diff --git a/.ci_fedora.sh b/.ci_fedora.sh index c865e8a0aa..0f21d156fd 100755 --- a/.ci_fedora.sh +++ b/.ci_fedora.sh @@ -23,7 +23,7 @@ then test . != ".$2" && mpi="$2" || mpi=openmpi time $cmd pull ghcr.io/boutproject/bout-container-base:main time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \ - --shm-size 256M \ + --shm-size 1G \ --name mobydick ghcr.io/boutproject/bout-container-base:main \ /tmp/BOUT-dev/.ci_fedora.sh $mpi time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev @@ -37,9 +37,15 @@ test . != ".$1" && mpi="$1" || mpi=openmpi cp -a /tmp/BOUT-dev /home/test/ . /etc/profile.d/modules.sh module load mpi/${1}-x86_64 - export OMPI_MCA_rmaps_base_oversubscribe=yes + sudo dnf install -y python3-pytest python3-pytest-xdist + # OpenMPI Oversubscription Overrides + export OMPI_MCA_rmaps_base_oversubscribe=1 + export OMPI_MCA_hwloc_base_binding_policy=none + export OMPI_MCA_rmaps_base_mapping_policy=core:OVERSUBSCRIBE + export PRTE_MCA_rmaps_default_mapping_policy=core:OVERSUBSCRIBE export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe export TRAVIS=true + export CI=true # Try limiting openmp threads export FLEXIBLAS=NETLIB export MKL_NUM_THREADS=1 diff --git a/.ci_with_cmake.sh b/.ci_with_cmake.sh index 71ea2204e2..c664d3d66e 100755 --- a/.ci_with_cmake.sh +++ b/.ci_with_cmake.sh @@ -13,7 +13,7 @@ fi cmake --build build --target build-check -j 2 cd build -ctest --output-on-failure --timeout 300 +cmake --build . --target check export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ff11a2a4c9..92171444e0 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -133,39 +133,48 @@ jobs: echo CMake options: ${{ matrix.config.cmake_options }} - name: Install dependencies - run: sudo apt update && - sudo apt install -y - libfftw3-dev - libnetcdf-dev - libnetcdf-c++4-dev - netcdf-bin - python3 - python3-pip - python3-pytest - python3-numpy - python3-scipy - lcov - openmpi-bin - libopenmpi-dev - petsc-dev - slepc-dev - liblapack-dev - libparpack2-dev - libhypre-dev + run: | + sudo apt update + sudo apt install -y \ + libfftw3-dev \ + libnetcdf-dev \ + libnetcdf-c++4-dev \ + netcdf-bin \ + lcov \ + openmpi-bin \ + libopenmpi-dev \ + petsc-dev \ + slepc-dev \ + liblapack-dev \ + libparpack2-dev \ + libhypre-dev - uses: actions/checkout@v6 with: submodules: true + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + - uses: actions/setup-python@v6 with: python-version: '3.x' - cache: 'pip' - - name: Install pip packages + - name: Setup virtual environment with uv run: | - python -m pip install --upgrade pip setuptools - python -m pip install -r requirements.txt + # uv sync automatically creates a .venv and installs the groups + uv sync --no-dev --group pytest --inexact + + # Install the core requirements into the same venv + uv pip install -r requirements.txt + + # Put the venv in the PATH + echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH + + # Force CMake to recognize the virtual environment + echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> $GITHUB_ENV - name: Cache Zenodo test data uses: actions/cache@v5 @@ -190,7 +199,9 @@ jobs: run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh - name: Build BOUT++ - run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }} + run: | + UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }} \ + -DPython3_EXECUTABLE=$GITHUB_WORKSPACE/.venv/bin/python Fedora: # This is its own job as it doesn't use most of the steps of the diff --git a/CMakeLists.txt b/CMakeLists.txt index 67e2337210..d2258cca77 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -741,6 +741,7 @@ option( OFF ) if(BOUT_TESTS) + set(CMAKE_CTEST_ARGUMENTS "--output-on-failure" "--timeout" "300") enable_testing() # Targets for just building the tests # Tests need to add themselves as dependencies to these targets @@ -768,7 +769,8 @@ if(BOUT_TESTS) endif() add_custom_target( - check-integrated-tests COMMAND ctest -R "test-" --output-on-failure + check-integrated-tests + COMMAND bash "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh" ) add_dependencies(check-integrated-tests build-check-integrated-tests) @@ -782,6 +784,30 @@ if(BOUT_TESTS) add_dependencies(check check-unit-tests) endif() + # Copy the pytest config file + configure_file( + "${PROJECT_SOURCE_DIR}/tests/conftest.py" + "${PROJECT_BINARY_DIR}/tests/conftest.py" + ) + + # Copy the pyproject.toml file + configure_file( + "${PROJECT_SOURCE_DIR}/pyproject.toml" + "${PROJECT_BINARY_DIR}/pyproject.toml" + ) + + # Copy the pytest config file for the boutpp tests + configure_file( + "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py" + "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py" + ) + + # Copy the pytest shell script + configure_file( + "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh" + "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh" @ONLY + ) + endif() option(BOUT_BUILD_EXAMPLES "Build the examples" ON) diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake index 9b64f643c6..c5abb1169c 100644 --- a/cmake/BOUT++functions.cmake +++ b/cmake/BOUT++functions.cmake @@ -172,7 +172,9 @@ endfunction() # function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME) set(options USE_RUNTEST USE_DATA_BOUT_INP) - set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME) + set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME + PYTHON_TEST_FILE + ) set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS EXTRA_DEPENDS ) @@ -256,16 +258,29 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME) # Set the actual test command if(BOUT_TEST_OPTIONS_USE_RUNTEST) - add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS}) + if(BOUT_TEST_OPTIONS_PYTHON_TEST_FILE) + # It's an integrated test with a specific python file + add_test(NAME ${TESTNAME} + COMMAND pytest ${BOUT_TEST_OPTIONS_PYTHON_TEST_FILE} + ${BOUT_TEST_OPTIONS_TESTARGS} + ) + else() + # It's an MMS test still using the 'runtest' script + add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS}) + endif() + set_tests_properties( ${TESTNAME} PROPERTIES ENVIRONMENT PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ) - bout_copy_file(runtest) else() add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS}) endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest) + bout_copy_file(runtest) + endif() + set_tests_properties( ${TESTNAME} PROPERTIES PROCESSORS ${BOUT_TEST_OPTIONS_PROCESSORS} PROCESSOR_AFFINITY ON @@ -286,11 +301,23 @@ endfunction() # Add a new integrated test. See `bout_add_integrated_or_mms_test` for arguments function(bout_add_integrated_test TESTNAME) + # Construct the Python test filename + string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME + "${TESTNAME}" + ) + string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}") + string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}") + bout_add_integrated_or_mms_test( - build-check-integrated-tests ${TESTNAME} ${ARGV} + build-check-integrated-tests ${TESTNAME} PYTHON_TEST_FILE ${TEST_FILENAME} + ${ARGV} ) -endfunction() + # Only copy the file if the test wasn't skipped due to missing requirements + if(TARGET ${TESTNAME}) + bout_copy_file(${TEST_FILENAME}) + endif() +endfunction() # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments function(bout_add_mms_test TESTNAME) bout_add_integrated_or_mms_test(build-check-mms-tests ${TESTNAME} ${ARGV}) diff --git a/externalpackages/googletest b/externalpackages/googletest index 8736d2cd5c..d72f9c8aea 160000 --- a/externalpackages/googletest +++ b/externalpackages/googletest @@ -1 +1 @@ -Subproject commit 8736d2cd5c1dcba41170ed2fddca14021d4916c3 +Subproject commit d72f9c8aea6817cdf1ca0ac10887f328de7f3da2 diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst index 062415af04..02dda06a0a 100644 --- a/manual/sphinx/developer_docs/contributing.rst +++ b/manual/sphinx/developer_docs/contributing.rst @@ -196,6 +196,23 @@ formatters and run them according to the next section. Usually this is just: which will format just the parts of C++ files that have changed since ``next``. +The "integrated" tests are run via pytest . To install the required packages using `uv +`_ (from the top of your BOUT++ directory): + +.. code-block:: console + + uv sync --group pytest --inexact + +They can be run via cmake in the same way as the other tests: + +.. code-block:: console + + cmake --build build --target check-integrated-tests + +or directly, by running the script `tests/run_integrated_tests.sh`. + +For test isolation, pytest automatically copies each test to a temporary directory when running them. + Formatting and Linters ~~~~~~~~~~~~~~~~~~~~~~ diff --git a/pyproject.toml b/pyproject.toml index 3e75bb39c5..4a76c03fd2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,9 @@ requires = [] build-backend = "backend" backend-path = ["tools/pylib/_boutpp_build/"] +[tool.pytest.ini_options] +console_output_style = "plain" + [dependency-groups] dev = [ "cmake~=4.2", @@ -19,6 +22,10 @@ dev = [ "sphinx-lint~=1.0", "sync-with-uv~=0.5.0", ] +pytest = [ + "pytest~=8.4", + "pytest-xdist~=3.8", +] maint = [ "pygithub~=2.8", "ruamel-yaml~=0.19", diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000000..f04f85e562 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,60 @@ +import pytest +import shutil +import os +import subprocess +import time +from pathlib import Path + + +def pytest_configure(config): + config.addinivalue_line( + "markers", + "serial: mark that the test should not be run concurrently with other. ", + ) + + +@pytest.fixture +def test_dir(request) -> Path: + return Path(request.fspath).parent + + +@pytest.fixture(scope="function", autouse=True) +def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch): + """ + For each test function, create a unique temporary copy of the test directory + and change cwd to it. + """ + + test_file_dir = Path(request.fspath).parent + + if not test_file_dir.is_dir(): + pytest.fail(f"Expected test directory '{test_file_dir}' not found") + + # Create a unique temp dir for this test + run_dir = tmp_path_factory.mktemp(test_file_dir.name) + + # Copy the original test directory into it + shutil.copytree(test_file_dir, run_dir, dirs_exist_ok=True) + + # Change working directory to the copy + monkeypatch.chdir(run_dir) + + +@pytest.fixture +def assert_success_in_shell(test_dir): + + def inner_function(command: str): + # MPI oversubscribe for communications test + os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1" # Allows 18 procs + start = time.time() + result = subprocess.run( + command, shell=True, capture_output=True, text=True, timeout=600 + ) + elapsed = time.time() - start + assert result.returncode == 0, ( + f"Failed after {elapsed:.3f}s in {test_dir}\n" + f"Stderr: {result.stderr}\n" + f"Output: {result.stdout}" + ) + + return inner_function diff --git a/tests/integrated/test-backtrace/runtest b/tests/integrated/test-backtrace/runtest deleted file mode 100755 index c4020e6d99..0000000000 --- a/tests/integrated/test-backtrace/runtest +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env python3 - -# Test enabling/disabling exception backtrace from environment variable - -# requires all_tests - -from boututils.run_wrapper import build_and_log, shell -import os - -build_and_log("backtrace environment variable test") - -try: - del os.environ["BOUT_SHOW_BACKTRACE"] -except KeyError: - pass - -success = True -errors = [] - -_, output = shell("BOUT_SHOW_BACKTRACE=0 ./boutexcept", pipe=True) - -if "troublemaker" in output: - success = False - print( - f"Fail: detected offending function name in output when not expected:\n{output}" - ) - -_, output = shell("./boutexcept", pipe=True) - -if "troublemaker" not in output: - success = False - print( - f"Fail: did not detect offending function name in output when expected:\n{output}" - ) - -if success: - print("=> All BoutException backtrace tests passed") - exit(0) - -print("=> Some failed tests") -exit(1) diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py new file mode 100755 index 0000000000..4572010c62 --- /dev/null +++ b/tests/integrated/test-backtrace/test_backtrace.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python3 + +# Test enabling/disabling exception backtrace from environment variable + +# requires all_tests + +from boututils.run_wrapper import shell +import os + + +def test_backtrace(): + try: + del os.environ["BOUT_SHOW_BACKTRACE"] + except KeyError: + pass + + _, output = shell(["BOUT_SHOW_BACKTRACE=0 ./boutexcept"], pipe=True) + + assert "troublemaker" not in output, ( + f"Fail: detected offending function name in output when not expected\n{output}" + ) + + _, output = shell(["./boutexcept"], pipe=True) + + assert "troublemaker" in output, ( + f"Fail: did not detect offending function name in output when expected\n{output}" + ) diff --git a/tests/integrated/test-beuler/runtest b/tests/integrated/test-beuler/runtest deleted file mode 100755 index 00fb93708c..0000000000 --- a/tests/integrated/test-beuler/runtest +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env python3 - -# requires: petsc - -from boututils.run_wrapper import shell_safe, launch_safe - -from sys import exit - -nthreads = 1 -nproc = 1 - -print("Making solver test") -shell_safe("make > make.log") - -print("Running solver test") -status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True) -with open("run.log", "w") as f: - f.write(out) - -if status: - print(out) - -exit(status) diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py new file mode 100755 index 0000000000..ab028a9c2e --- /dev/null +++ b/tests/integrated/test-beuler/test_beuler.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 + +# requires: petsc + +from boututils.run_wrapper import shell_safe + + +def test_beuler(): + print("Running solver test") + status, out = shell_safe("./test_beuler", pipe=True) + with open("run.log", "w") as f: + f.write(out) + + assert status == 0, out diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py new file mode 100644 index 0000000000..1095b40a70 --- /dev/null +++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./runtest") diff --git a/tests/integrated/test-boutpp/collect-staggered/runtest b/tests/integrated/test-boutpp/collect-staggered/runtest deleted file mode 100755 index 25477c05ee..0000000000 --- a/tests/integrated/test-boutpp/collect-staggered/runtest +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env python3 -import boutpp as bc - -# requires boutpp -# requires not make - -bc.init("-q -q -q") - -fail = 0 -f = bc.create3D("sin(y)", outloc="YLOW") - -dump = bc.Options() -dump["f3d_evolve"].assignRepeat(f) -dump["f3d_once"] = f -bc.writeDefaultOutputFile(dump) - - -fc = bc.create3D("sin(y)", outloc="CENTRE") - -fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False) -fo = bc.Field3D.fromCollect("f3d_once", path="data", info=False) - -if fe.getLocation() == fc.getLocation(): - print("The loaded field should not be at CELL_CENTRE") - fail = 1 - -if fo.getLocation() == fc.getLocation(): - print("The loaded field should not be at CELL_CENTRE") - fail = 1 - - -def compare(a, b): - diff = a - bc.interp_to(b, a.getLocation()) - err = bc.max(bc.sqrt(diff * diff)) - return err - - -if compare(fc, f) > 1e-3: - print("Something is wrong. Maybe interpolation is broken") - fail = 1 - -if compare(fc, fe) > 1e-3: - print("Something is wrong. Maybe setting the location from field failed.") - fail = 1 - -if compare(fc, fo) > 1e-3: - print("Something is wrong. Maybe setting the location from field failed.") - fail = 1 - -exit(fail) diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py new file mode 100755 index 0000000000..d88595e434 --- /dev/null +++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py @@ -0,0 +1,54 @@ +#!/usr/bin/env python3 + +import boutpp as bc + +# requires boutpp +# requires not make + + +def test_boutpp_collect_staggered(run_isolated): + + if run_isolated(): + return + + bc.init("-q -q -q") + + fail = 0 + f = bc.create3D("sin(y)", outloc="YLOW") + + dump = bc.Options() + dump["f3d_evolve"].assignRepeat(f) + dump["f3d_once"] = f + bc.writeDefaultOutputFile(dump) + + fc = bc.create3D("sin(y)", outloc="CENTRE") + + fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False) + fo = bc.Field3D.fromCollect("f3d_once", path="data", info=False) + + if fe.getLocation() == fc.getLocation(): + print("The loaded field should not be at CELL_CENTRE") + fail = 1 + + if fo.getLocation() == fc.getLocation(): + print("The loaded field should not be at CELL_CENTRE") + fail = 1 + + def compare(a, b): + diff = a - bc.interp_to(b, a.getLocation()) + err = bc.max(bc.sqrt(diff * diff)) + return err + + if compare(fc, f) > 1e-3: + print("Something is wrong. Maybe interpolation is broken") + fail = 1 + + if compare(fc, fe) > 1e-3: + print("Something is wrong. Maybe setting the location from field failed.") + fail = 1 + + if compare(fc, fo) > 1e-3: + print("Something is wrong. Maybe setting the location from field failed.") + fail = 1 + + assert fail == 0 diff --git a/tests/integrated/test-boutpp/collect/runtest b/tests/integrated/test-boutpp/collect/runtest deleted file mode 100755 index 31d228d518..0000000000 --- a/tests/integrated/test-boutpp/collect/runtest +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env python3 -import boutpp as bc -import numpy as np -from boutdata import collect - -# requires boutpp -# requires not make - -bc.init("-d input".split(" ")) - -f = bc.Field3D.fromMesh(None) -f.setAll(np.array([[[1.0]]])) -f2 = bc.Field3D.fromMesh(None) -f2.setAll(np.array([[[2.0]]])) -print(f.getAll()) - -dump = bc.Options(f3d=f, f2d=f2) -bc.writeDefaultOutputFile(dump) - -errorlist = "" -n = collect("f2d", path="input", tind=-1, yguards=True) -print(n.shape) -T = collect("f3d", path="input", tind=-1, yguards=True) -print(n.shape) - -print("initialized mesh") -mesh = bc.Mesh.getGlobal() -print("initialized mesh") - -dens = bc.Field3D.fromMesh(mesh) -dens[:, :, :] = n.reshape((1, 1, 1)) -temp = bc.Field3D.fromCollect("f3d", path="input") -pres = dens + temp -print(slice(None, None, -2).indices(5)) -p = pres[::5, 0, ::-2] -pn = n + T -pn = pn.reshape(p.shape) -if not ((p == pn).all()): - errorlist += "addition not working\n" -pres = dens * temp * 1 -p = pres.getAll() -pn = n * T -pn = pn.reshape(p.shape) -if not ((p == pn).all()): - errorlist += "multiplication not working\n" -print(p.shape) -print(pn.shape) diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py new file mode 100755 index 0000000000..89ad9d6b5b --- /dev/null +++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py @@ -0,0 +1,53 @@ +#!