Merge branch 'master' into 2755_psyad_array_notn_bug

changelog

@@ -255,13 +255,17 @@
 	88) PR #2753 towards #2717. Adds DataNode.is_character method.
 
 	89) PR #2712 for #2711. Adds support for user-supplied Kernels that
-        operate on dofs (in the LFRic API).
+	operate on dofs (in the LFRic API).
 
 	99) PR #2685 for #2027. Improves datatype and shape inference.
 
 	100) PR #2694 for #2690. Extends the PSyData NaN-checking tooling to
 	perform value verification.
 
+	101) PR #2749 for #2311. Alters test-harness generation for the LFRic
+	API in PSyAD to base the generated test-code filenames on the name of
+	the supplied LFRic Algorithm file.
+
 release 2.5.0 14th of February 2024
 
 	1) PR #2199 for #2189. Fix bugs with missing maps in enter data

examples/psyad/eg2/Makefile

@@ -64,8 +64,8 @@ TL_KERNEL_TYPE = ${TL_KERNEL_NAME}_type
 ADJ_KERNEL_TYPE = $(subst tl_,adj_,${TL_KERNEL_TYPE})
 
 # The name of the file that will contain the generated test harness.
-HARNESS_X90_FILE = adjoint_test_mod.x90
-HARNESS_F90_FILE = adjoint_test_mod.F90
+HARNESS_X90_FILE = adjt_hydrostatic_alg_mod.x90
+HARNESS_F90_FILE = adjt_hydrostatic_alg_mod.F90
 
 GENERATED_FILES += adj_*.[fF]90 test_harness.exe \
                    *.x90 ${HARNESS_F90_FILE} psy.f90 *.mod *.o

examples/psyad/eg2/README.md

@@ -18,9 +18,9 @@ make
 
 This will construct the adjoint of the kernel (written to
 `adj_hydrostatic_kernel_mod.x90`) and a test harness in the form of LFRic
-Algorithm-layer code (`adjoint_test_mod.x90`). The Makefile then proceeds to
+Algorithm-layer code (`adjt_hydrostatic_alg_mod.x90`). The Makefile then proceeds to
 use PSyclone to process the test harness Algorithm code to generate algorithm
-(`adjoint_test_mod.F90`) and PSy layer (`psy.f90`) code.
+(`adjt_hydrostatic_alg_mod.F90`) and PSy layer (`psy.f90`) code.
 
 There is no `compile` target for this example because the generated code
 requires the full LFRic infrastructure. However, it is straightforward
@@ -36,9 +36,9 @@ psyad tl_hydrostatic_kernel_mod.F90 -a r_u exner theta moist_dyn_gas moist_dyn_t
 In this case, the adjoint of the tangent-linear kernel is written to
 `stdout`.
 
-## Using the generated test harness in the LFRic skeleton mini-app
+## Using the generated test harness in the LFRic core skeleton application
 
-These instructions assume that you have a local, compiled version of LFRic
+These instructions assume that you have a local, compiled version of LFRic core
 in `<lfric-root>` and that the directory containing this file is `<work-dir>`.
 
 1. Create the adjoint kernel and test harness code:
@@ -51,7 +51,7 @@ make
    test-harness code and the TL and adjoint kernels:
 ```sh
 cd <lfric-root>/miniapps/skeleton
-cp <work-dir>/adjoint_test_mod.x90 source/algorithm/.
+cp <work-dir>/adjt_hydrostatic_alg_mod.x90 source/algorithm/.
 cp <work-dir>/tl_hydrostatic_kernel_mod.F90 source/kernel/.
 cp <work-dir>/adj_hydrostatic_kernel_mod.F90 source/kernel/.
 ```
@@ -61,12 +61,12 @@ cp <work-dir>/adj_hydrostatic_kernel_mod.F90 source/kernel/.
    example - if the skeleton mini-app is modified on LFRic trunk then it will
    need to be updated):
 ```sh
-sed -e 's/  subroutine run()/  subroutine run()\n    use adjoint_test_mod, only: adjoint_test/' -e 's/call skeleton_alg(field_1)/call adjoint_test(mesh, chi, panel_id)/' source/driver/skeleton_driver_mod.f90 > new_driver.f90
+sed -e 's/  subroutine run()/  subroutine run()\n    use adjt_hydrostatic_alg_mod, only: adjt_hydrostatic_alg/' -e 's/call skeleton_alg(field_1)/call adjt_hydrostatic_alg(mesh, chi, panel_id)/' source/driver/skeleton_driver_mod.f90 > new_driver.f90
 mv source/driver/skeleton_driver_mod.f90{,.bak}
 mv new_driver.f90 source/driver/skeleton_driver_mod.f90
 ```
 
