))
```
%% Cell type:code id: tags:
``` python
substitutions = {m: m_func(T),
ε: εVal}
fe_i = interface_free_energy_density.subs(substitutions)
fe_b = bulk_free_energy_density.subs(substitutions)
μ_if = ps.fd.expand_diff_full(ps.fd.functional_derivative(fe_i, φ), functions=[φ])
μ_b = ps.fd.expand_diff_full(ps.fd.functional_derivative(fe_b, φ), functions=[φ])
```
%% Cell type:code id: tags:
``` python
dF_dφ = μ_b + sp.Piecewise((μ_if, nLen**2 > 1e-10), (0, True))
```
%% Cell type:code id: tags:
``` python
parameters = {
τ: 0.0003,
κ: 1.8,
εb: 0.01,
δ: 0.3,
γ: 10,
j: 6,
α: 0.9,
Teq: 1.0,
θzero: 0.2,
sp.pi: sp.pi.evalf()
}
parameters
```
%% Output
$\displaystyle \left\{ \pi : 3.14159265358979, \ T_{eq} : 1.0, \ \bar{\epsilon} : 0.01, \ j : 6, \ α : 0.9, \ γ : 10, \ δ : 0.3, \ θ_{0} : 0.2, \ κ : 1.8, \ τ : 0.0003\right\}$
{π: 3.14159265358979, T_eq: 1.0, \bar{\epsilon}: 0.01, j: 6, α: 0.9, γ: 10, δ:
0.3, θ₀: 0.2, κ: 1.8, τ: 0.0003}
%% Cell type:code id: tags:
``` python
dφ_dt = - dF_dφ / τ
assignments = [
ps.Assignment(φ_delta_field.center, discretize(dφ_dt.subs(parameters))),
]
φEqs = ps.simp.sympy_cse_on_assignment_list(assignments)
φEqs.append(ps.Assignment(φ, discretize(ps.fd.transient(φ) - φ_delta_field.center)))
temperatureEvolution = -ps.fd.transient(T) + ps.fd.diffusion(T, 1) + κ * φ_delta_field.center
temperatureEqs = [
ps.Assignment(T, discretize(temperatureEvolution.subs(parameters)))
]
```
%% Cell type:code id: tags:
``` python
temperatureEqs
```
%% Output
$\displaystyle \left[ {{T}_{(0,0,0)}} \leftarrow 0.0111111111111111 {{T}_{(-1,0,0)}} + 0.0111111111111111 {{T}_{(0,-1,0)}} + 0.0111111111111111 {{T}_{(0,0,-1)}} + 0.933333333333333 {{T}_{(0,0,0)}} + 0.0111111111111111 {{T}_{(0,0,1)}} + 0.0111111111111111 {{T}_{(0,1,0)}} + 0.0111111111111111 {{T}_{(1,0,0)}} + 1.8 \cdot 10^{-5} {{φ_D}_{(0,0,0)}}\right]$
[T_C := 0.0111111111111111⋅T_W + 0.0111111111111111⋅T_S + 0.0111111111111111⋅T
_B + 0.933333333333333⋅T_C + 0.0111111111111111⋅T_T + 0.0111111111111111⋅T_N +
0.0111111111111111⋅T_E + 1.8e-5⋅phidelta_C]
%% Cell type:code id: tags:
``` python
φ_kernel = ps.create_kernel(φEqs, cpu_openmp=4, target=target).compile()
temperatureKernel = ps.create_kernel(temperatureEqs, cpu_openmp=4, target=target).compile()
```
%% Cell type:code id: tags:
``` python
def time_loop(steps):
φ_sync = dh.synchronization_function(['phi'], target=target)
temperature_sync = dh.synchronization_function(['T'], target=target)
dh.all_to_gpu()
for t in range(steps):
φ_sync()
dh.run_kernel(φ_kernel)
temperature_sync()
dh.run_kernel(temperatureKernel)
dh.all_to_cpu()
def init(nucleus_size=np.sqrt(5)):
for b in dh.iterate():
x, y, z = b.cell_index_arrays
x, y, z = x - b.shape[0] // 2, y - b.shape[1] // 2, z - b.shape[2] // 2
b['phi'].fill(0)
b['phi'][(x ** 2 + y ** 2 + z ** 2) < nucleus_size ** 2] = 1.0
b['T'].fill(0.0)
def plot(slice_obj=ps.make_slice[:, :, 0.5]):
plt.subplot(1, 3, 1)
plt.scalar_field(dh.gather_array('phi', slice_obj).squeeze())
plt.title("φ")
plt.colorbar()
plt.subplot(1, 3, 2)
plt.title("T")
plt.scalar_field(dh.gather_array('T', slice_obj).squeeze())
plt.colorbar()
plt.subplot(1, 3, 3)
plt.title("∂φ")
plt.scalar_field(dh.gather_array('phidelta', slice_obj).squeeze())
plt.colorbar()
```
%% Cell type:code id: tags:
``` python
init()
plot()
print(dh)
```
%% Output
Name| Inner (min/max)| WithGl (min/max)
----------------------------------------------------
T| ( 0, 0)| ( 0, 0)
phi| ( 0, 1)| ( 0, 1)
phidelta| ( 0, 0)| ( 0, 0)
%% Cell type:code id: tags:
``` python
if 'is_test_run' in globals():
time_loop(2)
assert np.isfinite(dh.max('phi'))
assert np.isfinite(dh.max('T'))
assert np.isfinite(dh.max('phidelta'))
else:
from time import perf_counter
vtk_writer = dh.create_vtk_writer('dentritic_growth_large', ['phi'])
last = perf_counter()
for i in range(300):
time_loop(100)
vtk_writer(i)
print("Step ", i, perf_counter() - last, dh.max('phi'))
last = perf_counter()
```
......
......@@ -17,6 +17,9 @@ def test_print_infinity(type, negative, target):
assignment = pystencils.Assignment(x.center, oo)
ast = pystencils.create_kernel(assignment, data_type=type, target=target)
if target == 'gpu':
pytest.importorskip('pycuda')
ast.compile()
print(ast.compile().code)
import numpy as np
import pytest
import pystencils as ps
from pystencils.rng import PhiloxFourFloats, PhiloxTwoDoubles, AESNIFourFloats, AESNITwoDoubles
......@@ -12,6 +14,9 @@ philox_reference = np.array([[[3576608082, 1252663339, 1987745383, 348040302],
def test_philox_double():
for target in ('cpu', 'gpu'):
if target == 'gpu':
pytest.importorskip('pycuda')
dh = ps.create_data_handling((2, 2), default_ghost_layers=0, default_target=target)
f = dh.add_array("f", values_per_cell=2)
......@@ -39,6 +44,9 @@ def test_philox_double():
def test_philox_float():
for target in ('cpu', 'gpu'):
if target == 'gpu':
pytest.importorskip('pycuda')
dh = ps.create_data_handling((2, 2), default_ghost_layers=0, default_target=target)
f = dh.add_array("f", values_per_cell=4)
......
......@@ -3,7 +3,6 @@ python_files = test_*.py *_test.py scenario_*.py
norecursedirs = *.egg-info .git .cache .ipynb_checkpoints htmlcov
addopts = --doctest-modules --durations=20 --cov-config pytest.ini
markers =
gpu: test that require a gpu
kerncraft: tests depending on kerncraft
[run]
......
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