Merge branch 'master' into feature/acc-wait-directive

.github/workflows/compilation.yml

@@ -38,14 +38,24 @@
 # Modified by N. M. Nobre, STFC Daresbury Lab
 
 # This workflow will use a self-hosted runner to perform the more expensive
-# integrations tests that are not run on GHA systems. At the moment it only
-# runs the test suite with compilation enabled (using gfortran).
+# compilation tests that are not run on GHA systems. At the moment it:
+#
+#  * Runs the test suite with compilation with gfortran and nvfortran;
+#  * Builds the examples with gfortran and nvfortran (the latter with
+#    OpenACC enabled).
+#  * Builds the tutorials with gfortran and nvfortran.
 
 name: Compilation tests
 
 on:
   push
 
+env:
+  PYTHON_VERSION: 3.11.4
+  GFORTRAN_VERSION: 13.2.0
+  NVFORTRAN_VERSION: 23.7
+  CUDA_VERSION: 12.2
+
 jobs:
   run_if_on_mirror:
     # Only PSyclone-mirror has the necessary self-hosted runner.
@@ -66,17 +76,60 @@ jobs:
         commit-filter: '[skip ci]'
     - name: Install dependencies
       run: |
-        module load python/3.11.3
+        module load python/${PYTHON_VERSION}
         python -m venv .runner_venv
         . .runner_venv/bin/activate
         python -m pip install --upgrade pip
         # If you wish to install the version of fparser pointed to by the
         # submodule instead of the released version (from PyPI) then
         # uncomment the following line:
         pip install external/fparser
-        pip install .[test]
-    - name: Test with pytest and compilation
+        pip install .[test,psydata]
+    - name: Unit tests with compilation - gfortran
+      run: |
+        module load python/${PYTHON_VERSION}
+        . .runner_venv/bin/activate
+        module load gcc/${GFORTRAN_VERSION} openmpi netcdf_fortran
+        pytest -n 2 --f90=gfortran --compile --compileopencl src/psyclone/tests
+        module rm netcdf_fortran gcc
+    - name: Unit tests with compilation - nvfortran
+      run: |
+        module load python/${PYTHON_VERSION}
+        . .runner_venv/bin/activate
+        module load nvidia-hpcsdk/${NVFORTRAN_VERSION} netcdf_fortran
+        # We have to tell nvfortran where to find the OpenCL library.
+        pytest -n 2 --f90=nvfortran --f90flags="-L/apps/packages/compilers/nvidia-hpcsdk/Linux_x86_64/${NVFORTRAN_VERSION}/cuda/${CUDA_VERSION}/targets/x86_64-linux/lib" --compile --compileopencl src/psyclone/tests
+        module rm netcdf_fortran nvidia-hpcsdk
+    - name: Examples with compilation - gfortran
+      run: |
+        module load python/${PYTHON_VERSION}
+        . .runner_venv/bin/activate
+        module load gcc/${GFORTRAN_VERSION} openmpi netcdf_fortran
+        # Although we're using gfortran, we link with the OpenCL lib that comes
+        # with CUDA.
+        make -C examples allclean
+        F90=gfortran F90FLAGS="-L/apps/packages/compilers/nvidia-hpcsdk/Linux_x86_64/${NVFORTRAN_VERSION}/cuda/${CUDA_VERSION}/targets/x86_64-linux/lib" make -C examples compile
+    - name: Tutorials with compilation - gfortran
+      run: |
+        module load python/${PYTHON_VERSION}
+        . .runner_venv/bin/activate
+        make -C tutorial/practicals allclean
+        module load gcc/${GFORTRAN_VERSION} openmpi netcdf_fortran
+        make -C tutorial/practicals compile
+    - name: Examples with compilation - nvfortran
+      run: |
+        module load python/${PYTHON_VERSION}
+        . .runner_venv/bin/activate
+        make -C examples allclean
+        module load nvidia-hpcsdk/${NVFORTRAN_VERSION} netcdf_fortran
+        # We have to tell nvfortran where to find the OpenCL library.
+        F90=nvfortran F90FLAGS="-acc -Minfo=all -L/apps/packages/compilers/nvidia-hpcsdk/Linux_x86_64/${NVFORTRAN_VERSION}/cuda/${CUDA_VERSION}/targets/x86_64-linux/lib" make -C examples compile
+    - name: Tutorials with compilation - nvfortran
       run: |
-        module load python/3.11.3
+        module load python/${PYTHON_VERSION}
         . .runner_venv/bin/activate
-        pytest -n 2 --f90=gfortran --compile src/psyclone/tests
+        make -C tutorial/practicals allclean
+        module load nvidia-hpcsdk/${NVFORTRAN_VERSION} netcdf_fortran
+        # TODO #2251. Cannot build the LFRic practicals with 23.5/7 of nvfortran
+        # because the compilation of nan_test.f90 gives an ICE.
+        F90=nvfortran F90FLAGS="-acc -Minfo=all" make -C tutorial/practicals/nemo compile

