Add Intel tests to devel branch (#1547)

Add the configuration files to run tests with an Intel compiler. Add
an environment variable `PYCCEL_DEFAULT_COMPILER` which
specifies the default compiler.

There are 3 failing tests due to:
- passing NaN as an argument
- #1540 

Additionally some array tests were modified to use `isclose` for
comparisons instead of `np.all_equal` these tests all involve divisions
and should have been using `isclose` anyway.

This is related to #542 but does not fully fix the issue as it only adds
Intel.

---------

Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com>

.github/actions/intel_install/action.yml

@@ -0,0 +1,68 @@
+name: 'Intel installation commands'
+
+runs:
+  using: "composite"
+  steps:
+    - name: update the package list
+      run:
+        sudo apt-get update
+      shell: bash
+    - name: Restore cached Intel
+      id: cache-intel-restore
+      uses: actions/cache/restore@v3
+      with:
+        path: |
+          /opt/intel/oneapi/
+        key: ${{ runner.os }}-intel-2023
+        restore-keys: |
+          ${{ runner.os }}-intel-
+    - name: Install Intel OneAPI
+      if: steps.cache-intel-restore.outputs.cache-hit != 'true'
+      run: |
+        # See https://github.com/oneapi-src/oneapi-ci
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+        echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        sudo apt-get update -o Dir::Etc::sourcelist="sources.list.d/oneAPI.list" -o APT::Get::List-Cleanup="0"
+        sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-openmp intel-oneapi-mkl intel-oneapi-mpi-devel
+      shell: bash
+    - name: Save Intel environment variables
+      run: |
+        source /opt/intel/oneapi/setvars.sh
+        echo "$PATH" > $GITHUB_PATH
+        echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "LIBRARY_PATH=$LIBRARY_PATH" >> $GITHUB_ENV
+        echo "ONEAPI_ROOT=$ONEAPI_ROOT" >> $GITHUB_ENV
+        echo "MANPATH=$MANPATH" >> $GITHUB_ENV
+        echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH" >> $GITHUB_ENV
+        echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH" >> $GITHUB_ENV
+        echo "TBB_ROOT=$TBB_ROOT" >> $GITHUB_ENV
+        echo "ONEAPI_ROOT=$ONEAPI_ROOT" >> $GITHUB_ENV
+        echo "ACL_BOARD_VENDOR_PATH=$ACL_BOARD_VENDOR_PATH" >> $GITHUB_ENV
+        echo "FPGA_VARS_DIR=$FPGA_VARS_DIR" >> $GITHUB_ENV
+        echo "I_MPI_ROOT=$I_MPI_ROOT" >> $GITHUB_ENV
+        echo "FI_PROVIDER_PATH=$FI_PROVIDER_PATH" >> $GITHUB_ENV
+        echo "DIAGUTIL_PATH=$DIAGUTIL_PATH" >> $GITHUB_ENV
+        echo "GDB_INFO=$GDB_INFO" >> $GITHUB_ENV
+        echo "CMPLR_ROOT=$CMPLR_ROOT" >> $GITHUB_ENV
+        echo "INFOPATH=$INFOPATH" >> $GITHUB_ENV
+        echo "OCL_ICD_FILENAMES=$OCL_ICD_FILENAMES" >> $GITHUB_ENV
+        echo "CLASSPATH=$CLASSPATH" >> $GITHUB_ENV
+        echo "INTELFPGAOCLSDKROOT=$INTELFPGAOCLSDKROOT" >> $GITHUB_ENV
+        echo "MKLROOT=$MKLROOT" >> $GITHUB_ENV
+        echo "NLSPATH=$NLSPATH" >> $GITHUB_ENV
+        echo "INTEL_PYTHONHOME=$INTEL_PYTHONHOME" >> $GITHUB_ENV
+        echo "CPATH=$CPATH" >> $GITHUB_ENV
+        mpicc --version
+      shell: bash
+    - name: Save Intel Cache
+      id: cache-intel-save
+      uses: actions/cache/save@v3
+      with:
+        path: |
+          /opt/intel/oneapi/
+        key: ${{ steps.cache-intel-restore.outputs.cache-primary-key }}
+    - name: Install Valgrind
+      run:
+        sudo apt-get install valgrind
+      shell: bash

