Merge m-to-n with main

.github/workflows/ci.yaml

@@ -18,9 +18,9 @@ jobs:
         name: Flake8
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         -
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             # matches compat target in setup.py
             python-version: '3.8'
@@ -36,9 +36,9 @@ jobs:
         name: Mypy
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v3
+        -   uses: actions/checkout@v4
         -
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: '3.x'
         -   name: Install
@@ -55,9 +55,9 @@ jobs:
         name: Pylint
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         -
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: '3.x'
         - name: Install
@@ -73,9 +73,9 @@ jobs:
     pydocstyle:
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         -
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: '3.x'
         - name: Run Pydocstyle
@@ -91,7 +91,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         - name: Install
           run: |
             . .ci-support/install.sh
@@ -112,7 +112,7 @@ jobs:
             os: [ubuntu-latest, porter]
 
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         - name: Install
           run: |
             . .ci-support/install.sh
@@ -124,6 +124,9 @@ jobs:
             . "$MINIFORGE_INSTALL_DIR/bin/activate" testing
             export XDG_CACHE_HOME=/tmp
             mamba install vtk  # needed for the accuracy comparison
+
+            # Temporary workaround for https://github.com/conda-forge/openvino-feedstock/pull/73
+
             [[ $(hostname) == "porter" ]] && export PYOPENCL_TEST="port:nv" && unset XDG_CACHE_HOME
 
              # This is only possible because actions run sequentially on porter
@@ -136,7 +139,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         - name: Install
           run: |
             . .ci-support/install.sh
@@ -168,11 +171,11 @@ jobs:
             os: [ubuntu-latest, macos-latest]
 
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         - name: Install emirge
           run: |
             [[ $(uname) == Linux ]] && sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev
-            [[ $(uname) == Darwin ]] && brew upgrade && brew install mpich
+            [[ $(uname) == Darwin ]] && ( brew upgrade || true; brew install mpich )
             cd ..
             git clone https://github.com/illinois-ceesd/emirge
             cd emirge
@@ -194,14 +197,14 @@ jobs:
             os: [ubuntu-latest, macos-latest, porter]
 
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
           with:
             fetch-depth: '0'
         - name: Prepare production environment
           run: |
             set -x
             [[ $(uname) == Linux ]] && [[ $(hostname) != "porter" ]] && sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev
-            [[ $(uname) == Darwin ]] && brew upgrade && brew install mpich
+            [[ $(uname) == Darwin ]] && ( brew upgrade || true; brew install mpich )
 
             # This is only possible because actions run sequentially on porter
             [[ $(hostname) == "porter" ]] && rm -rf /tmp/githubrunner/pocl-scratch && rm -rf /tmp/githubrunner/xdg-scratch
@@ -222,4 +225,7 @@ jobs:
         - name: Run production test
           run: |
             source ../config/activate_env.sh
+
+            # Temporary workaround for https://github.com/conda-forge/openvino-feedstock/pull/73
+
             scripts/run-integrated-tests.sh --production

.gitignore

@@ -48,3 +48,9 @@ test/nodal-dg
 # Emacs backups
 .\#*
 \#*
+
+
+# disk caches
+xdg-cache/
+pocl-cache/
+cuda-cache/

.rtd-env-py3.yml

@@ -18,6 +18,7 @@ dependencies:
   - "git+https://github.com/inducer/leap.git#egg=leap"
   - "git+https://github.com/inducer/modepy.git#egg=modepy"
   - "git+https://github.com/illinois-ceesd/arraycontext.git@production#egg=arraycontext"
+  - "git+https://github.com/illinois-ceesd/pytato.git@production#egg=pytato"
   - "git+https://github.com/illinois-ceesd/meshmode.git@production#egg=meshmode"
   - "git+https://github.com/illinois-ceesd/grudge.git@production#egg=grudge"
   - "sphinx-math-dollar"

conda-env.yml

@@ -23,7 +23,7 @@ dependencies:
 - pytest
 - pylint
 - pydocstyle
-- cantera
+- cantera=3.0.0
 - h5py * nompi_*  # Make sure cantera does not pull in MPI through h5py
 - gmsh
 - vtk

