Merge branch 'master' into 2588_get_routine_psyir

.github/linkspector.yml

@@ -0,0 +1,13 @@
+dirs:
+  - .
+useGitIgnore: true
+ignorePatterns:
+  - pattern: '^https://mybinder.org/v2/gh/stfc/psyclone'
+replacementPatterns:
+  - pattern: '^https:\/\/(psyclone.*\.readthedocs\.io\/en)\/stable$'
+    replacement: 'https://$1/latest'
+aliveStatusCodes:
+  - 200
+  - 401
+  - 502
+  - 503

.github/workflows/linkcheck.yml

@@ -0,0 +1,16 @@
+name: Linkspector
+on: [pull_request]
+jobs:
+  check-links:
+    if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
+    name: Run linkspector
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run linkspector
+        uses: umbrelladocs/action-linkspector@v1
+        with:
+          github_token: ${{ secrets.github_token }}
+          reporter: github-pr-check
+          fail_on_error: true
+          config_file: '.github/linkspector.yml'

.github/workflows/nemo_tests.yml

@@ -82,6 +82,28 @@ jobs:
         cd lib/profiling/nvidia/
         F90=nvfortran make
 
+    # PSyclone passthrough for 5.0-beta of NEMO.
+    - name: NEMO 5.0 beta passthrough without optimisation
+      run: |
+        . .runner_venv/bin/activate
+        export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
+        # PSYCLONE_HOME has `/bin` appended to it by the build system.
+        export PSYCLONE_HOME=${PWD}/.runner_venv
+        export NEMO_DIR=${HOME}/NEMOv5
+        cd $NEMO_DIR
+        module load nvidia-hpcsdk/${NVFORTRAN_VERSION}
+        module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION}
+        module load perl/${PERL_VERSION}
+        # We compile at -O1 to permit comparison of the results. (N.B. this test
+        # passes at -O3 with the Intel ifx compiler.)
+        ./makenemo -r BENCH -m linux_nvidia_O1 -n BENCH_PASSTHROUGH -p passthrough del_key "key_xios key_iomput key_top" add_key "key_nosignedzero" clean -y
+        ./makenemo -r BENCH -m linux_nvidia_O1 -n BENCH_PASSTHROUGH -p passthrough del_key "key_xios key_iomput key_top" add_key "key_nosignedzero" -j 4
+        cd $NEMO_DIR/tests/BENCH_PASSTHROUGH/EXP00
+        mpirun -np 4 ./nemo
+        diff run.stat ${PSYCLONE_NEMO_DIR}/KGOs/run.stat.bench.orca2.4mpi.10steps
+        export VAR_TIME=$(awk '/ step /{print $3}' timing.output | head -n 1 | sed -e 's/s//')
+        echo "Time-stepping duration = " $VAR_TIME
+
     # PSyclone passthrough for MetOffice NEMO
     - name: NEMO MetOffice Passthrough
       run: |

.github/workflows/python-package.yml

@@ -52,26 +52,17 @@ on:
   workflow_dispatch:
 
 jobs:
-  markdown-link-check:
-    if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
-    # Check all markdown files for dead links. See the 'mlc_config.json'
-    # file in the project root directory for configuration.
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@master
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        use-verbose-mode: 'yes'
-        config-file: '.github/workflows/mlc_config.json'
   sphinx-link-check:
     if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
     # Check all Sphinx documentation for dead links.
     runs-on: ubuntu-latest
     env:
       GITHUB_PR_NUMBER: ${{ github.event.number }}
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
     - run: sudo apt-get install -y graphviz doxygen
     - run: python -m pip install --upgrade pip
     - run: pip install .[doc]
@@ -89,8 +80,10 @@ jobs:
     # Check doctests of developer's guide
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
     - run: python -m pip install --upgrade pip
     - run: pip install .[doc]
     # Sphinx since version 7.2 (7.2.0/1/2) aborts with
@@ -108,7 +101,7 @@ jobs:
       matrix:
         python-version: [3.7, 3.8, 3.12]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         # This is required to get the commit history for merge commits for
@@ -146,7 +139,8 @@ jobs:
     - name: Run tutorials
       run: |
         ( make -C tutorial/practicals transform > /dev/null )
-        ( make -C tutorial/notebooks notebook )
+        # Jupyter notebooks are out-of-date
+        # ( make -C tutorial/notebooks notebook )
     - name: Test with pytest
       if: ${{ !(matrix.python-version == 3.8) }}
       run: |

README.md

@@ -53,6 +53,7 @@ cloning this repository and using:
 For more information about the installation process see
 [this section of the User Guide](https://psyclone.readthedocs.io/en/latest/system_specific_setup.html).
 
