Merge remote-tracking branch 'origin/master' into nemo_v5

.github/workflows/compilation.yml

@@ -51,14 +51,14 @@ on:
   push
 
 env:
-  CUDA_VERSION: 12.6.3
+  CUDA_VERSION: 12.8.0
   GFORTRAN_VERSION: 14.2.0
   HDF5_VERSION: 1.14.5
   NETCDF_C_VERSION: 4.9.2
   NETCDF_FORTRAN_VERSION: 4.6.1
-  NVFORTRAN_VERSION: 24.11
+  NVFORTRAN_VERSION: 25.1
   OPENMPI_VERSION: 5.0.6
-  PYTHON_VERSION: 3.13.0
+  PYTHON_VERSION: 3.13.2
 
 jobs:
   run_if_on_mirror:

.github/workflows/lfric_test.yml

@@ -47,7 +47,7 @@ jobs:
     runs-on: self-hosted
     env:
       LFRIC_APPS_REV: 3269
-      PYTHON_VERSION: 3.13.0
+      PYTHON_VERSION: 3.13.2
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/nemo_tests.yml

@@ -51,8 +51,8 @@ jobs:
       NETCDF_FORTRAN_VERSION: 4.6.1
       NVFORTRAN_VERSION: 23.7
       ONEAPI_VERSION: 2024.2.1
-      PERL_VERSION: 5.40.0
-      PYTHON_VERSION: 3.13.0
+      PERL_VERSION: 5.40.1
+      PYTHON_VERSION: 3.13.2
 
     steps:
     - uses: actions/checkout@v3

changelog

@@ -47,6 +47,20 @@
 	16) PR #2857 for 2854. Excludes character assignments from ACC KERNELS
 	regions to avoid issues in NEMO.
 
+	17) PR #2829 for #2826. Adds a --config command-line argument to the
+	PSyAD script (to replicate that for psyclone).
+
+	18) PR #2280 for #2723. Add support for depencency analysis involving
+	array ranges.
+
+	19) PR #2885. Update integration test dependencies.
+
+	20) PR #2799 for #2779. Implement split finite-element order for
+	function spaces in the LFRic API and update Adjoint tests to use it.
+
+	21) PR #2883 for #2875. Fix issues cannonicalising WHEREs with elemental
+	functions.
+
 release 3.0.0 6th of December 2024
 
 	1) PR #2477 for #2463. Add support for Fortran Namelist statements.

doc/psyad/user_guide/implementation.rst

@@ -447,7 +447,7 @@ tangent-linear code it is first transformed into equivalent inline
 code before the code is transformed to its adjoint form. The PSyIR
 ``DotProduct2CodeTrans`` or ``Matmul2CodeTrans`` transformations are
 used to perform these manipulations. See the
-:ref:`user_guide:available_trans` section of the user guide for more
+:ref:`user_guide:sec_transformations_available` section of the user guide for more
 information on these transformations.
 
 .. note:: At the moment all ``dot_product`` and ``matmul`` intrinsics

doc/psyad/user_guide/psyad_command.rst

@@ -62,7 +62,7 @@ by the command:
 .. parsed-literal::
 		
   >>> psyad -h
-    usage: psyad [-h] [-oad OAD] [-v] [-t] [-api API] [-coord-arg COORD_ARG] [-panel-id-arg PANEL_ID_ARG] [-otest TEST_FILENAME] -a ACTIVE [ACTIVE ...] -- filename
+    usage: psyad [-h] [-oad OAD] [-c CONFIG] [-v] [-t] [-api API] [-coord-arg COORD_ARG] [-panel-id-arg PANEL_ID_ARG] [-otest TEST_FILENAME] -a ACTIVE [ACTIVE ...] -- filename
 
     Run the PSyclone adjoint code generator on a tangent-linear kernel file
 
@@ -73,6 +73,8 @@ by the command:
       -h, --help            show this help message and exit
       -a ACTIVE [ACTIVE ...], --active ACTIVE [ACTIVE ...]
                             name of active variables
+      -c CONFIG, --config CONFIG
+                            config file with PSyclone specific options
       -v, --verbose         increase the verbosity of the output
       -t, --gen-test        generate a standalone unit test for the adjoint code
       -api API              the PSyclone API that the TL kernel conforms to (if any)
@@ -207,3 +209,11 @@ internally you can specify the ``-v`` option. For example
 ::
 