/usr/bin/env python3 +import boutpp as bc +import numpy as np +from boutdata import collect + +# requires boutpp +# requires not make + + +def test_boutpp_collect(run_isolated): + + if run_isolated(): + return + + bc.init("-d input".split(" ")) + + f = bc.Field3D.fromMesh(None) + f.setAll(np.array([[[1.0]]])) + f2 = bc.Field3D.fromMesh(None) + f2.setAll(np.array([[[2.0]]])) + print(f.getAll()) + + dump = bc.Options(f3d=f, f2d=f2) + bc.writeDefaultOutputFile(dump) + + errorlist = "" + n = collect("f2d", path="input", tind=-1, yguards=True) + print(n.shape) + T = collect("f3d", path="input", tind=-1, yguards=True) + print(n.shape) + + print("initialized mesh") + mesh = bc.Mesh.getGlobal() + print("initialized mesh") + + dens = bc.Field3D.fromMesh(mesh) + dens[:, :, :] = n.reshape((1, 1, 1)) + temp = bc.Field3D.fromCollect("f3d", path="input") + pres = dens + temp + print(slice(None, None, -2).indices(5)) + p = pres[::5, 0, ::-2] + pn = n + T + pn = pn.reshape(p.shape) + if not ((p == pn).all()): + errorlist += "addition not working\n" + pres = dens * temp * 1 + p = pres.getAll() + pn = n * T + pn = pn.reshape(p.shape) + if not ((p == pn).all()): + errorlist += "multiplication not working\n" + print(p.shape) + print(pn.shape) diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py new file mode 100644 index 0000000000..09631a1fe6 --- /dev/null +++ b/tests/integrated/test-boutpp/conftest.py @@ -0,0 +1,98 @@ +import pytest +import os +import sys +import subprocess + + +@pytest.fixture(autouse=True, scope="function") +def unique_xdist_group(request): + # Unique group per test function (nodeid is unique, e.g., test_file.py::test_func) + group_name = ( + f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}" + ) + request.node.add_marker(pytest.mark.xdist_group(name=group_name)) + + +@pytest.fixture(scope="function") +def run_isolated(request): + """ + Spawns a fresh, isolated process for tests. + This prevents C++ singleton/MPI conflicts in xdist workers. + Returns a function that evaluates to True in the parent (to abort test execution) + and False in the child (to run the actual test). + """ + if os.environ.get("BOUT_ISOLATED_RUN") == "1": + return lambda: False + + # In the parent process, set up and run the child + nodeid = request.node.nodeid + + # Use the absolute path to the test file to avoid directory resolution issues + # fspath is the local path to the test file + root_dir = str(request.config.rootpath) + + env = os.environ.copy() + env["BOUT_ISOLATED_RUN"] = "1" + + # Disable xdist (-p no:xdist) in the subprocess to ensure a clean single-process run + # Use -o to disable the cache entirely in the subprocess + # Remove -c /dev/null so it stays in the project context + cmd = [ + sys.executable, + "-m", + "pytest", + nodeid, + "--rootdir", + root_dir, + "-p", + "no:xdist", + "-o", + "cache_dir=/tmp/pytest-cache", # Redirect cache to a writable place + "-c", + str(request.config.inifile or root_dir), # Point to actual config if it exists + ] + + result = subprocess.run(cmd, env=env, cwd=root_dir, capture_output=True, text=True) + + if result.returncode != 0: + pytest.fail( + f"Isolated test failed with exit code {result.returncode}\n" + f"--- STDERR ---\n{result.stderr}\n" + f"--- STDOUT ---\n{result.stdout}", + pytrace=False, + ) + + # Return True so the parent can exit the test cleanly without skipping. + return lambda: True + + +@pytest.fixture(autouse=True) +def sanitize_openmpi_env(): + """ + OpenMPI leaks state via environment variables (PMIX_*, OPAL_*). + This fixture removes them so subprocesses called via `mpirun` + don't crash thinking they are already initialized. + """ + # Find all problematic OpenMPI state variables + bad_prefixes = ("PMIX_", "OPAL_") + bad_exact = ( + "OMPI_COMM_WORLD_SIZE", + "OMPI_COMM_WORLD_RANK", + "OMPI_COMM_WORLD_LOCAL_RANK", + ) + + mpi_vars_to_remove = [ + k for k in os.environ if k.startswith(bad_prefixes) or k in bad_exact + ] + + # Save original variables + saved_env = {k: os.environ[k] for k in mpi_vars_to_remove} + + # Delete them from the current environment + for k in mpi_vars_to_remove: + del os.environ[k] + + yield # Run the test + + # Restore the environment after the test finishes + os.environ.update(saved_env) diff --git a/tests/integrated/test-boutpp/legacy-model/runtest b/tests/integrated/test-boutpp/legacy-model/runtest deleted file mode 100755 index ea5d06a06e..0000000000 --- a/tests/integrated/test-boutpp/legacy-model/runtest +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python3 -import boutpp -import sys - -# requires boutpp -# requires not make - -boutpp.init(sys.argv[1:]) - -dens = boutpp.create3D("0") - - -def rhs(time): - n_ddt = dens.ddt() - n_ddt[:, :, :] = dens * 0 - n_ddt += 1 - - -model = boutpp.PhysicsModelBase() -model.setRhs(rhs) -model.solve_for(n=dens) -model.solve() diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py new file mode 100755 index 0000000000..d1f6ea736a --- /dev/null +++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python3 +import boutpp + +# requires boutpp +# requires not make + + +def test_boutpp_legacy_model(run_isolated): + + if run_isolated(): + return + + boutpp.init([]) + + dens = boutpp.create3D("0") + + def rhs(time): + n_ddt = dens.ddt() + n_ddt[:, :, :] = dens * 0 + n_ddt += 1 + + model = boutpp.PhysicsModelBase() + model.setRhs(rhs) + model.solve_for(n=dens) + model.solve() diff --git a/tests/integrated/test-boutpp/mms-ddz/runtest b/tests/integrated/test-boutpp/mms-ddz/runtest deleted file mode 100755 index 02e87ae63a..0000000000 --- a/tests/integrated/test-boutpp/mms-ddz/runtest +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env python3 -import boutpp -import numpy as np - -# requires boutpp -# requires not make - -errorlist = "" -boutpp.init("-d data -q -q -q") # +" -f BOUT.settings") - -shapes = [] -errors = [] -mmax = 7 -start = 6 -doPlot = False -nzs = np.logspace(start, mmax, num=mmax - start + 1, base=2) -for nz in nzs: - boutpp.setOption("meshz:nz", "%d" % nz, force=True) - boutpp.setOption("meshz:dz", "2*pi/%d" % nz, force=True) - mesh = boutpp.Mesh(section="meshz") - f = boutpp.create3D("sin(z)", mesh) - sim = boutpp.DDZ(f) - ana = boutpp.create3D("cos(z)", mesh) - err = sim - ana - err = np.max(np.abs(err.getAll())) - errors.append(err) - -if doPlot: - from matplotlib import pyplot as plt - - plt.plot(1 / np.array(nzs), errors, "-o") - plt.show() - -errc = np.log(errors[-2] / errors[-1]) -difc = np.log(nzs[-1] / nzs[-2]) -conv = errc / difc - -if 1.9 < conv < 2.1: - print("The convergence is: %f" % conv) -else: - errorlist += "DDZ is not working\n" - -if errorlist != "": - print("Found errors:\n%s" % errorlist) - exit(1) diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py new file mode 100755 index 0000000000..1e2421e59b --- /dev/null +++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py @@ -0,0 +1,50 @@ +#!/usr/bin/env python3 +import boutpp +import numpy as np + +# requires boutpp +# requires not make + + +def test_boutpp_mms_ddz(run_isolated): + + if run_isolated(): + return + + errorlist = "" + boutpp.init("-d data -q -q -q") # +" -f BOUT.settings") + + errors = [] + mmax = 7 + start = 6 + doPlot = False + nzs = np.logspace(start, mmax, num=mmax - start + 1, base=2) + for nz in nzs: + boutpp.setOption("meshz:nz", "%d" % nz, force=True) + boutpp.setOption("meshz:dz", "2*pi/%d" % nz, force=True) + mesh = boutpp.Mesh(section="meshz") + f = boutpp.create3D("sin(z)", mesh) + sim = boutpp.DDZ(f) + ana = boutpp.create3D("cos(z)", mesh) + err = sim - ana + err = np.max(np.abs(err.getAll())) + errors.append(err) + + if doPlot: + from matplotlib import pyplot as plt + + plt.plot(1 / np.array(nzs), errors, "-o") + plt.show() + + errc = np.log(errors[-2] / errors[-1]) + difc = np.log(nzs[-1] / nzs[-2]) + conv = errc / difc + + if 1.9 < conv < 2.1: + print("The convergence is: %f" % conv) + else: + errorlist += "DDZ is not working\n" + + if errorlist != "": + print("Found errors:\n%s" % errorlist) + exit(1) diff --git a/tests/integrated/test-boutpp/print/CMakeLists.txt b/tests/integrated/test-boutpp/print/CMakeLists.txt index 84b005df89..edc17cd407 100644 --- a/tests/integrated/test-boutpp/print/CMakeLists.txt +++ b/tests/integrated/test-boutpp/print/CMakeLists.txt @@ -1,6 +1,5 @@ bout_add_integrated_test( test-boutpp-print - USE_RUNTEST EXTRA_FILES test/BOUT.inp test.py REQUIRES BOUT_ENABLE_PYTHON ) diff --git a/tests/integrated/test-boutpp/print/runtest b/tests/integrated/test-boutpp/print/runtest deleted file mode 100755 index 4b68c692aa..0000000000 --- a/tests/integrated/test-boutpp/print/runtest +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh -# requires boutpp -# requires not make - -set -ex - -testit() { - msg="$@" - python3 test.py $msg > out.log - grep "$msg" out.log - grep "$msg" test/BOUT.log.0 -} - -testit Can we print to the log from python? 🎉 '__does_it_still__work {} {:s}' diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py new file mode 100644 index 0000000000..26934a0080 --- /dev/null +++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py @@ -0,0 +1,20 @@ +import subprocess + + +def test_boutpp_print(run_isolated): + + if run_isolated(): + return + + msg = "Can we print to the log from python? 