Merge branch 'development' into remove_old_fortran_make

AMReX-Astro · Feb 13, 2025 · a7e65c4 · a7e65c4
2 parents d541ea3 + 5886c9c
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diff --git a/.github/workflows/dependencies/dependencies_hip.sh b/.github/workflows/dependencies/dependencies_hip.sh
@@ -33,7 +33,9 @@ sudo apt-key add rocm.gpg.key
 
 source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
 
-echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+VERSION=${1-6.3.2}
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${VERSION} ${UBUNTU_CODENAME} main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -53,16 +55,16 @@ sudo apt-get install -y --no-install-recommends \
     libnuma-dev     \
     libopenmpi-dev  \
     openmpi-bin     \
-    rocm-dev        \
-    roctracer-dev   \
-    rocprofiler-dev \
-    rocrand-dev     \
-    rocfft-dev      \
-    rocprim-dev     \
-    rocsparse-dev
+    rocm-dev${VERSION}        \
+    roctracer-dev${VERSION}   \
+    rocprofiler-dev${VERSION} \
+    rocrand-dev${VERSION}     \
+    rocfft-dev${VERSION}      \
+    rocprim-dev${VERSION}     \
+    rocsparse-dev${VERSION}
 
 # hiprand-dev is a new package that does not exist in old versions
-sudo apt-get install -y --no-install-recommends hiprand-dev || true
+sudo apt-get install -y --no-install-recommends hiprand-dev${VERSION} || true
 
 # activate
 #

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   hip-compile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
         with:
@@ -27,7 +27,7 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies/dependencies_hip.sh
+        run: .github/workflows/dependencies/dependencies_hip.sh 6.3.2
 
       - name: compile test_react with HIP (iso7)
         run: |

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

diff --git a/Docs/source/comprehensive_tests.rst b/Docs/source/comprehensive_tests.rst
@@ -1,3 +1,5 @@
+.. _sec:comprehensive_tests:
+
 ************************
 Comprehensive Unit Tests
 ************************

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

diff --git a/Docs/source/index.rst b/Docs/source/index.rst
@@ -92,6 +92,7 @@ system.
    :hidden:
 
    unit_tests
+   unit_test_runtime_parameters
    comprehensive_tests
    one_zone_tests
 

diff --git a/Docs/source/jac_cell.rst b/Docs/source/jac_cell.rst
@@ -38,14 +38,15 @@ The parameters that affect the thermodynamics are:
 
 * ``unit_test.temperature`` : the initial temperature
 
-* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
+The composition can be set either by specifying individual mass fractions
+or setting ``unit_test.uniform_xn`` as described in :ref:`sec:defining_unit_test_composition`.
 
-* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
+If the values don't sum to ``1`` initially, then the test will do a
+normalization.  This normalization can be disabled by setting:
 
-While the mass fractions can be set individually (using
-``unit_test.X1``, ``unit_test.X2``, ...), it is recommended to use
-``unit_test.uniform_xn=1`` to initialize all the mass fractions to be
-equal.
+::
+
+    unit_test.skip_initial_normalization = 1
 
 
 Building and Running the Code

diff --git a/Docs/source/one_zone_tests.rst b/Docs/source/one_zone_tests.rst
@@ -1,3 +1,5 @@
+.. _sec:one_zone_tests:
+
 **************
 One Zone Tests
 **************