doc/misc.rst

@@ -93,3 +93,6 @@ References
    `(DOI) <https://doi.org/10.4208/cicp.170712.010313a>`__
 .. [Renac_2021] Florent Renac, Entropy stable, robust and high-order DGSEM for the compressible multicomponent \
    Euler equations, Journal of Computational Physics, 445 `(DOI) <https://doi.org/10.1016/j.jcp.2021.110584>`__
+.. [Ern_2008] Daniele A. Di Pietro, Alexandre Ern, Jean-Luc Guermond, Discontinuous Galerkin Methods for \
+   Anisotropic Semidefinite Diffusion with Advection, SIAM Journal on Numerical Analysis 46 2 \
+   `(DOI) <https://www.jstor.org/stable/40233233?seq=12>`__

doc/running/caching.rst

@@ -1,11 +1,12 @@
 OpenCL kernel caching
 =====================
 
-OpenCL kernels are cached on hard disk on multiple levels during a |mirgecom|
-execution. This has the advantage of reducing the compilation time of kernels
-when running the same driver multiple times.
+OpenCL kernels are cached in memory and on hard disk on multiple levels during
+a |mirgecom| execution. This has the advantage of reducing the compilation time
+of kernels when running the same driver multiple times.
 
-The following sections discuss |mirgecom|-related packages that use caching.
+The following sections discuss |mirgecom|-related packages that use caching,
+with a focus on configuring the disk-based caching.
 
 .. note::
 
@@ -19,6 +20,21 @@ The following sections discuss |mirgecom|-related packages that use caching.
    ~/.cache/pyopencl  ~/Library/Caches/pyopencl $POCL_CACHE_DIR
    $XDG_CACHE_HOME/pocl ~/.cache/pocl ~/.nv/ComputeCache $CUDA_CACHE_PATH``
 
+.. note::
+
+   The following bash code can be used to disable all disk caches::
+
+      $ export LOOPY_NO_CACHE=1
+      $ export PYOPENCL_NO_CACHE=1
+      $ export POCL_KERNEL_CACHE=0
+      $ export CUDA_CACHE_DISABLE=1
+
+.. note::
+
+   Disabling disk caching for a specific package only affects
+   that particular package. For example, disabling disk caching for :mod:`loopy`
+   does not affect the caching behavior of :mod:`pyopencl` or *PoCL*.
+
 
 Loopy
 -----
@@ -64,21 +80,22 @@ for details.
    PyOpenCL uses ``clCreateProgramWithSource`` on the first compilation and
    caches the OpenCL binary it retrieves. The second time the same source
    is compiled, it uses ``clCreateProgramWithBinary`` to hand the binary
-   to the CL runtime (such as PoCL). This can lead to different caching behaviors on the first three compilations depending on how the CL runtime
+   to the CL runtime (such as PoCL). This can lead to different caching
+   behaviors on the first three compilations depending on how the CL runtime
    itself performs caching.
 
 
 PoCL
 ----
 
-PoCL stores compilation results (LLVM bitcode and shared libraries) in
-``$POCL_CACHE_DIR`` or ``$XDG_CACHE_HOME/pocl`` by default. You can export
-``POCL_KERNEL_CACHE=0`` to disable caching. See `here
+*PoCL* stores compilation results (LLVM bitcode and shared
+libraries) in ``$POCL_CACHE_DIR`` or ``$XDG_CACHE_HOME/pocl`` by default. You
+can export ``POCL_KERNEL_CACHE=0`` to disable caching. See `here
 <http://portablecl.org/docs/html/using.html#tuning-pocl-behavior-with-env-variables>`__ for details.
 
 .. note::
 
-   When ``$POCL_CACHE_DIR`` and ``$XDG_CACHE_HOME`` are not set, PoCL's cache
+   When ``$POCL_CACHE_DIR`` and ``$XDG_CACHE_HOME`` are not set, *PoCL*'s cache
    dir defaults to ``~/.cache/pocl`` on Linux and MacOS.
 