🎉 __does_it_still__work {} {:s}" + cmd = ["python3", "test.py", msg] + + print(f"+ python3 test.py {msg} > out.log") + with open("out.log", "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + with open("out.log", "r") as f: + assert msg in f.read(), f"Error: '{msg}' not found in out.log" + + with open("test/BOUT.log.0", "r") as f: + assert msg in f.read(), f"Error: '{msg}' not found in test/BOUT.log.0" diff --git a/tests/integrated/test-boutpp/simple-model/runtest b/tests/integrated/test-boutpp/simple-model/runtest deleted file mode 100755 index d1a6b573b7..0000000000 --- a/tests/integrated/test-boutpp/simple-model/runtest +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env python3 - -# requires boutpp -# requires not make - -from boutpp import * - -init("-d mini") - - -class MyModel(PhysicsModel): - def init(self, restart): - self.n = create3D("dens:function") - self.solve_for(dens=self.n) - - def rhs(self, time): - self.n.ddt(DDX(self.n)) - - -model = MyModel() -model.solve() diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py new file mode 100755 index 0000000000..a443f22cd8 --- /dev/null +++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python3 + +# requires boutpp +# requires not make + +import boutpp + + +def test_boutpp_simple_model(run_isolated): + + if run_isolated(): + return + + boutpp.init("-d mini") + + class MyModel(boutpp.PhysicsModel): + def init(self, restart): + self.n = boutpp.create3D("dens:function") + self.solve_for(dens=self.n) + + def rhs(self, time): + self.n.ddt(boutpp.DDX(self.n)) + + model = MyModel() + model.solve() diff --git a/tests/integrated/test-boutpp/slicing/runtest b/tests/integrated/test-boutpp/slicing/runtest deleted file mode 100755 index 781e3593a4..0000000000 --- a/tests/integrated/test-boutpp/slicing/runtest +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env python3 -# requires boutpp -# requires not make - -import numpy as np -import boutpp as bc -import inspect - -bc.init("-d test") -mesh = bc.Mesh.getGlobal() -field = bc.Field3D.fromMesh(mesh) -ndat = np.random.random(field.shape) -field[:] = ndat - -assert np.all(ndat == field[:]) - -examples = [ - lambda x: x[2], - lambda x: x[-2], - lambda x: x[1, 3], - lambda x: x[1, -1], - lambda x: x[0], - lambda x: x[0][2], - lambda x: x[1:7:2], - lambda x: x[-2:10], - lambda x: x[-3:3:-1], - lambda x: x[5:], - lambda x: x[1:2], - lambda x: x[..., 0], - lambda x: x[:, :, 0], - lambda x: x[np.array([3, 3, 1, 8])], - lambda x: x[np.array([3, 3, -3, 8])], - lambda x: x[np.array([1, -1])], - lambda x: x[np.array([3, 4])], - lambda x: x[[0, 1, 2], [0, 1, 0]], - lambda x: x[1:2, 1:3], - lambda x: x[1:2, [1, 2]], - lambda x: x[ndat < 0], -] - -print(field.shape) -for ex in examples: - print("testing", inspect.getsource(ex)) - try: - nout = ex(ndat) - fout = ex(field) - assert ( - fout.shape == nout.shape - ), f"Field3D returned {{ fout.shape }} but numpy {{ nout.shape }}" - assert np.all(fout == nout), f"data mismatch, {{ fout == nout }}" - except: - print("Failed to test", inspect.getsource(ex)) - raise diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py new file mode 100755 index 0000000000..cffc767bf8 --- /dev/null +++ b/tests/integrated/test-boutpp/slicing/test_slicing.py @@ -0,0 +1,54 @@ +#!/usr/bin/env python3 +# requires boutpp +# requires not make +import numpy as np +import numpy.testing as npt +import boutpp as bc +import inspect + + +def test_slicing(): + + bc.init("-d test") + + mesh = bc.Mesh.getGlobal() + field = bc.Field3D.fromMesh(mesh) + ndat = np.random.random(field.shape) + field[:] = ndat + + npt.assert_allclose(ndat, field[:]) + + examples = [ + lambda x: x[2], + lambda x: x[-2], + lambda x: x[1, 3], + lambda x: x[1, -1], + lambda x: x[0], + lambda x: x[0][2], + lambda x: x[1:7:2], + lambda x: x[-2:10], + lambda x: x[-3:3:-1], + lambda x: x[5:], + lambda x: x[1:2], + lambda x: x[..., 0], + lambda x: x[:, :, 0], + lambda x: x[np.array([3, 3, 1, 8])], + lambda x: x[np.array([3, 3, -3, 8])], + lambda x: x[np.array([1, -1])], + lambda x: x[np.array([3, 4])], + lambda x: x[[0, 1, 2], [0, 1, 0]], + lambda x: x[1:2, 1:3], + lambda x: x[1:2, [1, 2]], + lambda x: x[ndat < 0], + ] + + print(field.shape) + for ex in examples: + print("testing", inspect.getsource(ex)) + nout = ex(ndat) + fout = ex(field) + npt.assert_allclose( + fout, + nout, + err_msg=f"data mismatch, {{ fout == nout }}. Failed to test {inspect.getsource(ex)}", + ) diff --git a/tests/integrated/test-code-style/README.md b/tests/integrated/test-code-style/README.md deleted file mode 100644 index 602c41d8d5..0000000000 --- a/tests/integrated/test-code-style/README.md +++ /dev/null @@ -1,9 +0,0 @@ -Coding Style Test -================= - -Test for a few parts of the coding style. -For example options should be passed as non-const value for small datatypes (`int`,`char`,`BoutReal`,...) - -```C++ -void fu(int a); -``` \ No newline at end of file diff --git a/tests/integrated/test-code-style/runtest b/tests/integrated/test-code-style/runtest deleted file mode 100755 index d392f9110f..0000000000 --- a/tests/integrated/test-code-style/runtest +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env bash - -#requires not make - -BOUT_TOP=../../.. -error= - -paths="src include examples tests" - - -# Check that exceptions are caught by reference -for path in $paths -do - catch_errors=$(grep catch[^\(]*\([^\(]*Bout $BOUT_TOP/$path --include=*xx -r|grep -v '&') - ex=$? - if test $ex -eq 0 - then - error=yes - echo "Found catch by value - not by reference:" - echo "$catch_errors" - fi -done - - -# Return -if test $error -then - echo "-> Errors listed above" - exit 1 -else - echo "No Errors detected" - exit 0 -fi diff --git a/tests/integrated/test-collect/runtest b/tests/integrated/test-collect/runtest deleted file mode 100755 index a1ebb8e3c7..0000000000 --- a/tests/integrated/test-collect/runtest +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env python3 - -# requires: all_tests - -from boututils.run_wrapper import shell, shell_safe - -from boutdata import collect -import numpy as np - -shell_safe("make > make.log") - -shell_safe("./test-collect") - -# Try collecting data using incorrect case -# This should be corrected automatically -a = collect("A", path="data") - -if not np.allclose(a, 1.23): - print("Wrong value => Failed") - print(a) - exit(1) - -print("Passed") -exit(0) diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py new file mode 100755 index 0000000000..eade57557a --- /dev/null +++ b/tests/integrated/test-collect/test_collect.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 + +# requires: all_tests + +from boututils.run_wrapper import shell_safe + +from boutdata import collect +import numpy.testing as npt + + +def test_collect(): + + shell_safe("./test-collect") + + # Try collecting data using incorrect case + # This should be corrected automatically + a = collect("A", path="data") + + npt.assert_allclose(a, 1.23, err_msg=f"Wrong value => Failed: {a}") diff --git a/tests/integrated/test-command-args/runtest b/tests/integrated/test-command-args/test_command_args.py similarity index 89% rename from tests/integrated/test-command-args/runtest rename to tests/integrated/test-command-args/test_command_args.py index a8dc3f020c..c8f786ef4f 100755 --- a/tests/integrated/test-command-args/runtest +++ b/tests/integrated/test-command-args/test_command_args.py @@ -1,25 +1,26 @@ #!/usr/bin/env python3 -from boututils.run_wrapper import build_and_log, launch_safe -import os +from boututils.run_wrapper import launch_safe +from pathlib import Path import re import shutil import unittest import platform -OUTPUT_FILE = "stdout.log" if platform.system() == "FreeBSD" else "stderr.log" + +OUTPUT_FILE = Path("stdout.log") if platform.system() == "FreeBSD" else "stderr.log" class TestCommandLineArgs(unittest.TestCase): command = "./command-args >stdout.log 2>stderr.log" def makeDirAndCopyInput(self, path): - os.mkdir(path) + Path.mkdir(path) shutil.copy("BOUT.inp", path) def setUp(self): try: - os.remove(OUTPUT_FILE) + Path.unlink(OUTPUT_FILE) except OSError: pass shutil.rmtree("./data", ignore_errors=True) @@ -52,11 +53,11 @@ def testNoArgumentsDefaultDirectory(self): self.makeDirAndCopyInput("data") launch_safe(self.command, pipe=True, nproc=1, mthread=1) self.assertTrue( - os.path.exists("data/BOUT.settings"), + Path("data/BOUT.settings").exists(), msg="FAIL: No BOUT.settings file in data directory", ) self.assertTrue( - os.path.exists("data/BOUT.log.0"), + Path("data/BOUT.log.0").exists(), msg="FAIL: No BOUT.log.0 file in data directory", ) @@ -64,11 +65,11 @@ def testShortLogArgument(self): self.makeDirAndCopyInput("data") launch_safe(self.command + " -l different.log", pipe=True, nproc=1, mthread=1) self.assertFalse( - os.path.exists("data/BOUT.log.0"), + Path("data/BOUT.log.0").exists(), msg="FAIL: BOUT.log.0 file in data directory", ) self.assertTrue( - os.path.exists("data/different.log.0"), + Path("data/different.log.0").exists(), msg="FAIL: no different.log.0 file in data directory", ) @@ -76,22 +77,22 @@ def testLongLogArgument(self): self.makeDirAndCopyInput("data") launch_safe(self.command + " --log log", pipe=True, nproc=1, mthread=1) self.assertFalse( - os.path.exists("data/BOUT.log.0"), + Path("data/BOUT.log.0").exists(), msg="FAIL: BOUT.log.0 file in data directory", ) self.assertTrue( - os.path.exists("data/log.0"), msg="FAIL: no log.0 file in data directory" + Path("data/log.0").exists(), msg="FAIL: no log.0 file in data directory" ) def testDirectoryArgument(self): self.makeDirAndCopyInput("test") launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1) self.assertTrue( - os.path.exists("test/BOUT.settings"), + Path("test/BOUT.settings").exists(), msg="FAIL: No BOUT.settings file in test directory", ) self.assertTrue( - os.path.exists("test/BOUT.log.0"), + Path("test/BOUT.log.0").exists(), msg="FAIL: No BOUT.log.0 file in data directory", ) @@ -114,7 +115,7 @@ def testDirectoryArgumentNonDirectory(self): with open(OUTPUT_FILE) as f: contents = f.read() self.assertIn( - '"runtest" is not a directory', + 'DataDir "runtest" does not exist or is not accessible', contents, msg="FAIL: Error message not printed when missing input directory", ) @@ -199,5 +200,4 @@ def testCommandLineOptionsArePrinted(self): if __name__ == "__main__": - build_and_log("Command arguments test") unittest.main(verbosity=2) diff --git a/tests/integrated/test-communications/runtest b/tests/integrated/test-communications/runtest deleted file mode 100755 index 7c89f0630a..0000000000 --- a/tests/integrated/test-communications/runtest +++ /dev/null @@ -1,429 +0,0 @@ -#!