diff --git a/Docs/source/unit_test_runtime_parameters.rst b/Docs/source/unit_test_runtime_parameters.rst
@@ -0,0 +1,58 @@
+***********************************
+Unit Test Common Runtime Parameters
+***********************************
+
+There are a number of runtime parameters that are common to all (or most) of the unit tests.
+These are defined in the top-level ``unit_test/_parameters`` file.
+
+Thermodynamics
+==============
+
+The equation of state enforces minimum density and temperatures, which must be set
+upon initialization.  These are controlled by the following runtime parameters:
+
+* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
+
+* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
+
+
+.. _sec:defining_unit_test_composition:
+
+Defining composition
+====================
+
+Most of the unit tests require a composition to be defined (for the
+initial mass-fractions, $X_k$).  There are a few ways this can be done
+(depending on the test).
+
+* One-zone (``*_cell``) tests (see :ref:`sec:one_zone_tests`) usually do one of:
+
+  * *Explicitly setting the individual mass fractions.*  This is
+    controlled by the parameters ``unit_test.X1``, ``unit_test.X2``, ..., ``unit_test.X35``,
+    e.g.:
+
+    ::
+
+        unit_test.X1 = 0.5
+        unit_test.X2 = 0.2
+        unit_test.X3 = 0.2
+        unit_test.X4 = 0.1
+
+    While many of the tests will renormalize the abundances, the user
+    should take care to ensure that the mass fractions sum to unity.
+
+  * *Setting the composition to be uniform.*  This is controlled by
+    ``unit_test.uniform_xn``.  If this is set to ``1``, then each mass fraction
+    is initialized to ``1 / NumSpec``.
+
+* Comprehensive tests (see :ref:`sec:comprehensive_tests`) need many different compositions, since they are creating a cube
+  of varying thermodynamic properties, and thus require a prescription
+  to create the composition.  This is done by setting ``unit_test.primary_species_1``,
+  ``unit_test.primary_species_2``, and ``unit_test.primary_species_3`` to one of the
+  *names* of the species in the network.
+
+  The function ``setup_composition()`` is then used to set limits on
+  the species abundances (it takes a parameter which is the index into
+  the cube of data that is being initialized) which is then used by
+  ``get_xn()`` to create the individual mass fractions.  Both of these
+  routines are contained in ``react_util.H``.
diff --git a/Make.Microphysics b/Make.Microphysics
@@ -64,17 +64,6 @@ ifeq ($(USE_REACT), TRUE)
   DEFINES += -DREACTIONS
 endif
 
-ifeq ($(USE_REACT_SPARSE_JACOBIAN), TRUE)
-  DEFINES += -DREACT_SPARSE_JACOBIAN
-
-  # The following is sometimes useful to turn on for debugging sparse J indices
-  # (if a get/set/scale is called with (row, col) not in the sparse J, stop)
-  # Otherwise, set/scale do nothing, and get returns 0.
-  ifeq ($(USE_SPARSE_STOP_ON_OOB), TRUE)
-    DEFINES += -DSPARSE_STOP_ON_OOB
-  endif
-endif
-
 
 #------------------------------------------------------------------------------
 # AMReX

diff --git a/unit_test/_parameters b/unit_test/_parameters
@@ -40,5 +40,12 @@ X33           real       0.0e0
 X34           real       0.0e0
 X35           real       0.0e0
 
+# do we set all of the mass fractions equal (to 1/NumSpec)?
 uniform_xn    bool        0
 
+# lowest temperature allowed in the EOS
+small_temp    real       1.e5
+
+# lowest density allowed in the EOS
+small_dens    real       1.e5
+
diff --git a/unit_test/burn_cell/_parameters b/unit_test/burn_cell/_parameters
@@ -1,8 +1,5 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 # the final time to integrate to
 tmax          real       1.e-2
 

diff --git a/unit_test/burn_cell_metal_chem/_parameters b/unit_test/burn_cell_metal_chem/_parameters
@@ -3,8 +3,8 @@
 run_prefix    string  "burn_cell_metal_chem"
 
 # floor values of temperature and density
-small_temp    real       1.e1
-small_dens    real       1.e-30
+small_temp    real       1.e1           100
+small_dens    real       1.e-30         100
 
 # the final time to integrate to
 tmax          real       1.e20

diff --git a/unit_test/burn_cell_primordial_chem/_parameters b/unit_test/burn_cell_primordial_chem/_parameters
@@ -3,8 +3,8 @@
 run_prefix    string  "burn_cell_primordial_chem"
 
 # floor values of temperature and density
-small_temp    real       1.e1
-small_dens    real       1.e-30
+small_temp    real       1.e1           100
+small_dens    real       1.e-30         100
 