 

doc/running/large-systems.rst

@@ -45,9 +45,9 @@ In order to avoid these issues, users should direct the packages to create
 cache files in directories that are private to each rank by using the ``XDG_CACHE_HOME`` and ``POCL_CACHE_DIR``
 environment variables, such as in the following example::
 
-   $ export XDG_CACHE_ROOT="/tmp/$USER/xdg-scratch"
-   $ export POCL_CACHE_ROOT="/tmp/$USER/pocl-scratch"
-   $ srun -n 512 bash -c 'POCL_CACHE_DIR=$POCL_CACHE_ROOT/$$ XDG_CACHE_HOME=$XDG_CACHE_ROOT/$$ python -m mpi4py examples/wave-mpi.py'
+   $ export XDG_CACHE_ROOT="/tmp/$USER/xdg-cache"
+   $ export POCL_CACHE_ROOT="/tmp/$USER/pocl-cache"
+   $ srun -n 512 bash -c 'POCL_CACHE_DIR=$POCL_CACHE_ROOT/$$ XDG_CACHE_HOME=$XDG_CACHE_ROOT/$$ python -m mpi4py examples/wave.py'
 
 
 There is also on-disk caching of compiled kernels done by CUDA itself.

doc/support/arrays.rst

@@ -43,24 +43,25 @@ To demonstrate the effect of this, first we need some setup:
 .. doctest::
 
    >>> import pyopencl as cl
-   >>> from arraycontext import PyOpenCLArrayContext, thaw
+   >>> from arraycontext import thaw
+   >>> from meshmode.array_context import PyOpenCLArrayContext
    >>> ctx = cl.create_some_context()
    >>> queue = cl.CommandQueue(ctx)
    >>> actx = PyOpenCLArrayContext(queue)
    >>> from meshmode.mesh.generation import generate_regular_rect_mesh
    >>> mesh = generate_regular_rect_mesh(a=(0, 0), b=(1, 1), nelements_per_axis=(10, 10))
-   >>> from grudge import DiscretizationCollection
-   >>> dcoll = DiscretizationCollection(actx, mesh, order=5)
+   >>> from grudge import make_discretization_collection
+   >>> dcoll = make_discretization_collection(actx, mesh, order=5)
 
 Most quantities that are maintained by the discretization will be frozen. For example,
 if one wanted to grab the nodes of the mesh or normals of a named surface in the mesh:
 
 .. doctest::
 
-   >>> from grudge.dof_desc import DOFDesc
-   >>> nodes = thaw(dcoll.nodes(), actx)
-   >>> dd = DOFDesc("all_faces")
-   >>> nhat = thaw(dcoll.normal(dd), actx)
+   >>> from grudge.dof_desc import as_dofdesc
+   >>> nodes = actx.thaw(dcoll.nodes())
+   >>> dd = as_dofdesc("all_faces")
+   >>> nhat = actx.thaw(dcoll.normal(dd))
 
 What can go wrong?  Attempts to operate on frozen data will yield errors similar to
 the following:
@@ -76,7 +77,7 @@ Fortunately, recovering from this is straightforward:
 
 .. doctest::
 
-   >>> nodes = thaw(dcoll.nodes(), actx)
+   >>> nodes = actx.thaw(dcoll.nodes())
    >>> result = nodes * 5
 
 Array Containers

examples/README.md

@@ -13,6 +13,7 @@ The examples and the unique features they exercise are as follows:
 - `sod.py`: Sod's shock case: Fluid test case with strong shock
 - `vortex.py`: Isentropic vortex advection: outflow boundaries, verification
 - `hotplate.py`: Isothermal BC verification (prescribed exact soln)
+- `blasius.py`: Inflow, outflow and no-slip wall BC verification
 - `doublemach.py`: AV test case
 - `poiseuille.py`: Poiseuille flow verification case
 - `poiseuille-multispecies.py`: Poiseuille flow with passive scalars