    > psyad -a var1 var2 -oad ad_kern.f90 -v tl_kern.f90
+
+Configuration Options
+---------------------
+
+By default PSyAD uses the same configuration file used by PSyclone. To
+use a custom configuration file use the ``--config`` command-line option.
+Further documentation of the configuration options can be found in
+:ref:`user_guide:configuration`.

doc/user_guide/psyclone_kern.rst

@@ -32,7 +32,7 @@
 .. POSSIBILITY OF SUCH DAMAGE.
 .. -----------------------------------------------------------------------------
 .. Written by R. W. Ford and A. R. Porter, STFC Daresbury Lab
-.. Modified by I. Kavcic and L. Turner, Met Office
+.. Modified by I. Kavcic, L. Turner and J. Dendy, Met Office
 
 PSyclone Kernel Tools
 =====================
@@ -558,14 +558,15 @@ gives the following algorithm layer code:
       use mesh_mod, only : mesh_type
       use simple_mod, only : simple_type
       use constants_mod, only : i_def, r_def
-      integer(kind=i_def), parameter :: element_order = 1_i_def
+      integer(kind=i_def), parameter :: element_order_h = 1_i_def
+      integer(kind=i_def), parameter :: element_order_v = 1_i_def
       type(mesh_type), pointer, intent(in) :: mesh
       type(field_type), dimension(3), intent(in), optional :: chi
       type(field_type), intent(in), optional :: panel_id
       TYPE(function_space_type), POINTER :: vector_space_w1_ptr
       type(field_type) :: field_1
 
-      vector_space_w1_ptr => function_space_collection % get_fs(mesh, element_order, w1)
+      vector_space_w1_ptr => function_space_collection % get_fs(mesh, element_order_h, element_order_v, w1)
       call field_1 % initialise(vector_space=vector_space_w1_ptr, name='field_1')
       call invoke(setval_c(field_1, 1.0_r_def), simple_type(field_1))
 

doc/user_guide/transformations.rst

@@ -34,6 +34,7 @@
 .. Written by: R. W. Ford, A. R. Porter and S. Siso, STFC Daresbury Lab
 ..             A. B. G. Chalk and N. Nobre, STFC Daresbury Lab
 ..             I. Kavcic, Met Office
+..             J. Dendy, Met Office
 
 .. _transformations:
 
@@ -216,7 +217,7 @@ process, optional parameters for the transformation are also
 provided this way. A simple example::
 
     kctrans = Dynamo0p3KernelConstTrans()
-    kctrans.apply(kernel, {"element_order": 0, "quadrature": True})
+    kctrans.apply(kernel, {"element_order_h": 0, "element_order_v": 0, "quadrature": True})
 
 The same ``options`` dictionary will be used when calling ``validate``.
 
@@ -287,19 +288,19 @@ can be found in the API-specific sections).
 .. autoclass:: psyclone.psyir.transformations.AllArrayAccess2LoopTrans
     :members: apply
     :noindex:
-  
+
 ####
 
 .. autoclass:: psyclone.psyir.transformations.ArrayAccess2LoopTrans
     :members: apply
     :noindex:
-  
+
 ####
 
 .. autoclass:: psyclone.psyir.transformations.ArrayAssignment2LoopsTrans
     :members: apply
     :noindex:
-  
+
 ####
 
 .. autoclass:: psyclone.psyir.transformations.ChunkLoopTrans
@@ -802,7 +803,7 @@ PSyclone supports OpenMP Tasking, through the `OMPTaskloopTrans` and
 transformations can be applied to loops, whilst the `OMPTaskwaitTrans`
 operator is applied to an OpenMP Parallel Region, and computes the dependencies
 caused by Taskloops, and adds OpenMP Taskwait statements to satisfy those
-dependencies. An example of using OpenMP tasking is available in 
+dependencies. An example of using OpenMP tasking is available in
 `PSyclone/examples/nemo/eg1/openmp_taskloop_trans.py`.
 