 # the final time to integrate to
 tmax          real       1.e20

diff --git a/unit_test/burn_cell_sdc/_parameters b/unit_test/burn_cell_sdc/_parameters
@@ -1,8 +1,5 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 # the final time to integrate to
 tmax          real       1.e-2
 

diff --git a/unit_test/eos_cell/_parameters b/unit_test/eos_cell/_parameters
@@ -1,7 +1,4 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 density       real       1.e7
 temperature   real       3.e9
diff --git a/unit_test/jac_cell/_parameters b/unit_test/jac_cell/_parameters
@@ -1,8 +1,5 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 density       real       1.e7
 
 temperature   real       3.e9

diff --git a/unit_test/nse_net_cell/_parameters b/unit_test/nse_net_cell/_parameters
@@ -2,9 +2,6 @@
 
 run_prefix    string     ""
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 density       real       1.e7
 
 temperature   real       3.e9

diff --git a/unit_test/nse_net_cell/make_table/_parameters b/unit_test/nse_net_cell/make_table/_parameters
@@ -1,8 +1,5 @@
 @namespace: unit_test
 
-small_dens  real  1.e5
-small_temp  real  1.e5
-
 rho_min   real   1.e6
 rho_max   real   1.e10
 

diff --git a/unit_test/nse_table_cell/_parameters b/unit_test/nse_table_cell/_parameters
@@ -1,8 +1,5 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 density       real    1.23e9
 temperature   real    5.18e9
 ye            real    0.472

diff --git a/unit_test/part_func_cell/_parameters b/unit_test/part_func_cell/_parameters
@@ -1,7 +1,4 @@
 @namespace: unit_test
 
-small_temp    real       1.e5
-small_dens    real       1.e5
-
 temperature   real    5.e9
 
diff --git a/unit_test/test_aprox_rates/_parameters b/unit_test/test_aprox_rates/_parameters
@@ -6,6 +6,3 @@ temp_min      real       1.e6
 temp_max      real       1.e12
 
 metalicity_max  real     0.1e0
-
-small_temp    real        1.e4
-small_dens    real        1.e-4
diff --git a/unit_test/test_aprox_rates/aprox_rates_util.cpp b/unit_test/test_aprox_rates/aprox_rates_util.cpp
@@ -24,7 +24,8 @@ void aprox_rates_test(const Box& bx,
 
   const int ini56 = network_spec_index("nickel-56");
 
-  AMREX_PARALLEL_FOR_3D(bx, i, j, k,
+  amrex::ParallelFor(bx,
+  [=] AMREX_GPU_HOST_DEVICE (int i, int j, int k)
   {
 
     eos_extra_t eos_state;
@@ -444,7 +445,8 @@ void aprox_rates_extra_c12ag(const Box& bx,
 
     const int ini56 = network_spec_index("nickel-56");
 
-    AMREX_PARALLEL_FOR_3D(bx, i, j, k,
+    amrex::ParallelFor(bx,
+    [=] AMREX_GPU_HOST_DEVICE (int i, int j, int k)
     {
 
         eos_extra_t eos_state;

diff --git a/unit_test/test_conductivity/_parameters b/unit_test/test_conductivity/_parameters
@@ -6,6 +6,3 @@ temp_min      real       1.e6
 temp_max      real       1.e12
 
 metalicity_max  real     0.1e0
-
-small_temp    real        1.e4
-small_dens    real        1.e-4
diff --git a/unit_test/test_conductivity/conductivity_util.cpp b/unit_test/test_conductivity/conductivity_util.cpp
@@ -22,7 +22,8 @@ void cond_test_C(const amrex::Box& bx,
   const int ih1 = network_spec_index("hydrogen-1");
   const int ihe4 = network_spec_index("helium-4");
 
-  AMREX_PARALLEL_FOR_3D(bx, i, j, k,
+  amrex::ParallelFor(bx,
+  [=] AMREX_GPU_HOST_DEVICE (int i, int j, int k)
   {
 
     // set the composition -- approximately solar

diff --git a/unit_test/test_eos/_parameters b/unit_test/test_eos/_parameters
@@ -6,6 +6,3 @@ temp_min      real       1.e6
 temp_max      real       1.e12
 
 metalicity_max  real     0.1e0
-
-small_temp    real        1.e4
-small_dens    real        1.e-4