[JAX-CFD] tweak installation & tests

The tweaks to the test suite ensure everything passes on my local installation on my MacBook, and shave a few minutes off the execution time. If the README instructions are followed, the whole test-suite runs in about two and a half minutes on my Mac. It excludes the "validation tests", which are too slow to run on CPU. PiperOrigin-RevId: 374442976
google · May 18, 2021 · b47e8df · b47e8df
1 parent dfc7eec
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diff --git a/README.md b/README.md
@@ -25,13 +25,17 @@ We are currently preparing more example notebooks, inculding:
 JAX-CFD is organized around sub-modules:
 
 - `jax_cfd.base`: core numerical methods for CFD, written in JAX.
-- `jax_cfd.ml` (not yet released): machine learning augmented models for CFD,
+- `jax_cfd.ml`: machine learning augmented models for CFD,
   written in JAX and [Haiku](https://dm-haiku.readthedocs.io/en/latest/).
 - `jax_cfd.data`: data processing utilities for preparing, evaluating and
   post-processing data created with JAX-CFD, written in
   [Xarray](http://xarray.pydata.org/) and
   [Pillow](https://pillow.readthedocs.io/).
 
+A base install with `pip install jax-cfd` only requires NumPy, SciPy and JAX.
+To install dependencies for the other submodules, use `pip install jax-cfd[ml]`,
+`pip install jax-cfd[data]` or `pip install jax-cfd[complete]`.
+
 ## Numerics
 
 JAX-CFD is currently focused on unsteady turbulent flows:
@@ -93,3 +97,18 @@ Did we miss something? Please let us know!
       primaryClass={physics.flu-dyn}
 }
 ```
+
+## Local development
+
+To locally install for development:
+```
+git clone https://github.com/google/jax-cfd.git
+cd jax-cfd
+pip install jaxlib
+pip install -e ".[complete]"
+```
+
+Then to manually run the test suite:
+```
+pytest -n auto jax_cfd --dist=loadfile --ignore=jax_cfd/base/validation_test.py
+```
diff --git a/jax_cfd/__init__.py b/jax_cfd/__init__.py
@@ -14,5 +14,6 @@
 
 """Defines the JAX-CFD module for computational fluid dynamics."""
 
+__version__ = '0.1.0'
+
 import jax_cfd.base
-import jax_cfd.data
diff --git a/jax_cfd/base/advection_test.py b/jax_cfd/base/advection_test.py
@@ -93,7 +93,7 @@ class AdvectionTest(test_util.TestCase):
            cfl_number=0.5,
            atol=7e-2),
       dict(testcase_name='upwind_3D',
-           shape=(101, 101, 101),
+           shape=(101, 5, 5),
            method=_euler_step(adv.advect_upwind),
            num_steps=100,
            cfl_number=0.5,
@@ -112,7 +112,7 @@ class AdvectionTest(test_util.TestCase):
            atol=2e-2,
            v_sign=-1.),
       dict(testcase_name='van_leer_3D',
-           shape=(101, 101, 101),
+           shape=(101, 5, 5),
            method=_euler_step(adv.advect_van_leer),
            num_steps=100,
            cfl_number=0.5,
@@ -124,7 +124,7 @@ class AdvectionTest(test_util.TestCase):
            cfl_number=0.5,
            atol=2e-2),
       dict(testcase_name='van_leer_using_limiters_3D',
-           shape=(101, 101, 101),
+           shape=(101, 5, 5),
            method=_euler_step(adv.advect_van_leer_using_limiters),
            num_steps=100,
            cfl_number=0.5,
@@ -136,7 +136,7 @@ class AdvectionTest(test_util.TestCase):
            cfl_number=0.5,
            atol=7e-2),
       dict(testcase_name='semilagrangian_3D',
-           shape=(101, 101, 101),
+           shape=(101, 5, 5),
            method=adv.advect_step_semilagrangian,
            num_steps=100,
            cfl_number=0.5,

diff --git a/jax_cfd/base/equations_test.py b/jax_cfd/base/equations_test.py
@@ -83,7 +83,7 @@ class SemiImplicitNavierStokesTest(test_util.TestCase):
            dt=1e-3,
            time_steps=1000,
            divergence_atol=1e-3,
-           momentum_atol=1e-3),
+           momentum_atol=2e-3),
       dict(testcase_name='gaussian_force_upwind',
            velocity=zero_field,
            forcing=lambda v, g: gaussian_field(g),
