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‎.github/workflows/dependencies/dependencies_hip.sh

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@@ -33,7 +33,9 @@ sudo apt-key add rocm.gpg.key
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source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
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echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
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VERSION=${1-6.3.2}
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echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${VERSION} ${UBUNTU_CODENAME} main" \
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| sudo tee /etc/apt/sources.list.d/rocm.list
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echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
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| sudo tee -a /etc/profile.d/rocm.sh
@@ -53,16 +55,16 @@ sudo apt-get install -y --no-install-recommends \
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libnuma-dev \
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libopenmpi-dev \
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openmpi-bin \
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rocm-dev \
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roctracer-dev \
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rocprofiler-dev \
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rocrand-dev \
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rocfft-dev \
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rocprim-dev \
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rocsparse-dev
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rocm-dev${VERSION} \
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roctracer-dev${VERSION} \
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rocprofiler-dev${VERSION} \
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rocrand-dev${VERSION} \
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rocfft-dev${VERSION} \
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rocprim-dev${VERSION} \
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rocsparse-dev${VERSION}
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# hiprand-dev is a new package that does not exist in old versions
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sudo apt-get install -y --no-install-recommends hiprand-dev || true
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sudo apt-get install -y --no-install-recommends hiprand-dev${VERSION} || true
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# activate
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#

‎.github/workflows/hip.yml

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@@ -8,7 +8,7 @@ concurrency:
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jobs:
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hip-compile:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@v4
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with:
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cd ../..
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- name: Dependencies
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run: .github/workflows/dependencies/dependencies_hip.sh
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run: .github/workflows/dependencies/dependencies_hip.sh 6.3.2
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- name: compile test_react with HIP (iso7)
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run: |

‎Docs/source/burn_cell.rst

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@@ -52,39 +52,17 @@ The parameters that affect the thermodynamics are:
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* ``unit_test.temperature`` : the initial temperature
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* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
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The composition can be set either by specifying individual mass fractions
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or setting ``unit_test.uniform_xn`` as described in :ref:`sec:defining_unit_test_composition`.
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* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
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The composition can be set either by setting each mass fraction explicitly via the
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parameters, ``unit_test.X1``, ``unit_test.X2``, ...,
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e.g.:
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::
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unit_test.X1 = 0.5
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unit_test.X2 = 0.2
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unit_test.X3 = 0.2
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unit_test.X4 = 0.1
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where parameters up to ``X35`` are available. If the values don't sum to ``1``
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initially, then the test will do a normalization. This normalization can be
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disabled by setting:
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If the values don't sum to ``1`` initially, then the test will do a
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normalization. This normalization can be disabled by setting:
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::
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unit_test.skip_initial_normalization = 1
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Alternately, the composition can be set automatically by initializing all
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of the mass fractions equally (to $1/N$, where $N$ is the number of species),
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by setting:
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::
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unit_test.uniform_xn = 1
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Controlling time
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----------------
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‎Docs/source/comprehensive_tests.rst

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@@ -1,3 +1,5 @@
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.. _sec:comprehensive_tests:
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13
************************
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Comprehensive Unit Tests
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************************