.github/workflows/intel.yml

@@ -0,0 +1,106 @@
+name: Intel unit tests
+
+on:
+  workflow_dispatch:
+    inputs:
+      python_version:
+        required: true
+        type: string
+      ref:
+        required: false
+        type: string
+      check_run_id:
+        required: false
+        type: string
+      pr_repo:
+        required: false
+        type: string
+  push:
+    branches: devel
+
+env:
+  COMMIT: ${{ inputs.ref || github.event.ref }}
+  PEM: ${{ secrets.BOT_PEM }}
+  GITHUB_RUN_ID: ${{ github.run_id }}
+  GITHUB_CHECK_RUN_ID: ${{ inputs.check_run_id }}
+  PR_REPO: ${{ inputs.pr_repo || github.repository }}
+  PYCCEL_DEFAULT_COMPILER: 'intel'
+
+jobs:
+  Python_version_picker:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    outputs:
+      python_version: ${{ steps.set-python_version.outputs.python_version }}
+    steps:
+    - if: github.event_name == 'push'
+      run: |
+        echo "version=3.9" >> $GITHUB_ENV
+      shell: bash
+    - id: dispatch-matrix
+      if: github.event_name == 'workflow_dispatch'
+      run: |
+        echo "version=${{ inputs.python_version }}" >> $GITHUB_ENV
+      shell: bash
+    - id: set-python_version
+      run: |
+        echo "python_version=$version" >> $GITHUB_OUTPUT
+      shell: bash
+
+  Intel:
+
+    runs-on: ubuntu-latest
+    name: Unit tests
+    needs: Python_version_picker
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ env.COMMIT }}
+          repository: ${{ env.PR_REPO }}
+      - name: Set up Python ${{ needs.Python_version_picker.outputs.python_version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ needs.Python_version_picker.outputs.python_version }}
+      - name: "Setup"
+        id: token
+        run: |
+          pip install jwt requests
+          python ci_tools/setup_check_run.py
+      - name: Install dependencies
+        uses: ./.github/actions/intel_install
+      - name: Install Pyccel with tests
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[test]
+        shell: bash
+      - name: Coverage install
+        uses: ./.github/actions/coverage_install
+      - name: Fortran/C tests with pytest
+        id: f_c_pytest
+        timeout-minutes: 60
+        uses: ./.github/actions/pytest_run
+      - name: Python tests with pytest
+        id: python_pytest
+        timeout-minutes: 20
+        uses: ./.github/actions/pytest_run_python
+      - name: Parallel tests with pytest
+        id: parallel
+        timeout-minutes: 20
+        uses: ./.github/actions/pytest_parallel
+      - name: Test with valgrind for memory leaks
+        id: valgrind
+        uses: ./.github/actions/valgrind_run
+      - name: Collect coverage information
+        continue-on-error: True
+        uses: ./.github/actions/coverage_collection
+      - name: Save code coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-artifact
+          path: .coverage
+          retention-days: 1
+      - name: "Post completed"
+        if: always()
+        run:
+          python ci_tools/complete_check_run.py ${{ steps.f_c_pytest.outcome }} ${{ steps.python_pytest.outcome }} ${{ steps.parallel.outcome }} ${{ steps.valgrind.outcome }}

CHANGELOG.md

@@ -10,6 +10,7 @@ All notable changes to this project will be documented in this file.
 -   #1492 : Types of arguments for class methods can be declared like function arguments.
 -   #1511 : Add support for the `cmath` library.
 -   Output readable header syntax errors.
+-   New environment variable `PYCCEL_DEFAULT_COMPILER`.
 
 ### Fixed
 

ci_tools/bot_messages/show_tests.txt

@@ -13,5 +13,6 @@ The following is a list of keywords which can be used to run tests. Tests in bol
 - pickle_wheel : Checks that .pyccel files have been correctly generated and packaged into the wheel.
 - linux_anaconda : Runs the unit tests on a linux system using anaconda for python.
 - windows_anaconda : Runs the unit tests on a windows system using anaconda for python.
+- intel : Runs the unit tests on a linux system using the intel compiler.
 