.github/workflows/lfric_test.yml

@@ -0,0 +1,113 @@
+# -----------------------------------------------------------------------------
+# BSD 3-Clause License
+#
+# Copyright (c) 2023, Science and Technology Facilities Council.
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+# -----------------------------------------------------------------------------
+# Author S. Siso, STFC Daresbury Lab
+
+# This workflow will use a self-hosted runner to perform the more expensive
+# integrations tests that are not run on GHA systems.
+
+name: LFRic Integration Tests
+
+on:
+  push
+
+jobs:
+  run_if_on_mirror:
+    if: ${{ github.repository == 'stfc/PSyclone-mirror' }}
+    runs-on: self-hosted
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        # This is required to get the commit history for merge commits for
+        # the ci-skip check below.
+        fetch-depth: '0'
+    - name: Check for [skip ci] in commit message
+      uses: mstachniuk/ci-skip@v1
+      with:
+        # This setting causes the tests to 'fail' if [skip ci] is specified
+        fail-fast: true
+        commit-filter: '[skip ci]'
+    - name: Install dependencies
+      run: |
+        python -m venv .runner_venv
+        . .runner_venv/bin/activate
+        python -m pip install --upgrade pip
+        # If you wish to install the version of fparser pointed to by the
+        # submodule instead of the released version (from PyPI) then
+        # uncomment the following line:
+        pip install external/fparser
+        pip install .[test]
+        pip install jinja2
+
+    # PSyclone, compile and run MetOffice LFRic with 6 MPI ranks
+    - name: LFRic passthrough (with DistributedMemory)
+      run: |
+        . .runner_venv/bin/activate
+        export PSYCLONE_LFRIC_DIR=${GITHUB_WORKSPACE}/examples/lfric/scripts
+        export MINIAPP_DIR=${HOME}/LFRic/miniapps/gungho_model
+        cd ${MINIAPP_DIR}
+        # Compile
+        module load lfric_env
+        export PSYCLONE_CONFIG=${HOME}/lfric_psyclone_config.cfg
+        make clean
+        make -j 6 build
+        # Run
+        cd example
+        cp ${HOME}/lfric_gunho_configuration.nml configuration.nml
+        mpirun -n 6 ../bin/gungho_model configuration.nml
+        tail PET0.gungho_model.Log
+        cat timer.txt
+
+    # PSyclone, compile and run MetOffice LFRic with all optimisations and 6 OpenMP threads
+    - name: LFRic with all transformations
+      run: |
+        . .runner_venv/bin/activate
+        export PSYCLONE_LFRIC_DIR=${GITHUB_WORKSPACE}/examples/lfric/scripts
+        export MINIAPP_DIR=${HOME}/LFRic/miniapps/gungho_model
+        cd ${MINIAPP_DIR}
+        # Prepare script (LFRics expects a folder with a global.py)
+        mkdir -p psyclone-test
+        cp ${PSYCLONE_LFRIC_DIR}/everything_everywhere_all_at_once.py psyclone-test/global.py
+        # Compile
+        module load lfric_env
+        export PSYCLONE_CONFIG=${HOME}/lfric_psyclone_config.cfg
+        make clean
+        make OPTIMISATION_PATH=${MINIAPP_DIR}/psyclone-test -j 6 build
+        # Run
+        cd example
+        cp ${HOME}/lfric_gunho_configuration.nml configuration.nml
+        export OMP_NUM_THREADS=6
+        mpirun -n 1 ../bin/gungho_model configuration.nml
+        cat timer.txt