/usr/bin/env python3 - -import numpy as np -from sys import exit - -from boututils.datafile import DataFile -from boututils.run_wrapper import build_and_log, shell, launch_safe - -# Cores: 18 -# Requires: netcdf - -# Note, the expected values for the communicated cells, which are used to test the -# results, are shown in corner_communication_diagram.ods - -################################################# -# Test disconnected-double-null diverted topology -################################################# - -nype = 6 # need at least 6 to include all regions - -# run with processor splitting at separatrices -################################################## - -# With nxpe=3, both separatrices are on processor boundaries -nxpe = 3 -command = "./test-communications NXPE=" + str(nxpe) - -build_and_log("Communications Test") - -# remove old outputs -shell("rm data/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run.log." + str(nxpe), "w") as f: - f.write(out) - - -def test(actual, expected, procnum, region, boundary): - if not np.all(np.array(np.rint(actual).astype(int)) == np.array(expected)): - print( - "failed in {} boundary of region {} ({}). Expected: {} Actual: {}".format( - boundary, procnum, region, expected, actual - ) - ) - exit(1) - - -region = "lower, inner PF" -f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [72, 73], 0, region, "inner x") -test(f[-1, 1:-1], [24, 25], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y") -test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y") - -region = "lower, inner between separatrices" -f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [12, 13], 0, region, "inner x") -test(f[-1, 1:-1], [48, 49], 0, region, "outer x") -test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y") -test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y") - -region = "lower, inner SOL" -f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [36, 37], 0, region, "inner x") -test(f[-1, 1:-1], [84, 85], 0, region, "outer x") -test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y") - -region = "inner core" -f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [74, 75], 0, region, "inner x") -test(f[-1, 1:-1], [26, 27], 0, region, "outer x") -test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y") -test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y") - -region = "inner between separatrices" -f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [14, 15], 0, region, "inner x") -test(f[-1, 1:-1], [50, 51], 0, region, "outer x") -test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y") -test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y") - -region = "inner SOL" -f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [38, 39], 0, region, "inner x") -test(f[-1, 1:-1], [86, 87], 0, region, "outer x") -test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y") -test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y") - -region = "upper inner PF" -f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [76, 77], 0, region, "inner x") -test(f[-1, 1:-1], [28, 29], 0, region, "outer x") -test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y") - -region = "upper inner SOL, nearer PF" -f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [16, 17], 0, region, "inner x") -test(f[-1, 1:-1], [52, 53], 0, region, "outer x") -test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y") -test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y") - -region = "upper inner SOL, further from PF" -f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [40, 41], 0, region, "inner x") -test(f[-1, 1:-1], [88, 89], 0, region, "outer x") -test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y") -test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y") - -region = "upper outer PF" -f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [78, 79], 0, region, "inner x") -test(f[-1, 1:-1], [30, 31], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y") -test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y") - -region = "upper outer SOL, nearer PF" -f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [18, 19], 0, region, "inner x") -test(f[-1, 1:-1], [54, 55], 0, region, "outer x") -test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y") -test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y") - -region = "upper outer SOL, further from PF" -f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [42, 43], 0, region, "inner x") -test(f[-1, 1:-1], [90, 91], 0, region, "outer x") -test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y") - -region = "outer core" -f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [80, 81], 0, region, "inner x") -test(f[-1, 1:-1], [32, 33], 0, region, "outer x") -test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y") -test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y") - -region = "outer between separatrices" -f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [20, 21], 0, region, "inner x") -test(f[-1, 1:-1], [56, 57], 0, region, "outer x") -test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y") -test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y") - -region = "outer SOL" -f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [44, 45], 0, region, "inner x") -test(f[-1, 1:-1], [92, 93], 0, region, "outer x") -test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y") -test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y") - -region = "lower outer PF" -f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [82, 83], 0, region, "inner x") -test(f[-1, 1:-1], [34, 35], 0, region, "outer x") -test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y") - -region = "lower outer between separatrices" -f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [22, 23], 0, region, "inner x") -test(f[-1, 1:-1], [58, 59], 0, region, "outer x") -test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y") -test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y") - -region = "lower outer SOL" -f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [46, 47], 0, region, "inner x") -test(f[-1, 1:-1], [94, 95], 0, region, "outer x") -test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y") -test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y") - -# run with processor splitting not at separatrices -################################################## - -# With nxpe=2, neither separatrix is on a processor boundary -nxpe = 2 -command = "./test-communications NXPE=" + str(nxpe) - -# remove old outputs -shell("rm data/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run.log." + str(nxpe), "w") as f: - f.write(out) - -region = "lower, inner leg, interior" -f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [72, 73], 0, region, "inner x") -test(f[-1, 1:-1], [36, 37], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y") -test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y") - -region = "lower, inner leg, exterior" -f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [24, 25], 0, region, "inner x") -test(f[-1, 1:-1], [84, 85], 0, region, "outer x") -test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y") - -region = "inner, interior" -f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [74, 75], 0, region, "inner x") -test(f[-1, 1:-1], [38, 39], 0, region, "outer x") -test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y") -test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y") - -region = "inner, exterior" -f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [26, 27], 0, region, "inner x") -test(f[-1, 1:-1], [86, 87], 0, region, "outer x") -test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y") -test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y") - -region = "upper, inner leg, interior" -f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [76, 77], 0, region, "inner x") -test(f[-1, 1:-1], [40, 41], 0, region, "outer x") -test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y") - -region = "upper, inner leg, exterior" -f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [28, 29], 0, region, "inner x") -test(f[-1, 1:-1], [88, 89], 0, region, "outer x") -test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y") -test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y") - -region = "upper, outer leg, interior" -f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [78, 79], 0, region, "inner x") -test(f[-1, 1:-1], [42, 43], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y") -test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y") - -region = "upper, outer leg, exterior" -f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [30, 31], 0, region, "inner x") -test(f[-1, 1:-1], [90, 91], 0, region, "outer x") -test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y") - -region = "outer, interior" -f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [80, 81], 0, region, "inner x") -test(f[-1, 1:-1], [44, 45], 0, region, "outer x") -test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y") -test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y") - -region = "outer, exterior" -f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [32, 33], 0, region, "inner x") -test(f[-1, 1:-1], [92, 93], 0, region, "outer x") -test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y") -test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y") - -region = "lower, outer leg, interior" -f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [82, 83], 0, region, "inner x") -test(f[-1, 1:-1], [46, 