-4. Build the modified miniapp:
+4. Build the modified application:
 ```sh
 make clean
 make
@@ -75,7 +75,7 @@ make
 Note that at this stage you may get errors relating to the LFRic unit-test
 framework. These can be ignored.
 
-5. Run the miniapp:
+5. Run the application:
 ```sh
 cd example
 ../bin/skeleton ./configuration.nml

src/psyclone/psyad/domain/lfric/lfric_adjoint_harness.py

@@ -34,6 +34,7 @@
 # Authors R. W. Ford and A. R. Porter, STFC Daresbury Lab
 # Modified by J. Henrichs, Bureau of Meteorology
 # Modified by L. Turner, Met Office
+# Modified by T. Vockerodt, Met Office
 
 ''' Provides LFRic-specific PSyclone adjoint test-harness functionality. '''
 
@@ -522,11 +523,13 @@ def _lfric_log_write(sym_table, kernel, var1, var2):
 
 
 def generate_lfric_adjoint_harness(tl_psyir, coord_arg_idx=None,
-                                   panel_id_arg_idx=None):
+                                   panel_id_arg_idx=None,
+                                   test_name="adjoint_test"):
     '''
     Constructs and returns the PSyIR for a Container and Routine that
     implements a test harness for the adjoint of the supplied tangent-linear
-    kernel.
+    kernel. The base name to use for the Container and Routine is given by
+    the test_name argument.
 
     :param tl_psyir: the PSyIR of an LFRic module defining a \
                      tangent-linear kernel.
@@ -535,6 +538,8 @@ def generate_lfric_adjoint_harness(tl_psyir, coord_arg_idx=None,
         field in the list of arguments in the kernel metadata (if present).
     :param Optional[int] panel_id_arg_idx: 1-indexed position of the panel-id \
         field in the list of arguments in the kernel metadata (if present).
+    :param Optional[str] test_name: Name of the adjoint test algorithm \
+        (if present).
 
     :returns: PSyIR of an Algorithm that tests the adjoint of the supplied \
               LFRic TL kernel.
@@ -555,7 +560,8 @@ def generate_lfric_adjoint_harness(tl_psyir, coord_arg_idx=None,
             f"does not have a Container node:\n{tl_psyir.view(colour=False)}")
 
     lfalg = LFRicAlg()
-    container = lfalg.create_alg_routine("adjoint_test")
+    # Variable test_name is validated inside create_alg_routine.
+    container = lfalg.create_alg_routine(test_name)
     routine = container.walk(Routine)[0]
     table = routine.symbol_table
 

src/psyclone/psyad/main.py

@@ -33,13 +33,16 @@
 # -----------------------------------------------------------------------------
 # Authors: R. W. Ford and A. R. Porter, STFC Daresbury Lab
 # Modified by J. Henrichs, Bureau of Meteorology
+#             T. Vockerodt, Met Office
 
 '''Top-level driver functions for PSyAD : the PSyclone Adjoint
 support. Transforms an LFRic tangent linear kernel to its adjoint.
 
 '''
 import argparse
 import logging
+import os
+import re
 import sys
 
 from psyclone.configuration import Config, LFRIC_API_NAMES
@@ -97,7 +100,7 @@ def msg():
                         help='the position of the panel-ID field in the '
                         'meta_args list of arguments in the kernel metadata '
                         '(LFRic only)')
-    parser.add_argument('-otest',
+    parser.add_argument('-otest', default=None,
                         help='filename for the unit test (implies -t)',
                         dest='test_filename')
     parser.add_argument('-oad', help='filename for the transformed code')
@@ -128,6 +131,22 @@ def msg():
                          "the 'lfric' API.")
             sys.exit(1)
 
+    # Processing test filename
+    test_name = "adjoint_test"
+    if generate_test:
+        if args.api in LFRIC_API_NAMES:
+            filename_standard = "adjt_.+_alg_mod.[Xx]90|atlt_.+_alg_mod.[Xx]90"
+            regex_search = re.search(filename_standard, args.test_filename)
+            if regex_search is None:
+                logger.error("Filename '%s' with 'lfric' API "
+                             "must be of the form "
+                             "<path>/adjt_<name>_alg_mod.[Xx]90 or "
+                             "<path>/atlt_<name>_alg_mod.[Xx]90.",
+                             args.test_filename)
+                sys.exit(1)
+            # At this stage filename should be valid, so we take the base name
+            test_name = os.path.basename(args.test_filename).split("_mod.")[0]
+
     # TL Fortran code
     filename = args.filename
     logger.info("Reading kernel file %s", filename)
@@ -145,7 +164,8 @@ def msg():
             tl_fortran_str, args.active, api=args.api,
             coord_arg_index=args.coord_arg,
             panel_id_arg_index=args.panel_id_arg,
-            create_test=generate_test)
+            create_test=generate_test,
+            test_name=test_name)
     except TangentLinearError as info:
         print(str(info.value))
         sys.exit(1)

src/psyclone/psyad/tl2ad.py

@@ -32,6 +32,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 # -----------------------------------------------------------------------------
 # Authors R. W. Ford, A. R. Porter and S. Siso, STFC Daresbury Lab
+# Modified by T. Vockerodt, Met Office
 