 These tests can be run with the command `/bot run X` (multiple tests can be specified separated by spaces), or with `try V X` to test on Python version V.

ci_tools/bot_tools/bot_funcs.py

@@ -14,6 +14,7 @@
         'anaconda_windows': '3.10',
         'coverage': '3.7',
         'docs': '3.8',
+        'intel': '3.9',
         'linux': '3.7',
         'macosx': '3.10',
         'pickle_wheel': '3.7',
@@ -30,6 +31,7 @@
         'anaconda_windows': "Unit tests on Windows with anaconda",
         'coverage': "Coverage verification",
         'docs': "Check documentation",
+        'intel': "Unit tests on Linux with Intel compiler",
         'linux': "Unit tests on Linux",
         'macosx': "Unit tests on MacOSX",
         'pickle_wheel': "Test pickling during wheel installation",
@@ -415,7 +417,7 @@ def is_test_required(self, commit_log, name, key, state):
             True if the test should be run, False otherwise.
         """
         print("Checking : ", name)
-        if key in ('linux', 'windows', 'macosx', 'anaconda_linux', 'anaconda_windows', 'coverage'):
+        if key in ('linux', 'windows', 'macosx', 'anaconda_linux', 'anaconda_windows', 'coverage', 'intel'):
             has_relevant_change = lambda diff: any((f.startswith('pyccel/') or f.startswith('tests/')) \
                                                     and f.endswith('.py') and f != 'pyccel/version.py' \
                                                     for f in diff) #pylint: disable=unnecessary-lambda-assignment

ci_tools/devel_branch_tests.py

@@ -14,3 +14,4 @@
     bot.run_tests(['pickle_wheel'], '3.7', force_run = True)
     bot.run_tests(['anaconda_linux'], '3.10', force_run = True)
     bot.run_tests(['anaconda_windows'], '3.10', force_run = True)
+    bot.run_tests(['intel'], '3.9', force_run = True)