47], 0, region, "outer x") -test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y") - -region = "lower, outer leg, exterior" -f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [34, 35], 0, region, "inner x") -test(f[-1, 1:-1], [94, 95], 0, region, "outer x") -test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y") -test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y") - -# run with no processor splitting in the x-direction -#################################################### - -nxpe = 1 -command = "./test-communications NXPE=" + str(nxpe) - -# remove old outputs -shell("rm data/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run.log." + str(nxpe), "w") as f: - f.write(out) - -region = "lower, inner leg" -f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [72, 73], 0, region, "inner x") -test(f[-1, 1:-1], [84, 85], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y") - -region = "inner" -f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [74, 75], 0, region, "inner x") -test(f[-1, 1:-1], [86, 87], 0, region, "outer x") -test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y") -test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y") - -region = "upper, inner leg" -f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [76, 77], 0, region, "inner x") -test(f[-1, 1:-1], [88, 89], 0, region, "outer x") -test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y") - -region = "upper, outer leg" -f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [78, 79], 0, region, "inner x") -test(f[-1, 1:-1], [90, 91], 0, region, "outer x") -test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y") -test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y") - -region = "outer" -f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [80, 81], 0, region, "inner x") -test(f[-1, 1:-1], [92, 93], 0, region, "outer x") -test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y") -test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y") - -region = "lower, outer leg" -f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [82, 83], 0, region, "inner x") -test(f[-1, 1:-1], [94, 95], 0, region, "outer x") -test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y") -test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y") - - -################################################# -# Test limiter topology -################################################# - -nype = 1 - -# run with processor splitting at the separatrix -#################################################### - -nxpe = 3 -command = "./test-communications -d data_limiter NXPE=" + str(nxpe) - -# remove old outputs -shell("rm data_limiter/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run_limiter.log." + str(nxpe), "w") as f: - f.write(out) - -region = "core" -f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [12, 13], 0, region, "inner x") -test(f[-1, 1:-1], [4, 5], 0, region, "outer x") -test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y") -test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y") - -region = "interior SOL" -f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [2, 3], 0, region, "inner x") -test(f[-1, 1:-1], [8, 9], 0, region, "outer x") -test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y") -test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y") - -region = "exterior SOL" -f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [6, 7], 0, region, "inner x") -test(f[-1, 1:-1], [14, 15], 0, region, "outer x") -test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y") -test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y") - -# run with processor splitting not at the separatrix -#################################################### - -nxpe = 2 -command = "./test-communications -d data_limiter NXPE=" + str(nxpe) - -# remove old outputs -shell("rm data_limiter/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run_limiter.log." + str(nxpe), "w") as f: - f.write(out) - -region = "interior" -f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [12, 13], 0, region, "inner x") -test(f[-1, 1:-1], [6, 7], 0, region, "outer x") -test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y") -test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y") - -region = "exterior" -f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [4, 5], 0, region, "inner x") -test(f[-1, 1:-1], [14, 15], 0, region, "outer x") -test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y") -test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y") - -# run with no processor splitting in the x-direction -#################################################### - -nxpe = 1 -command = "./test-communications -d data_limiter NXPE=" + str(nxpe) - -# remove old outputs -shell("rm data_limiter/BOUT.dmp.*") - -print("Running Communications Test, nproc=" + str(nxpe * nype)) - -s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) -with open("run_limiter.log." + str(nxpe), "w") as f: - f.write(out) - -region = "all" -f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] -test(f[0, 1:-1], [12, 13], 0, region, "inner x") -test(f[-1, 1:-1], [14, 15], 0, region, "outer x") -test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y") -test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y") - -# If we did not exit already, then all tests passed -print("Pass") -exit(0) diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py new file mode 100755 index 0000000000..75150ccde1 --- /dev/null +++ b/tests/integrated/test-communications/test_communications.py @@ -0,0 +1,426 @@ +#!/usr/bin/env python3 +import os +import numpy as np +import numpy.testing as npt +from boututils.datafile import DataFile +from boututils.run_wrapper import shell, launch_safe + +# Cores: 18 +# Requires: netcdf + +# Note, the expected values for the communicated cells, which are used to test the +# results, are shown in corner_communication_diagram.ods + + +def run_test(actual, expected, procnum, region, boundary): + npt.assert_allclose( + np.array(np.rint(actual).astype(int)), + np.array(expected), + err_msg=f"failed in {boundary} boundary of region {procnum} ({region}). " + f"Expected: {expected} Actual: {actual}", + ) + + +def test_communications(): + + ################################################# + # Test disconnected-double-null diverted topology + ################################################# + + nype = 6 # need at least 6 to include all regions + + # run with processor splitting at separatrices + ################################################## + + # MPI oversubscribe for communications test + os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1" # Allows 18 procs + + # With nxpe=3, both separatrices are on processor boundaries + nxpe = 3 + command = "./test-communications NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run.log." + str(nxpe), "w") as f: + f.write(out) + + region = "lower, inner PF" + f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [72, 73], 0, region, "inner x") + run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y") + run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y") + + region = "lower, inner between separatrices" + f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [12, 13], 0, region, "inner x") + run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x") + run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y") + run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y") + + region = "lower, inner SOL" + f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [36, 37], 0, region, "inner x") + run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x") + run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y") + + region = "inner core" + f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [74, 75], 0, region, "inner x") + run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x") + run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y") + run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y") + + region = "inner between separatrices" + f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [14, 15], 0, region, "inner x") + run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x") + run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y") + run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y") + + region = "inner SOL" + f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [38, 39], 0, region, "inner x") + run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x") + run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y") + run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y") + + region = "upper inner PF" + f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [76, 77], 0, region, "inner x") + run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x") + run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y") + + region = "upper inner SOL, nearer PF" + f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [16, 17], 0, region, "inner x") + run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x") + run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y") + run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y") + + region = "upper inner SOL, further from PF" + f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [40, 41], 0, region, "inner x") + run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x") + run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y") + run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y") + + region = "upper outer PF" + f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [78, 79], 