.github/workflows/nemo_tests.yml

@@ -100,7 +100,28 @@ jobs:
         tail -n 1 output.txt | grep -q "S_min:  0.482686"
         tail -n 1 output.txt | grep -q "S_max:  0.407622"
         grep -A 1 "Elapsed Time" output.txt
-        echo  $GITHUB_REF_NAME $GITHUB_SHA $(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1) >> ${NEMO_DIR}/performance_history
+        echo  $GITHUB_REF_NAME $GITHUB_SHA $(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1) >> ${NEMO_DIR}/performance_history_openmp_gpu
+
+    # PSyclone, compile and run MetOffice NEMO with OpenACC kernels for GPUs
+    - name: NEMO MetOffice OpenACC kernels for GPU
+      run: |
+        . .runner_venv/bin/activate
+        export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
+        export NEMO_DIR=${HOME}/NEMO
+        cd examples/nemo/scripts
+        make -j 4 openacc_kernels
+        module load nvidia-hpcsdk netcdf_fortran
+        COMPILER_ARCH=linux_nvidia_acc_gpu make -j 4 compile-openacc_kernels
+        export NV_ACC_POOL_THRESHOLD=75
+        make run-openacc_kernels | tee output.txt
+        # Check the output is as expected for the first 6 digits
+        tail -n 1 output.txt | grep -q " it :      10"
+        tail -n 1 output.txt | grep -q "|ssh|_max:  0.259483"
+        tail -n 1 output.txt | grep -q "|U|_max:  0.458515"
+        tail -n 1 output.txt | grep -q "S_min:  0.482686"
+        tail -n 1 output.txt | grep -q "S_max:  0.407622"
+        grep -A 1 "Elapsed Time" output.txt
+        echo  $GITHUB_REF_NAME $GITHUB_SHA $(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1) >> ${NEMO_DIR}/performance_history_openacc_kernels_gpu
 
     # PSyclone, compile and run ECMWF NEMO with OpenMP for CPUs
     - name: NEMO ECMWF OpenMP for CPU
@@ -129,4 +150,4 @@ jobs:
         tail -n 1 output.txt | grep -q "S_min:  0.108530"
         tail -n 1 output.txt | grep -q "S_max:  0.404045"
         grep -A 1 "Elapsed Time" output.txt
-        echo  $GITHUB_REF_NAME $GITHUB_SHA $(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1) >> ${NEMO_DIR}/performance_history
+        echo  $GITHUB_REF_NAME $GITHUB_SHA $(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1) >> ${NEMO_DIR}/performance_history_openmp_cpu

.github/workflows/python-package.yml

@@ -93,7 +93,14 @@ jobs:
     - uses: actions/setup-python@v4
     - run: python -m pip install --upgrade pip
     - run: pip install .[doc]
-    - run: cd doc/developer_guide; make doctest
+    # Sphinx since version 7.2 (7.2.0/1/2) aborts with
+    #   exec('from sympy import *', global_dict)
+    #   File "<string>", line 1, in <module>
+    #  AttributeError: module 'sympy' has no attribute 'external'
+    # when it is run without creating the documentation first.
+    # So till this is fixed in Sphinx, we trigger the creation
+    # of the html documents before actually running doctest
+    - run: cd doc/developer_guide; make html; make doctest
   build:
     if: ${{ github.repository != 'stfc/PSyclone-mirror' }}
     runs-on: ubuntu-latest

changelog

@@ -509,6 +509,79 @@
 	172) PR #2163 for #1537. Support array-slicing notation in SymPy
 	comparisons.
 