@@ -94,9 +94,9 @@ class SemiImplicitNavierStokesTest(test_util.TestCase):
            convect=_convect_upwind,
            pressure_solve=pressure.solve_cg,
            dt=1e-3,
-           time_steps=1000,
-           divergence_atol=1e-3,
-           momentum_atol=1e-3),
+           time_steps=100,
+           divergence_atol=1e-4,
+           momentum_atol=1e-4),
       dict(testcase_name='sinusoidal_velocity_fast_diag',
            velocity=sinusoidal_field,
            forcing=None,
@@ -145,5 +145,4 @@ def test_divergence_and_momentum(
 
 
 if __name__ == '__main__':
-  jax.config.update('jax_enable_x64', True)
   absltest.main()
diff --git a/jax_cfd/base/finite_differences_test.py b/jax_cfd/base/finite_differences_test.py
@@ -220,7 +220,7 @@ def test_divergence(self, grid_type, shape, offsets, f, g, atol):
           g=lambda x, y, z: np.array([[y - 1., jnp.zeros_like(x), z],
                                       [x, z - 2., jnp.zeros_like(x)],
                                       [jnp.zeros_like(x), y, x - 3.]]),
-          atol=1e-6),
+          atol=4e-6),
   )
   # pylint: enable=g-long-lambda
   def test_cell_centered_gradient(self, shape, f, g, atol):

diff --git a/jax_cfd/base/subgrid_models_test.py b/jax_cfd/base/subgrid_models_test.py
@@ -96,9 +96,9 @@ class SubgridModelsTest(test_util.TestCase):
           convect=_convect_upwind,
           pressure_solve=pressure.solve_cg,
           dt=1e-3,
-          time_steps=1000,
-          divergence_atol=1e-3,
-          momentum_atol=1e-3),
+          time_steps=100,
+          divergence_atol=1e-4,
+          momentum_atol=1e-4),
       dict(
           testcase_name='sinusoidal_velocity_with_subgrid_model',
           cs=0.12,

diff --git a/jax_cfd/data/visualization_test.py b/jax_cfd/data/visualization_test.py
@@ -15,16 +15,12 @@
 
 import os.path
 
-from absl import flags
 from absl.testing import absltest
 from jax_cfd.base import test_util
 from jax_cfd.data import visualization
 import numpy as np
 
 
-FLAGS = flags.FLAGS
-
-
 class VisualizationTest(test_util.TestCase):
 
   def test_trajectory_to_images_shape(self):
@@ -54,7 +50,7 @@ def test_horizontal_facet_shape(self):
 
   def test_save_movie_local(self):
     """Tests that save_movie write gif to a file."""
-    temp_dir = FLAGS.test_tmpdir
+    temp_dir = self.create_tempdir()
     temp_filename = os.path.join(temp_dir, 'tmp_file.gif')
     input_trajectory = np.random.uniform(size=(25, 32, 32))
     images = visualization.trajectory_to_images(input_trajectory)

diff --git a/jax_cfd/ml/__init__.py b/jax_cfd/ml/__init__.py
@@ -0,0 +1,36 @@
+# Copyright 2021 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""An ML modeling library built on Haiku and Gin-Config for JAX-CFD."""
+
+import jax_cfd.ml.advections
+import jax_cfd.ml.decoders
+import jax_cfd.ml.diffusions
+import jax_cfd.ml.encoders
+import jax_cfd.ml.equations
+import jax_cfd.ml.forcings
+import jax_cfd.ml.interpolations
+import jax_cfd.ml.layers
+import jax_cfd.ml.layers_util
+import jax_cfd.ml.model_builder
+import jax_cfd.ml.model_utils
+import jax_cfd.ml.networks
+import jax_cfd.ml.nonlinearities
+import jax_cfd.ml.optimizer_modules
+import jax_cfd.ml.physics_specifications
+import jax_cfd.ml.pressures
+import jax_cfd.ml.tiling
+import jax_cfd.ml.time_integrators
+import jax_cfd.ml.towers
+import jax_cfd.ml.viscosities
diff --git a/jax_cfd/ml/layers_test.py b/jax_cfd/ml/layers_test.py
@@ -451,10 +451,10 @@ def module_forward(x):
 
   @parameterized.named_parameters([
       ('interpolation', (128, 128), (0, 0),
-       lambda x, y: np.sin(2 * x + y), lambda x, y: np.sin(2 * x + y), 1e-1),
+       lambda x, y: np.sin(2 * x + y), lambda x, y: np.sin(2 * x + y), 0.2),
       ('first_derivative_x', (128, 128), (1, 0),
        lambda x, y: np.cos(2 * x + y), lambda x, y: -2 * np.sin(2 * x + y),
-       1e-1),
+       0.1),
   ])
   def test_2d(self, grid_shape, derivative, initial_fn, expected_fn, atol):
     """Tests SpatialDerivative module in 2d."""