0, region, "inner x") + run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y") + run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y") + + region = "upper outer SOL, nearer PF" + f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [18, 19], 0, region, "inner x") + run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x") + run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y") + run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y") + + region = "upper outer SOL, further from PF" + f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [42, 43], 0, region, "inner x") + run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x") + run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y") + + region = "outer core" + f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [80, 81], 0, region, "inner x") + run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x") + run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y") + run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y") + + region = "outer between separatrices" + f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [20, 21], 0, region, "inner x") + run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x") + run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y") + run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y") + + region = "outer SOL" + f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [44, 45], 0, region, "inner x") + run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x") + run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y") + run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y") + + region = "lower outer PF" + f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [82, 83], 0, region, "inner x") + run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x") + run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y") + + region = "lower outer between separatrices" + f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [22, 23], 0, region, "inner x") + run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x") + run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y") + run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y") + + region = "lower outer SOL" + f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [46, 47], 0, region, "inner x") + run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x") + run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y") + run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y") + + # run with processor splitting not at separatrices + ################################################## + + # With nxpe=2, neither separatrix is on a processor boundary + nxpe = 2 + command = "./test-communications NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run.log." + str(nxpe), "w") as f: + f.write(out) + + region = "lower, inner leg, interior" + f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [72, 73], 0, region, "inner x") + run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y") + run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y") + + region = "lower, inner leg, exterior" + f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [24, 25], 0, region, "inner x") + run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x") + run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y") + + region = "inner, interior" + f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [74, 75], 0, region, "inner x") + run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x") + run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y") + run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y") + + region = "inner, exterior" + f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [26, 27], 0, region, "inner x") + run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x") + run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y") + run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y") + + region = "upper, inner leg, interior" + f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [76, 77], 0, region, "inner x") + run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x") + run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y") + + region = "upper, inner leg, exterior" + f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [28, 29], 0, region, "inner x") + run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x") + run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y") + run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y") + + region = "upper, outer leg, interior" + f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [78, 79], 0, region, "inner x") + run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y") + run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y") + + region = "upper, outer leg, exterior" + f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [30, 31], 0, region, "inner x") + run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x") + run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y") + + region = "outer, interior" + f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [80, 81], 0, region, "inner x") + run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x") + run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y") + run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y") + + region = "outer, exterior" + f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [32, 33], 0, region, "inner x") + run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x") + run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y") + run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y") + + region = "lower, outer leg, interior" + f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [82, 83], 0, region, "inner x") + run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x") + run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y") + + region = "lower, outer leg, exterior" + f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [34, 35], 0, region, "inner x") + run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x") + run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y") + run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y") + + # run with no processor splitting in the x-direction + #################################################### + + nxpe = 1 + + command = "./test-communications NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run.log." + str(nxpe), "w") as f: + f.write(out) + + region = "lower, inner leg" + f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [72, 73], 0, region, "inner x") + run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y") + + region = "inner" + f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [74, 75], 0, region, "inner x") + run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x") + run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y") + run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y") + + region = "upper, inner leg" + f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [76, 77], 0, region, "inner x") + run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x") + run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y") + + region = "upper, outer leg" + f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [78, 79], 0, region, "inner x") + run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x") + run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y") + run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y") + + region = "outer" + f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [80, 81], 0, region, "inner x") + run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x") + run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y") + run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y") + + region = "lower, outer leg" + f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [82, 83], 0, region, "inner x") + run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x") + run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y") + run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y") + + ################################################# + # Test limiter topology + ################################################# + + nype = 1 + + # run with processor splitting at the separatrix + #################################################### + + nxpe = 3 + command = "./test-communications -d data_limiter NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data_limiter/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run_limiter.log." + str(nxpe), "w") as f: + f.write(out) + + region = "core" + f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [12, 13], 0, region, "inner x") + run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x") + run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y") + run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y") + + region = "interior SOL" + f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [2, 3], 0, region, "inner x") + run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x") + run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y") + run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y") + + region = "exterior SOL" + f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [6, 7], 0, region, "inner x") + run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x") + run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y") + run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y") + + # run with processor splitting not at the separatrix + #################################################### + + nxpe = 2 + command = "./test-communications -d data_limiter NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data_limiter/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run_limiter.log." + str(nxpe), "w") as f: + f.write(out) + + region = "interior" + f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [12, 13], 0, region, "inner x") + run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x") + run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y") + run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y") + + region = "exterior" + f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [4, 5], 0, region, "inner x") + run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x") + run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y") + run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y") + + # run with no processor splitting in the x-direction + #################################################### + + nxpe = 1 + command = "./test-communications -d data_limiter NXPE=" + str(nxpe) + + # remove old outputs + shell(["rm data_limiter/BOUT.dmp.