+	173) PR #2221 for #2214. Fix names of invokes containing a single
+	kernel in the PSyIR of the LFRic Alg layer.
+
+	174) PR #2225 for #2224. Fix erroneous CI link check error by
+	omitting test for the particular link.
+
+	175) PR #2172 for #1833. Fixes the LFRic tutorials so that they
+	build correctly.
+
+	176) PR #2227 for #2226. Adds new Node.path_from(ancestor) method.
+
+	177) PR #2158 for #81. Ensures all example/test Fortran code for
+	LFRic follows the LFRic naming convention.
+
+	178) PR #2218 towards #2132. Adds LFRic integration tests and
+	new, associated optimisation scripts. Includes bug fixes for
+	matmul inlining transformation.
+
+	179) PR #2230 for #2228. Improve reporting of errors due to kernel
+	functors not explicitly included in algorithm use statements.
+
+	180) PR #2207 for #1419. Split the DataSymbol constant_value attribute
+	into is_constant (bool) and initial_value (PSyIR Node). This allows
+	parsing Fortran declarations with initial_value that are not constant.
+
+	181) PR #2231 for #2213. The Fortran frontend and backend now also
+	consider that UnresolvedInterface symbols can come from the body of
+	a Fortran Interface.
+
+	182) PR #2240 for #2234. Fix WhileLoop issue in the NEMO OpenACC kernels
+	script.
+
+	183) PR #2182 for #2179. Fix LFRic eg14 nvfortran compilation and add
+	nvfortran examples and tutorials steps in the Integration tests. 
+
+	184) PR #2250 for #2248 and #1575. Fixes bug in line-length limiter
+	to prevent it breaking a line before the first non-whitepsace
+	character.
+
+	185) PR #2262 towards #446. Implement reference_access for Call nodes.
+
+	186) PR #2184 for #2166. Adds Sympy support for user-defined types.
+
+	187) PR #2270 for #1575. Fixes the line-length limiter for code that
+	has an indent greater than the max. line length.
+
+	188) PR #2259 for #1932. Adds support for the 'gang' and 'vector'
+	clauses on OpenACC Loop directives.
+
+	189) PR #2276 for #2274. Small fixes for various complaints
+	produced by latest version of pycodestyle.
+
+	190) PR #2291 for #2290. Bug fix to KernelModuleInlineTrans -
+	ensures that the new RoutineSymbol added to the Container is given
+	a DefaultModuleInterface.
+
+	191) PR #2238 for #2234. Adds support for a generic interface to
+	perform variable comparison when the datatype is unknown. (Required
+	for canonicalising SELECT CASE constructs.)
+
+	192) PR #2292 for #2288. Workaround for Sphinx-doctest bug by
+	building html dev guide before running the doctests.
+
+	193) PR #2260 for #2245. Splits LFRicLoopBounds class from
+	dynamo0.3.py.
+
+	194 PR #2241 for #2215. Adds support for Fortran names being the
+	same as Python keywords when using sympy within PSyclone, e.g. in
+	comparisons between expressions.
+
+  195) PR #2295 for #2294. Extends the PSyData extraction library
+  to support character variables
+
 release 2.3.1 17th of June 2022
 
 	1) PR #1747 for #1720. Adds support for If blocks to PSyAD.

doc/developer_guide/psy_data.rst

@@ -654,6 +654,8 @@ takes the following parameters:
         64-bit integer value
     ``logical``:
         32-bit logical value
+    ``char``:
+        A default string value
 
     Default value is ``real,double,int``.
 

doc/developer_guide/psyir.rst

@@ -507,6 +507,16 @@ var2, var3)` would be represented by a
 The PSyIR supports the concept of named arguments for operation
 nodes, see the :ref:`named_arguments-label` section for more details.
 
+.. note:: Similar to Fortran, the PSyIR has two comparison operators, one for
+        booleans (EQV) and one for non-booleans (EQ). These are not
+        interchangeable because they have different precedence priorities and
+        some compilers will not compile with the wrong operator. In some cases
+        we need to insert a comparison of two expressions and we don't know the
+        datatype of the operands (e.g. in the select-case canonicalisation).
+        A solution to this is to create an abstract interface with appropriate
+        implementations for each possible datatype.
+
+
 IntrinsicCall Nodes
 -------------------