 '''The implementation of PSyAD : the PSyclone Adjoint
 support. Transforms an LFRic tangent linear kernel to its adjoint.
@@ -66,7 +67,7 @@
 
 
 def generate_adjoint_str(tl_fortran_str, active_variables,
-                         api=None, create_test=False,
+                         api=None, create_test=False, test_name="adjoint_test",
                          coord_arg_index=None, panel_id_arg_index=None):
     '''Takes a tangent-linear kernel encoded as a string as input
     and returns its adjoint encoded as a string along with (if requested)
@@ -78,6 +79,8 @@ def generate_adjoint_str(tl_fortran_str, active_variables,
     :param Optional[str] api: the PSyclone API in use, if any.
     :param Optional[bool] create_test: whether or not to create test code for
         the adjoint kernel.
+    :param Optional[str] test_name: base name to use for the file containing
+        the created adjoint test.
     :param Optional[int] coord_arg_index: the (1-based) index of the kernel
         argument holding the mesh coordinates (if any). Only applies to the
         LFRic API.
@@ -139,7 +142,8 @@ def generate_adjoint_str(tl_fortran_str, active_variables,
         if create_test:
             test_psyir = generate_lfric_adjoint_harness(tl_psyir,
                                                         coord_arg_index,
-                                                        panel_id_arg_index)
+                                                        panel_id_arg_index,
+                                                        test_name)
     else:
         raise NotImplementedError(
             f"PSyAD only supports generic routines/programs or LFRic "

src/psyclone/tests/psyad/domain/lfric/test_lfric_adjoint_harness.py

@@ -572,11 +572,12 @@ def test_generate_lfric_adjoint_harness(fortran_reader, fortran_writer):
     '''Test that the generate_lfric_adjoint_harness() function generates the
     expected test-harness code.'''
     tl_psyir = fortran_reader.psyir_from_source(TL_CODE)
-    psyir = generate_lfric_adjoint_harness(tl_psyir)
+    adjt_name = "adjoint_test_alg"
+    psyir = generate_lfric_adjoint_harness(tl_psyir, test_name=adjt_name)
     gen = fortran_writer(psyir).lower()
     assert "use finite_element_config_mod, only : element_order" in gen
-    assert "module adjoint_test_mod" in gen
-    assert "subroutine adjoint_test(mesh, chi, panel_id)" in gen
+    assert "module adjoint_test_alg_mod" in gen
+    assert "subroutine adjoint_test_alg(mesh, chi, panel_id)" in gen
     # We should have a field, a copy of that field and an inner-product value
     # for that field.
     assert ("    real(kind=r_def) :: ascalar\n"

src/psyclone/tests/psyad/main_test.py

@@ -33,6 +33,7 @@
 # -----------------------------------------------------------------------------
 # Authors: R. W. Ford, A. R. Porter and N. Nobre, STFC Daresbury Lab
 # Modified by J. Henrichs, Bureau of Meteorology
+# Modified by T. Vockerodt, Met Office
 
 '''A module to perform pytest tests on the code in the main.py file
 within the psyad directory.
@@ -62,6 +63,59 @@
     "end module my_mod\n"
 )
 