+<!---  TODO #2627
 # Try it on Binder #
 
 Some of the examples are available as Jupyter notebooks. These may
@@ -62,12 +63,11 @@ software. This can take several minutes. You can track its progress
 by clicking the 'show' link next to the 'Build logs' heading.)
 
  * [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stfc/psyclone/master?filepath=tutorial%2Fnotebooks%2Fintroduction.ipynb) The **PSyclone Tutorial**. Note that we currently recommend following the more up-to-date README files under the `tutorials/practicals` directory.
- * [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stfc/psyclone/master?filepath=examples%2Fnemo%2Feg4%2Fcopy_stencil.ipynb) Uses PSyclone's NEMO API to process some simple Fortran code, display the resulting PSyIR and then re-generate Fortran.
 
  * [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stfc/psyclone/master?filepath=examples%2Fgocean%2Feg1%2Fopenmp.ipynb) Uses PSyclone's GOcean API to process example code that conforms to the PSyKAl separation of concerns. Transformations are applied in order to fuse various loops before parallelising the result with OpenMP.
  
  * [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stfc/psyclone/master?filepath=examples%2Fgocean%2Feg1%2Fdag.ipynb) demonstrates the generation of a DAG for the PSy layer of the previous example.
-
+--->
 
 # Structure #
 

changelog

@@ -107,6 +107,55 @@
 
 	39) PR #2564 for $2462. Generalise ModuleManager.
 
+	40) PR #2598 towards #2543. Refresh the PSyKAl-related documentation
+	in both the User and Developer Guides.
+
+	41) PR #2611. Update Integration tests nvhpc mpi library path. 
+
+	42) PR #2614 towards #2604. Fixes broken links to the docs in the
+	various tutorial READMEs.
+
+	43) PR #2587 for #1989. Improves the statistics produced by the
+	generated PSyKE driver code.
+
+	44) #PR #2602 for #1596. Exclude assumed-size variable references from
+	the ACCKernels regions.
+
+	45) PR #2603 for #1841. Refactors the ArrayRange2Loop transformation
+	(merging in functionality from the NEMO-specific version). Renames it
+	to ArrayAssignment2LoopsTrans.
+
+	46) PR #2615 for #2610. Fixes various spurious warnings that were
+	being produced by the lfric/eg17/full_example_extract example.
+
+	47) PR #2625 for #2619. Adds a create function for OMPParallelDoDirective
+	to avoid issues from using its parent class' create method.
+
+	48) PR #2609 for #2407. The OpenACC routine directive and transformation
+	now accept a "parallelism" attribute to set the level of parallelism, which
+	is mandatory in recent OpenACC standards.
+
+	49) PR #2626 for #2622. Adds convenience methods to the SymbolTable for
+	manipulating Routine argument lists.
+
+	50) PR #2607 FOR #2600. Update psyclone command and script interface
+	to remove mention of 'nemo' API.
+
+	51) PR #2575 towards #2201. Allow FileContainer to have symbols of their
+	inner subroutines. It also solves an issue with missing PURE, ELEMENTAL, ...
+
+	52) PR #2632 for #2116. Update the code-transformation tutorial.
+
+	53) PR #2639 for #2638. Upgrade CI markdown-linkcheck to linkspector.
+
+	54) PR #2583 towards #2577. Adds partial support for pointer
+	assignments. (Array accessors within structures are not supported.)
+	Pointer *declarations* will still result in symbols of
+	UnsupportedFortranType.
+
+	55) PR #2445 for #2444. Changes the kernel-extraction tooling so
+	that filenames are construction using dashes instead of colons.
+
 release 2.5.0 14th of February 2024
 
 	1) PR #2199 for #2189. Fix bugs with missing maps in enter data

doc/README.md

@@ -34,3 +34,11 @@ of the repository:
 In both cases ``latexmk`` is also required to be installed on
 the system in order to generate the
 [pdf documentation](../psyclone.pdf).
+
+The user documentation can make use of Sphinx's math support for
+html if `dvipng` is installed. This library is not listed as
+a dependency for the `doc` target due to its dependency on latex. But
+if `dvipng` is available on a system,
+Sphinx's math support can be enabled for the PSyclone documentation by
+setting the environment variable `$SPHINXTAG` to `-t has_dvipng`.
+The pdf output will always use Sphinx's math support.