 OpenCL

examples/lfric/code/gw_mixed_schur_preconditioner_alg_mod.x90

@@ -38,6 +38,7 @@
 ! -----------------------------------------------------------------------------
 ! Modified by I. Kavcic, Met Office
 ! Modified by R. W. Ford, STFC Daresbury Lab
+! Modified by J. Dendy, Met Office
 
 !>@brief Preconditioner for the gravity-wave system
 module gw_mixed_schur_preconditioner_alg_mod
@@ -125,7 +126,6 @@ contains
 						     result(self)
 
     use function_space_mod,            only: function_space_type
-    use finite_element_config_mod,     only: element_order
     use quadrature_xyoz_mod,           only: quadrature_xyoz_type
     use quadrature_rule_gaussian_mod,  only: quadrature_rule_gaussian_type
     use matrix_vector_kernel_mod,      only: matrix_vector_kernel_type

examples/lfric/eg13/kernel_constants.py

@@ -32,6 +32,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 # -----------------------------------------------------------------------------
 # Authors: R. W. Ford, N. Nobre and S. Siso, STFC Daresbury Lab
+# Modified by: J. Dendy, Met Office
 
 
 '''An example PSyclone transformation script which makes ndofs, nqp*
@@ -62,10 +63,11 @@
 # associated kernel value constant (rather than passing it in by
 # argument).
 NUMBER_OF_LAYERS = 20
-# The element order to use when modifying a kernel to make the
+# The element orders to use when modifying a kernel to make the
 # associated degrees of freedom values constant (rather than passing
 # them in by argument).
-ELEMENT_ORDER = 0
+ELEMENT_ORDER_H = 0
+ELEMENT_ORDER_V = 0
 # Whether or not to make the number of quadrature points constant in a
 # kernel (rather than passing them in by argument).
 CONSTANT_QUADRATURE = True
@@ -86,7 +88,8 @@ def trans(psyir):
         try:
             const_trans.apply(kernel,
                               {"number_of_layers": NUMBER_OF_LAYERS,
-                               "element_order": ELEMENT_ORDER,
+                               "element_order_h": ELEMENT_ORDER_H,
+                               "element_order_v": ELEMENT_ORDER_V,
                                "quadrature": CONSTANT_QUADRATURE})
         except TransformationError:
             print(f"    Failed to modify kernel '{kernel.name}'")

examples/lfric/eg14/main.x90

@@ -30,6 +30,7 @@
 ! -----------------------------------------------------------------------------
 ! Author: J. Henrichs, Bureau of Meteorology
 ! Modifications: A. R. Porter, STFC Daresbury Laboratory
+!                J. Dendy, Met Office
 
 program main
 
@@ -57,7 +58,8 @@ program main
     procedure (partitioner_interface), pointer :: partitioner_ptr
     type(field_type)                           :: field1, field2
     integer(kind=i_def)                        :: lfric_fs = W0   ! W0
-    integer(kind=i_def)                        :: element_order = 1
+    integer(kind=i_def)                        :: element_order_h = 1
+    integer(kind=i_def)                        :: element_order_v = 1
     integer(kind=i_def)                        :: ndata_sz, istp
     real(kind=r_def) :: chksm
 
@@ -84,9 +86,10 @@ program main
     mesh = mesh_type(global_mesh_ptr, partition, extrusion_ptr)
     write (*,*) "Mesh has", mesh%get_nlayers(), "layers."
     ndata_sz = 1
-    vector_space = function_space_type( mesh,          &
-                                        element_order, &
-                                        lfric_fs,      &
+    vector_space = function_space_type( mesh,            &
+                                        element_order_h, &
+                                        element_order_v, &
+                                        lfric_fs,        &
                                         ndata_sz)
     vector_space_ptr => vector_space
     call field1%initialise( vector_space = vector_space_ptr, name="field1" )

examples/lfric/eg17/full_example/README.md

@@ -9,7 +9,7 @@ The following steps are required for this (using simplified code examples):
     ```fortran
     global_mesh = global_mesh_type()
     ```
-   
+
 2) A 1x1 planar partition for one process is created:
     ```fortran
     partitioner_ptr => partitioner_planar
@@ -34,9 +34,10 @@ The following steps are required for this (using simplified code examples):
 