@@ -465,24 +465,25 @@ def test_2d(self, grid_shape, derivative, initial_fn, expected_fn, atol):
         _tower_factory, ndims=ndims, conv_block=layers.PeriodicConv2D)
 
     for extract_patches_method in ('conv', 'roll'):
-      def module_forward(inputs):
-        net = layers.SpatialDerivative(
-            stencil_sizes, grid.cell_center, grid.cell_center, derivative,
-            tower_factory, grid.step, extract_patches_method)  # pylint: disable=cell-var-from-loop
-        return net(inputs)
-
-      rng = jax.random.PRNGKey(14)
-      spatial_derivative_model = hk.without_apply_rng(
-          hk.transform(module_forward))
-
-      x, y = grid.mesh()
-      inputs = np.expand_dims(initial_fn(x, y), -1)  # add channel dimension
-      params = spatial_derivative_model.init(rng, inputs)
-      outputs = spatial_derivative_model.apply(params, inputs)
-      expected_outputs = np.expand_dims(expected_fn(x, y), -1)
-      np.testing.assert_allclose(
-          expected_outputs, outputs, atol=atol, rtol=0,
-          err_msg=f'Failed for method "{extract_patches_method}"')
+      with self.subTest(f'method_{extract_patches_method}'):
+        def module_forward(inputs):
+          net = layers.SpatialDerivative(
+              stencil_sizes, grid.cell_center, grid.cell_center, derivative,
+              tower_factory, grid.step, extract_patches_method)  # pylint: disable=cell-var-from-loop
+          return net(inputs)
+
+        rng = jax.random.PRNGKey(14)
+        spatial_derivative_model = hk.without_apply_rng(
+            hk.transform(module_forward))
+
+        x, y = grid.mesh()
+        inputs = np.expand_dims(initial_fn(x, y), -1)  # add channel dimension
+        params = spatial_derivative_model.init(rng, inputs)
+        outputs = spatial_derivative_model.apply(params, inputs)
+        expected_outputs = np.expand_dims(expected_fn(x, y), -1)
+        np.testing.assert_allclose(
+            expected_outputs, outputs, atol=atol, rtol=0,
+            err_msg=f'Failed for method "{extract_patches_method}"')
 
   def test_auxiliary_inputs(self):
     """Tests that auxiliary inputs don't change shape of the output."""

diff --git a/setup.py b/setup.py
@@ -15,25 +15,24 @@
 """Setup JAX-CFD."""
 import setuptools
 
-
-INSTALL_REQUIRES = [
-    'absl-py',
-    'jax',
-    'numpy',
-    'scipy',
-    'matplotlib',
-    'seaborn',
-    'Pillow',
-    'xarray',
-]
+base_requires = ['jax', 'numpy', 'scipy']
+data_requires = ['matplotlib', 'seaborn', 'Pillow', 'xarray']
+ml_requires = ['dm-haiku', 'einops', 'gin-config']
+tests_requires = ['absl-py', 'pytest', 'pytest-xdist', 'scikit-image']
 
 setuptools.setup(
     name='jax-cfd',
-    version='0.0.0',
+    version='0.1.0',
     license='Apache 2.0',
     author='Google LLC',
     author_email='[email protected]',
-    install_requires=INSTALL_REQUIRES,
+    install_requires=base_requires,
+    extras_require={
+        'data': data_requires,
+        'ml': ml_requires,
+        'tests': tests_requires,
+        'complete': data_requires + ml_requires + tests_requires,
+    },
     url='https://github.com/google/jax-cfd',
     packages=setuptools.find_packages(),
     python_requires='>=3',