diff --git a/pystencils/astnodes.py b/pystencils/astnodes.py
index 062d3687f582423bd38b8a1c2e9dae3ff95a6bfb..8ec80917af20aefc5883c68ac51f360005b4350b 100644
--- a/pystencils/astnodes.py
+++ b/pystencils/astnodes.py
@@ -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):
diff --git a/pystencils/backends/cbackend.py b/pystencils/backends/cbackend.py
index 9efca1f53a6870d2b0ce2bdd1da547d16beb6a6c..1c7c722cbe273329bc2a15521fbc933b00f56606 100644
--- a/pystencils/backends/cbackend.py
+++ b/pystencils/backends/cbackend.py
@@ -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:
diff --git a/pystencils_tests/test_boundary.py b/pystencils_tests/test_boundary.py
index 096b1348fc59181e14eb15042d8db0098e71c521..23770c8ef6d61c15110f94875b0000c3e7d11fac 100644
--- a/pystencils_tests/test_boundary.py
+++ b/pystencils_tests/test_boundary.py
@@ -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)
diff --git a/pystencils_tests/test_buffer_gpu.py b/pystencils_tests/test_buffer_gpu.py
index fc27a2331be1690b8bb1d0da043b47b3ba6fcfc9..f9ee96e9b19c147d95f006de4221980900375cb1 100644
--- a/pystencils_tests/test_buffer_gpu.py
+++ b/pystencils_tests/test_buffer_gpu.py
@@ -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']:
diff --git a/pystencils_tests/test_complex_numbers.py b/pystencils_tests/test_complex_numbers.py
index 9f9164640f50e417348ee635af620dd891249d77..b1c0569d05e73a786a780d7f4826eedf8d71b533 100644
--- a/pystencils_tests/test_complex_numbers.py
+++ b/pystencils_tests/test_complex_numbers.py
@@ -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)
diff --git a/pystencils_tests/test_cuda_known_functions.py b/pystencils_tests/test_cuda_known_functions.py
index fe33b98df27cc6a6c2ec77eda49e704b9afbec5e..99810a55af73907b686f342a8dba1f2053cbabe7 100644
--- a/pystencils_tests/test_cuda_known_functions.py
+++ b/pystencils_tests/test_cuda_known_functions.py
@@ -1,5 +1,7 @@
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)
diff --git a/pystencils_tests/test_datahandling.py b/pystencils_tests/test_datahandling.py
index 1b79fdbec5aa8bbbfb90450d2014d058065e998b..55b845f7b941316277cc9595058fdb42b07e665c 100644
--- a/pystencils_tests/test_datahandling.py
+++ b/pystencils_tests/test_datahandling.py
@@ -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)
diff --git a/pystencils_tests/test_phasefield_dentritic_3D.ipynb b/pystencils_tests/test_phasefield_dentritic_3D.ipynb
index aebdeefdddf53e9736feb7d8673c09bc5d8fa6d0..1a01f103891fb229385d8192f263fb53dd837a78 100644
--- a/pystencils_tests/test_phasefield_dentritic_3D.ipynb
+++ b/pystencils_tests/test_phasefield_dentritic_3D.ipynb
@@ -1,5 +1,15 @@
{
"cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pytest\n",
+ "pytest.importorskip('pycuda')"
+ ]
+ },
{
"cell_type": "code",
"execution_count": 1,
diff --git a/pystencils_tests/test_print_infinity.py b/pystencils_tests/test_print_infinity.py
index 4b1e488822163e684dcad4009fca1b72c7d87d2c..9e2dbd29b18389265b206513ec6c4625e0722a10 100644
--- a/pystencils_tests/test_print_infinity.py
+++ b/pystencils_tests/test_print_infinity.py
@@ -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)
diff --git a/pystencils_tests/test_random.py b/pystencils_tests/test_random.py
index 473aa3d1215449f51e70aa3b09f2c605ed13c313..1b3f89f2f81aa6e079f7bc030f27da74e778dd13 100644
--- a/pystencils_tests/test_random.py
+++ b/pystencils_tests/test_random.py
@@ -1,5 +1,7 @@
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)
diff --git a/pytest.ini b/pytest.ini
index 4e9f5caddfef20639da974ad9327e53fa8b6ced4..0070425966626449378fcd1ff9eabe468256a112 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -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]