+TEST_LFRIC_KERNEL = '''module tl_foo_kernel_mod
+
+  use argument_mod,      only : arg_type, func_type, &
+                                GH_FIELD, GH_REAL,   &
+                                GH_INC, CELL_COLUMN
+  use constants_mod,     only : r_def, i_def
+  use fs_continuity_mod, only : W2
+  use kernel_mod,        only : kernel_type
+
+  implicit none
+
+  private
+
+  type, public, extends(kernel_type) :: tl_foo_kernel_type
+    private
+    type(arg_type) :: meta_args(1) = (/            &
+         arg_type(GH_FIELD, GH_REAL, GH_INC,  W2)  &
+         /)
+    integer :: operates_on = CELL_COLUMN
+  contains
+    procedure, nopass :: tl_foo_kernel_code
+  end type
+
+  public :: tl_foo_kernel_code
+
+contains
+
+subroutine tl_foo_kernel_code(nlayers,           &
+                              field,             &
+                              ndf2, undf2, map2  &
+                              )
+
+  implicit none
+
+  ! Arguments
+  integer(kind=i_def),                      intent(in)    :: nlayers
+  integer(kind=i_def),                      intent(in)    :: ndf2, undf2
+  integer(kind=i_def), dimension(ndf2),     intent(in)    :: map2
+  real(kind=r_def), dimension(undf2),       intent(inout) :: field
+
+  ! Internal variables
+  integer(kind=i_def)            :: df2, k
+
+  do k = 0, nlayers-1
+    do df2 = 1,ndf2
+      field( map2(df2)+k ) = 0.0_r_def
+    end do
+  end do
+
+end subroutine tl_foo_kernel_code
+
+end module tl_foo_kernel_mod'''
+
 EXPECTED_HARNESS_CODE = '''program adj_test
   use my_mod, only : kern
   use adj_my_mod, only : adj_kern
@@ -512,3 +566,43 @@ def test_main_otest_verbose(tmpdir, caplog):
                      "github actions.")
     assert "Writing test harness for adjoint kernel to file" in caplog.text
     assert "/harness.f90" in caplog.text
+
+
+def test_main_otest_lfric(tmpdir, capsys):
+    ''' Test that the -otest option combined with LFRic API
+    generates the expected adjoint test. '''
+    filename_in = str(tmpdir.join("tl_foo_kernel_mod.f90"))
+    filename_out = str(tmpdir.join("atl_foo_kernel_mod.f90"))
+    harness_out = str(tmpdir.join("atlt_foo_alg_mod.x90"))
+    with open(filename_in, "w", encoding='utf-8') as my_file:
+        my_file.write(TEST_LFRIC_KERNEL)
+    main([filename_in, "-a", "field", "-api", "lfric", "-oad", filename_out,
+          "-otest", harness_out])
+    output, error = capsys.readouterr()
+    assert error == ""
+    assert output == ""
+    with open(harness_out, 'r', encoding='utf-8') as my_file:
+        data = my_file.read()
+    assert "module atlt_foo_alg_mod" in data.lower()
+    assert "subroutine atlt_foo_alg" in data.lower()
+
+
+def test_main_otest_lfric_error_name(capsys, caplog):
+    ''' Test that a bad -otest option combined with LFRic API
+    generates the expected error. '''
+    harness_out = "some/path/foo_alg_mod.x90"
+    logger = logging.getLogger("psyclone.psyad.main")
+    logger.propagate = True
+    with caplog.at_level(logging.ERROR, "psyclone.psyad.main"):
+        with pytest.raises(SystemExit) as err:
+            main(["input.f90", "-a", "field", "-api", "lfric", "-oad",
+                  "output.f90", "-otest", harness_out])
+    assert str(err.value) == "1"
+    x_fail_str = (rf"Filename '{harness_out}' with 'lfric' API "
+                  "must be of the form "
+                  "<path>/adjt_<name>_alg_mod.[Xx]90 or "
+                  "<path>/atlt_<name>_alg_mod.[Xx]90.")
+    assert x_fail_str in caplog.text
+    output, error = capsys.readouterr()
+    assert error == ""
+    assert output == ""

src/psyclone/tests/psyad/tl2ad_test.py

@@ -32,6 +32,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 # -----------------------------------------------------------------------------
 # Authors R. W. Ford, A. R. Porter and S. Siso, STFC Daresbury Lab
+# Modified by T. Vockerodt, Met Office
 
 '''A module to perform pytest tests on the code in the tl2ad.py file
 within the psyad directory.
@@ -137,10 +138,14 @@ def test_generate_adjoint_str_lfric_api():
     testkern = os.path.join(LFRIC_TEST_FILES_DIR, "tl_testkern_mod.F90")
     with open(testkern, mode="r", encoding="utf-8") as kfile:
         tl_code = kfile.read()
-    result, _ = generate_adjoint_str(tl_code,
+    adj, test = generate_adjoint_str(tl_code,
                                      ["xi", "u", "res_dot_product", "curl_u"],
-                                     api="lfric")
-    assert "subroutine adj_testkern_code" in result.lower()
+                                     api="lfric",
+                                     create_test=True,
+                                     test_name="atlt_testkern")
+    assert "subroutine adj_testkern_code" in adj.lower()
+    assert "module atlt_testkern_mod" in test.lower()
+    assert "subroutine atlt_testkern" in test.lower()
 
 
 def test_generate_adjoint_str_function():