doc/developer_guide/APIs.rst

@@ -224,7 +224,7 @@ indexed in the following way.
 	   :width: 120
 
 When the distributed memory option is switched on in the LFRic API
-(see the :ref:`distributed_memory` Section) the cells in the model are
+(see the :ref:`psykal_usage` Section) the cells in the model are
 partitioned amongst processors and halo cells are added at the
 boundaries to a depth determined by the LFRic infrastructure. In this
 case the LFRic infrastructure maintains the global cell index and
@@ -275,7 +275,7 @@ index 2 and the cell above that contains dof index 3 etc.
 
 As discussed in the previous section, when the distributed memory
 option is switched on in the LFRic API (see the
-:ref:`distributed_memory` Section) the cells in the model are
+:ref:`psykal_usage` Section) the cells in the model are
 partitioned amongst processors and halo cells are added at the
 boundaries to a depth determined by the LFRic infrastructure. This
 results in the dofs being replicated in the halo cells, leading to a
@@ -308,7 +308,7 @@ that contains dof index 3 etc.
 	   :width: 140
 
 As already explained, when the distributed memory option is switched
-on in the LFRic API (see the :ref:`distributed_memory` Section)
+on in the LFRic API (see the :ref:`psykal_usage` Section)
 the cells in the model are partitioned amongst processors and halo
 cells are added at the boundaries.
 
@@ -1259,22 +1259,6 @@ These scripts may be found in ``examples/nemo/scripts`` and their
 use is described in the ``README.md`` file in that directory.
 
 
-PSyIR Construction
-------------------
-
-Since NEMO is an existing code, the way it is handled in PSyclone is
-slightly different from those APIs that mandate a PSyKAl separation of
-concerns (LFRic and GOcean1.0).  As with the other APIs, fparser2 is
-used to parse the supplied Fortran source file and construct a parse
-tree (in ``psyclone.generator.generate``). This parse tree is then
-passed to the ``NemoPSy`` constructor which uses the ``fparser2`` PSyIR
-frontend to construct the equivalent PSyIR. (This PSyIR is
-'language-level' in that it does not contain any domain-specific
-constructs.) Finally, the PSyIR is passed to the ``NemoInvokes``
-constructor which applies various 'raising' transformations which
-raise the level of abstraction by introducing domain-specific
-information.
-
 Implicit Loops
 --------------
 
@@ -1283,7 +1267,7 @@ use of array notation is encouraged in the NEMO Coding Conventions
 :cite:`nemo_code_conv` and identifying these loops can be important
 when introducing, e.g. OpenMP. These implicit loops are not
 automatically represented as PSyIR Loop instances but can be converted
-to explicit loops using the ``NemoAllArrayRange2LoopTrans``
+to explicit loops using the ``ArrayAssignment2LoopsTrans``
 transformation.
 
 

doc/developer_guide/coding-style.rst

@@ -254,7 +254,7 @@ domain:
 
 psyir:
     This directory contains all classes and functions related to the PSyIR
-    (PSyclone Internal Representation). The directory itself does not contain
+    (PSyclone Intermediate Representation). The directory itself does not contain
     any source files (except `__init__.py` to shorten the import paths).
 
     psyir/transformations

doc/developer_guide/dependency.rst

@@ -43,11 +43,6 @@
     from psyclone.psyir.tools import DependencyTools
     from psyclone.transformations import OMPLoopTrans
 
-    # Make sure we use nemo here, otherwise depending on order the
-    # wrong API might be set.
-    from psyclone.configuration import Config
-    Config.get().api = "nemo"
-
     code = '''subroutine sub()
     integer :: i, j, k, a(11, 11)
     a(i,j) = 1

doc/developer_guide/index.rst

@@ -47,7 +47,7 @@
    psyir
    psyir_symbols
    psyir_backends
-   parsing
+   psykal
    module_manager
    APIs
    modules

doc/developer_guide/psyir.rst

@@ -37,8 +37,8 @@
 ..          L. Turner, Met Office
 
 
-The PSyclone Internal Representation (PSyIR)
-############################################
+The PSyclone Intermediate Representation (PSyIR)
+################################################
 
 The PSyclone Intermediate Representation (PSyIR) is a language-independent
 Intermediate Representation that PSyclone uses to represent the PSy (Parallel