 5) Create a function/vector space:
     ```fortran
-    vector_space = function_space_type( mesh,          &
-                                        element_order, &
-                                        lfric_fs,      &
+    vector_space = function_space_type( mesh,            &
+                                        element_order_h, &
+                                        element_order_v, &
+                                        lfric_fs,        &
                                         ndata_sz)
     ```
 

examples/lfric/eg17/full_example/main.x90

@@ -30,6 +30,7 @@
 ! -----------------------------------------------------------------------------
 ! Author: J. Henrichs, Bureau of Meteorology
 ! Modifications: A. R. Porter, STFC Daresbury Laboratory
+!                J. Dendy, Met Office
 
 program main
 
@@ -57,7 +58,8 @@ program main
     procedure (partitioner_interface), pointer :: partitioner_ptr
     type(field_type)                           :: field1, field2
     integer(kind=i_def)                        :: lfric_fs = W0   ! W0
-    integer(kind=i_def)                        :: element_order = 1
+    integer(kind=i_def)                        :: element_order_h = 1
+    integer(kind=i_def)                        :: element_order_v = 1
     integer(kind=i_def)                        :: ndata_sz
 
     ! Use the unit-testing constructor:
@@ -81,9 +83,10 @@ program main
     mesh = mesh_type(global_mesh_ptr, partition, extrusion_ptr)
     write (*,*) "Mesh has", mesh%get_nlayers(), "layers."
     ndata_sz = 1
-    vector_space = function_space_type( mesh,          &
-                                        element_order, &
-                                        lfric_fs,      &
+    vector_space = function_space_type( mesh,            &
+                                        element_order_h, &
+                                        element_order_v, &
+                                        lfric_fs,        &
                                         ndata_sz)
     vector_space_ptr => vector_space
     call field1%initialise( vector_space = vector_space_ptr, name="field1" )

examples/lfric/eg17/full_example_extract/main.X90

@@ -30,6 +30,7 @@
 ! -----------------------------------------------------------------------------
 ! Author: J. Henrichs, Bureau of Meteorology
 ! Modifications: A. R. Porter, STFC Daresbury Laboratory
+!                J. Dendy, Met Office
 
 program main
     !> This program is a simple LFRic program that contains two invokes,
@@ -70,7 +71,8 @@ program main
     type(field_type)                           :: field1, field2
     type(field_type)                           :: chi(3)
     integer(kind=i_def)                        :: lfric_fs = W0   ! W0
-    integer(kind=i_def)                        :: element_order = 1
+    integer(kind=i_def)                        :: element_order_h = 1
+    integer(kind=i_def)                        :: element_order_v = 1
     integer(kind=i_def)                        :: ndata_sz
     real(kind=r_def)                           :: one
     logical(kind=l_def)                        :: some_logical
@@ -101,9 +103,10 @@ program main
     mesh = mesh_type(global_mesh_ptr, partition, extrusion_ptr)
     write (*,*) "Mesh has", mesh%get_nlayers(), "layers."
     ndata_sz = 1
-    vector_space = function_space_type( mesh,          &
-                                        element_order, &
-                                        lfric_fs,      &
+    vector_space = function_space_type( mesh,            &
+                                        element_order_h, &
+                                        element_order_v, &
+                                        lfric_fs,        &
                                         ndata_sz)
     vector_space_ptr => vector_space
     do i=1, 3

examples/lfric/eg17/full_example_netcdf/README.md

@@ -9,7 +9,7 @@ steps are required for this (using simplified code examples):
     ```fortran
     global_mesh = global_mesh_type("mesh_BiP128x16-400x100.nc", "dynamics")
     ```
-   
+
 2) A 1x1 planar partition for one process is created:
     ```fortran
     partitioner_ptr => partitioner_planar
@@ -34,9 +34,10 @@ steps are required for this (using simplified code examples):
 
 5) Create a function/vector space:
     ```fortran
-    vector_space = function_space_type( mesh,          &
-                                        element_order, &
-                                        lfric_fs,      &
+    vector_space = function_space_type( mesh,            &
+                                        element_order_h, &
+                                        element_order_v, &
+                                        lfric_fs,        &
                                         ndata_sz)
     ```
 
@@ -61,7 +62,7 @@ steps are required for this (using simplified code examples):
 
 ## Compilation
 
-A simple makefile is provided to compile the example. It needs 
+A simple makefile is provided to compile the example. It needs
 a full installation of NetCDF, since it is using ``nf-config`` to
 query the required compiler and linker flags, and the
 infrastructure library ``liblfric_netcdf.a`` provided in