‎Docs/source/design.rst

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@@ -8,11 +8,11 @@ Structure
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The high-level directory structure delineates the types of microphysics
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and the generic solvers:
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* ``conductivity``: thermal conductivity routines
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* ``conductivity/``: thermal conductivity routines
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* ``constants``: fundamental constants
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* ``constants/``: fundamental constants
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* ``Docs``: the sphinx source for this documentation
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* ``Docs/``: the sphinx source for this documentation
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* ``EOS/``: the various equations of state
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@@ -41,7 +41,13 @@ and the generic solvers:
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* ``util/``: linear algebra solvers and other routines.
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Design Philosophy
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.. note::
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All quantities are assumed to be in CGS units, unless otherwise
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specified.
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Design philosophy
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=================
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Any application that uses Microphysics will at minimum need to
@@ -64,10 +70,33 @@ of the species defined by the network to interpret the state.
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We try to maximize code reuse in the Microphysics source, so the
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solvers (ODE integration for the network and Newton-Raphson root
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finding for the EOS) is separated from the specific implementations of
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finding for the EOS) are separated from the specific implementations of
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the microphysics.
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.. note::
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All quantities are assumed to be in CGS units, unless otherwise
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specified.
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GPU considerations
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==================
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.. index:: GPUs
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All of the Microphysics routines are written to run on GPUs. This is
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enabled in application codes by using the AMReX lambda-capturing
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mechanism (see the [AMReX GPU
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documentation](https://amrex-codes.github.io/amrex/docs_html/GPU.html)
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for more information).
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This means leveraging the AMReX data-structures, macros, and
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functions. The unit tests (see :ref:`sec:unit_tests`) provide a good
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reference for how to interface the Microphysics solvers and physics
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terms with an AMReX-based code.
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There are a few places where Microphysics behaves slightly differently
95+
when running on a CPU vs. a GPU:
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* In the VODE integrator, we disable Jacobian-caching to save memory.
98+
See :ref:`ch:networks:integrators`.
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* In general we disable printing from GPU kernels, due to register
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pressure. Some output can be enabled by compiling with
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``USE_GPU_PRINTF=TRUE``.

‎Docs/source/eos_cell.rst

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@@ -28,14 +28,8 @@ The parameters that affect the thermodynamics are:
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* ``unit_test.temperature`` : the initial temperature
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31-
* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
32-
33-
* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
34-
35-
The composition can be set in the same way as in ``burn_cell``, either
36-
by setting each mass fraction explicitly via the parameters,
37-
``unit_test.X1``, ``unit_test.X2``, ..., or forcing them to be all
38-
equal via ``unit_test.uniform_xn=1``.
31+
The composition can be set either by specifying individual mass fractions
32+
or setting ``unit_test.uniform_xn`` as described in :ref:`sec:defining_unit_test_composition`.
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Building and Running the Code

‎Docs/source/index.rst

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@@ -46,7 +46,6 @@ system.
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getting_started
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design
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data_structures
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autodiff
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rp_intro
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.. toctree::
@@ -85,13 +84,15 @@ system.
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:hidden:
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util
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autodiff
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.. toctree::
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:maxdepth: 1
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:caption: Unit tests
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:hidden:
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unit_tests
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unit_test_runtime_parameters
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comprehensive_tests
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one_zone_tests
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‎Docs/source/integrators.rst

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@@ -88,7 +88,7 @@ routine (at the moment this can be ``VODE``, ``BackwardEuler``, ``ForwardEuler``
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.. code-block:: c++
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AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
91-
void burner (burn_t& state, Real dt)
91+
void burner (burn_t& state, amrex::Real dt)
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The input is a ``burn_t``.
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@@ -198,7 +198,7 @@ be computed as:
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.. code-block:: c++
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Array1D<Real, 1, NumSpec> y;
201+
amrex::Array1D<amrex::Real, 1, NumSpec> y;
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...
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for (int i = 1; i <= NumSpec; ++i) {
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y(i) = state.xn[i-1] * aion_inv[i-1];

‎Docs/source/jac_cell.rst

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@@ -38,14 +38,15 @@ The parameters that affect the thermodynamics are:
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* ``unit_test.temperature`` : the initial temperature
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* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
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The composition can be set either by specifying individual mass fractions
42+
or setting ``unit_test.uniform_xn`` as described in :ref:`sec:defining_unit_test_composition`.
4243

43-
* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
44+
If the values don't sum to ``1`` initially, then the test will do a
45+
normalization. This normalization can be disabled by setting:
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45-
While the mass fractions can be set individually (using
46-
``unit_test.X1``, ``unit_test.X2``, ...), it is recommended to use
47-
``unit_test.uniform_xn=1`` to initialize all the mass fractions to be
48-
equal.
47+
::
48+
49+
unit_test.skip_initial_normalization = 1
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Building and Running the Code

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