docs/compiler.md

@@ -21,6 +21,8 @@ or
 epyccel(my_func, compiler='intel')
 ```
 
+It is also possible to change the default compiler family by setting the environment variable `PYCCEL_DEFAULT_COMPILER`.
+
 ## User-defined compiler
 
 The user can also define their own compiler in a JSON file. To use this definition, the location of the JSON file must be passed to the _compiler_ argument. The JSON file must define the following:

pyccel/codegen/pipeline.py

@@ -178,7 +178,7 @@ def handle_error(stage):
 
     # Choose Fortran compiler
     if compiler is None:
-        compiler = 'GNU'
+        compiler = os.environ.get('PYCCEL_DEFAULT_COMPILER', 'GNU')
 
     fflags = [] if fflags is None else fflags.split()
     wrapper_flags = [] if wrapper_flags is None else wrapper_flags.split()

pyccel/compilers/default_compilers.py

@@ -75,7 +75,7 @@
 
 #------------------------------------------------------------
 nvfort_info = {'exec' : 'nvfort',
-              'mpi_exec' : 'nvfort',
+              'mpi_exec' : 'mpifort',
               'language': 'fortran',
               'module_output_flag': '-module',
               'debug_flags': ("-Mbounds","-g","-O0"),
@@ -123,8 +123,8 @@
     gcc_info['mpi']['libdirs']  = (os.environ["MSMPI_LIB64"].rstrip('\\'),)
 
 #------------------------------------------------------------
-icc_info = {'exec' : 'icc',
-            'mpi_exec' : 'mpiicc',
+icc_info = {'exec' : 'icx',
+            'mpi_exec' : 'mpicc',
             'language': 'c',
             'debug_flags': ("-g","-O0"),
             'release_flags': ("-O3","-funroll-loops",),
@@ -158,7 +158,7 @@
 
 #------------------------------------------------------------
 nvc_info = {'exec' : 'nvc',
-            'mpi_exec' : 'nvc',
+            'mpi_exec' : 'mpicc',
             'language': 'c',
             'debug_flags': ("-g","-O0"),
             'release_flags': ("-O3","-Munroll",),

tests/epyccel/recognised_functions/test_cmath_funcs.py

@@ -1,5 +1,6 @@
 # pylint: disable=missing-function-docstring, missing-module-docstring
 from cmath import nanj, infj, pi
+import os
 import sys
 
 import pytest
@@ -257,6 +258,7 @@ def tanh_phrase(x : complex, y : complex):
         )
     )
 )
+@pytest.mark.skipif(os.environ.get('PYCCEL_DEFAULT_COMPILER', None) == 'intel', reason='Nan not correctly passed to intel function')
 def test_isfinite_call(language): # isfinite
     @template('T', [float, complex])
     def isfinite_call(x : 'T'):

tests/epyccel/recognised_functions/test_math_funcs.py

@@ -1,5 +1,6 @@
 # pylint: disable=missing-function-docstring, missing-module-docstring
 from math import nan, inf, modf
+import os
 import sys
 import pytest
 from numpy.random import rand, randint, uniform
@@ -539,6 +540,7 @@ def copysign_return_type(x : 'float', y : 'int'):
         )
     )
 )
+@pytest.mark.skipif(os.environ.get('PYCCEL_DEFAULT_COMPILER', None) == 'intel', reason='Nan not correctly passed to intel function')
 def test_isfinite_call(language): # isfinite
     def isfinite_call(x : 'float'):
         from math import isfinite

tests/epyccel/test_arrays.py

@@ -7,6 +7,9 @@
 from pyccel.epyccel import epyccel
 from modules        import arrays
 
+RTOL = 1e-12
+ATOL = 1e-16
+
 def check_array_equal(a, b):
     """
     Check that two arrays are equal.
@@ -1102,7 +1105,7 @@ def test_array_float_1d_scalar_div(language):
     f1(x1, a)
     f2(x2, a)
 
-    assert np.array_equal( x1, x2 )
+    assert np.allclose(x1, x2, rtol=RTOL, atol=ATOL)
 
 def test_array_float_1d_scalar_mod(language):
     f1 = arrays.array_float_1d_scalar_mod
@@ -1273,7 +1276,7 @@ def test_array_float_2d_C_scalar_div(language):
     f1(x1, a)
     f2(x2, a)
 
-    assert np.array_equal( x1, x2 )
+    assert np.allclose(x1, x2, rtol=RTOL, atol=ATOL)
 
 def test_array_float_2d_C_scalar_mod(language):
 
@@ -1476,7 +1479,7 @@ def test_array_float_2d_F_scalar_div(language):
     f1(x1, a)
     f2(x2, a)
 
-    assert np.array_equal( x1, x2 )
+    assert np.allclose(x1, x2, rtol=RTOL, atol=ATOL)
 
 def test_array_float_2d_F_scalar_mod(language):
 
@@ -1802,13 +1805,13 @@ def test_multiple_stack_array_1(language):
 
     f1 = arrays.multiple_stack_array_1
     f2 = epyccel(f1, language = language)
-    assert np.equal(f1(), f2())
+    assert np.allclose(f1(), f2(), rtol=RTOL, atol=ATOL)
 
 def test_multiple_stack_array_2(language):
 
     f1 = arrays.multiple_stack_array_2
     f2 = epyccel(f1, language = language)
-    assert np.equal(f1(), f2())
+    assert np.allclose(f1(), f2(), rtol=RTOL, atol=ATOL)
 
 #==============================================================================
 # TEST: 2D Stack ARRAYS OF REAL
@@ -1834,13 +1837,13 @@ def test_multiple_2d_stack_array_1(language):
 
     f1 = arrays.multiple_2d_stack_array_1
     f2 = epyccel(f1, language = language)
-    assert np.equal(f1(), f2())
+    assert np.allclose(f1(), f2(), rtol=RTOL, atol=ATOL)
 
 def test_multiple_2d_stack_array_2(language):
 
     f1 = arrays.multiple_2d_stack_array_2
     f2 = epyccel(f1, language = language)
-    assert np.equal(f1(), f2())
+    assert np.allclose(f1(), f2(), rtol=RTOL, atol=ATOL)
 
 #==============================================================================
 # TEST: Product and matrix multiplication
@@ -3569,8 +3572,6 @@ def test_arrs_2d_negative_index(language):
 #==============================================================================
 # TEST : NUMPY ARANGE
 #==============================================================================
-RTOL = 1e-12
-ATOL = 1e-16
 
 def test_numpy_arange_one_arg(language):
     f1 = arrays.arr_arange_1

tests/epyccel/test_epyccel_openmp.py

@@ -380,6 +380,7 @@ def test_omp_arraysum_combined(language):
     assert f1(x) == np.sum(x)
 
 @pytest.mark.external
+@pytest.mark.xfail(os.environ.get('PYCCEL_DEFAULT_COMPILER', None) == 'intel', reason='#1539')
 def test_omp_range_sum_critical(language):
     f1 = epyccel(openmp.omp_range_sum_critical, fflags = '-Wall', accelerators=['openmp'], language=language)