*"]) + + print("Running Communications Test, nproc=" + str(nxpe * nype)) + + s, out = launch_safe(command, nproc=nxpe * nype, pipe=True) + with open("run_limiter.log." + str(nxpe), "w") as f: + f.write(out) + + region = "all" + f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0] + run_test(f[0, 1:-1], [12, 13], 0, region, "inner x") + run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x") + run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y") + run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y") diff --git a/tests/integrated/test-compile-examples-petsc/README.md b/tests/integrated/test-compile-examples-petsc/README.md deleted file mode 120000 index 77bd1f7308..0000000000 --- a/tests/integrated/test-compile-examples-petsc/README.md +++ /dev/null @@ -1 +0,0 @@ -../test-compile-examples/README.md \ No newline at end of file diff --git a/tests/integrated/test-compile-examples-petsc/runtest b/tests/integrated/test-compile-examples-petsc/runtest deleted file mode 100755 index 0f9625af40..0000000000 --- a/tests/integrated/test-compile-examples-petsc/runtest +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env bash - -#requires: all_tests -#requires: not make -#requires: petsc - -BOUT_TOP=../../.. -export PATH=$(pwd)/$BOUT_TOP/bin:$PATH - -error=0 - -failed= -for target in $(find $BOUT_TOP/examples/ -name makefile) -do - dir=$(dirname ${target}) - if grep ":.*requires_petsc" $target -q; - then - echo "Trying to compile ${dir}" - - (cd ${dir} && make 2>&1) - ex=$? - - if test $ex -gt 0 - then - echo $(basename $dir) failed - error=1 - failed="$failed\n$(basename $dir) failed" - fi - else - echo "Skipping $dir - requires PETSc" - fi -done - -echo -e $failed - -exit $error diff --git a/tests/integrated/test-compile-examples/README.md b/tests/integrated/test-compile-examples/README.md deleted file mode 100644 index 2fa005c7c4..0000000000 --- a/tests/integrated/test-compile-examples/README.md +++ /dev/null @@ -1,13 +0,0 @@ -test-compile-examples -===================== - -This test ensures that all models in examples can be compiled. - -This currently works by finding any makefile located beneath -examples. It skips any directories matching doc in order to skip -documentation. Building documentation requires often additional -tools, and is thus skipped. The test is split in two parts, one for -examples without PETSc, and one for examples that require PETSc. - -PETSc detection works by checking the makefile whether any target -requires `requires_petsc`. diff --git a/tests/integrated/test-compile-examples/runtest b/tests/integrated/test-compile-examples/runtest deleted file mode 100755 index 765ea2cbfd..0000000000 --- a/tests/integrated/test-compile-examples/runtest +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env bash - -#requires: all_tests -#requires: not make - -BOUT_TOP=../../.. -export PATH=$(pwd)/$BOUT_TOP/bin:$PATH - -error=0 - -failed= -for target in $(find $BOUT_TOP/examples/ -name makefile | grep -v doc) -do - dir=$(dirname ${target}) - if grep ":.*requires_petsc" $target -q; - then - echo "Skipping $dir - requires PETSc" - else - echo "Trying to compile ${dir}" - - (cd ${dir} && make 2>&1) - ex=$? - - if test $ex -gt 0 - then - dir=${dir#../../../examples/} - echo $dir failed - error=1 - failed="$failed\n$dir failed" - fi - fi -done - -echo -e $failed - -exit $error diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py new file mode 100644 index 0000000000..64a438d1dc --- /dev/null +++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py @@ -0,0 +1,6 @@ +import pytest + + +@pytest.mark.serial +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./runtest") diff --git a/tests/integrated/test-cyclic/runtest b/tests/integrated/test-cyclic/runtest deleted file mode 100755 index c68f9b033e..0000000000 --- a/tests/integrated/test-cyclic/runtest +++ /dev/null @@ -1,54 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, check it completed successfully -# - -# Requires: netcdf -# Cores: 4 - -from __future__ import print_function - -try: - from builtins import str -except: - pass -from boututils.run_wrapper import build_and_log, shell, launch -from boutdata.collect import collect -from sys import stdout, exit - -build_and_log("Cyclic Reduction test") - -flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"] - -code = 0 # Return code -for nproc in [1, 2, 4]: - cmd = "./test_cyclic" - - print(" %d processors...." % (nproc)) - r = 0 - for f in flags: - stdout.write("\tflags '" + f + "' ... ") - - shell("rm data/BOUT.dmp.* 2> err.log") - - # Run the case - status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True) - with open(f"run.log.{nproc}.{r}", "w") as f: - f.write(out) - - r = r + 1 - - # Find out if it worked - if status: - print("PASSED") - else: - print("FAILED") - code = 1 - -if code == 0: - print(" => All cyclic reduction tests passed") -else: - print(" => Some failed tests") - -exit(code) diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py new file mode 100755 index 0000000000..38a2d70012 --- /dev/null +++ b/tests/integrated/test-cyclic/test_cyclic.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python3 + +# +# Run the test, check it completed successfully +# + +# Requires: netcdf +# Cores: 4 + +from boututils.run_wrapper import shell, launch +from sys import stdout + + +flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"] + + +def test_cyclic(): + + code = 0 # Return code + for nproc in [1, 2, 4]: + cmd = "./test_cyclic" + + print(" %d processors...." % (nproc)) + r = 0 + for f in flags: + stdout.write("\tflags '" + f + "' ... ") + + shell(["rm data/BOUT.dmp.* 2> err.log"]) + + # Run the case + status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True) + with open(f"run.log.{nproc}.{r}", "w") as f: + f.write(out) + + r = r + 1 + + # Find out if it worked + if status: + print("PASSED") + else: + print("FAILED") + code = 1 + assert status, f"Test failed for flag={f}" + + if code == 0: + print(" => All cyclic reduction tests passed") + else: + print(" => Some failed tests") diff --git a/tests/integrated/test-datafilefacade/runtest b/tests/integrated/test-datafilefacade/runtest deleted file mode 100755 index 213b64e26b..0000000000 --- a/tests/integrated/test-datafilefacade/runtest +++ /dev/null @@ -1,78 +0,0 @@ -#!/usr/bin/env python3 -# -# Test the DataFileFacade interface by writing to dump files using the SAVE_ONCE macro -# -# requires: netcdf -# cores: 2 - -from boutdata.collect import collect -from boututils.run_wrapper import build_and_log, shell, launch_safe -import numpy -from sys import exit - -build_and_log("DataFileFacade test") - - -success = True - -testvars = { - "f2d": 0.1, - "f3d": 0.2, - "fperp": 1.1, - "v2d_contravariantx": 2.2, - "v2d_contravarianty": 3.3, - "v2d_contravariantz": 4.4, - "v3d_contravariantx": 5.5, - "v3d_contravarianty": 6.6, - "v3d_contravariantz": 7.7, - "v2d_covariant_x": 12.12, - "v2d_covariant_y": 13.13, - "v2d_covariant_z": 14.14, - "v3d_covariant_x": 15.15, - "v3d_covariant_y": 16.16, - "v3d_covariant_z": 17.17, - "integer": 42, - "boolean": True, - "real": 3.14, - "name": "test string", -} - - -for nproc in [1, 2]: - # delete any existing output - shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc") - - print(f" {nproc} processor....") - - # run the test executable - s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True) - with open(f"run.log.{nproc}", "w") as f: - f.write(out) - - # check the results - for name, expected in testvars.items(): - # check non-evolving version - result = collect(name, path="data", info=False) - - if result.dtype.kind in ("S", "U"): - if str(result) != expected: - success = False - print( - f"{name} is different: got '{str(result)}', expected '{expected}'" - ) - continue - - if not numpy.allclose(expected, result): - success = False - print(f"{name} is different: {numpy.max(numpy.abs(expected - result))}") - -if success: - print("=> All DataFileFacade tests passed") - # clean up binary files - shell( - "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc" - ) - exit(0) - -print("=> Some failed tests") -exit(1) diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py new file mode 100755 index 0000000000..7a4d947f27 --- /dev/null +++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py @@ -0,0 +1,76 @@ +#!/usr/bin/env python3 +# +# Test the DataFileFacade interface by writing to dump files using the SAVE_ONCE macro +# +# requires: netcdf +# cores: 2 + +from boutdata.collect import collect +from boututils.run_wrapper import shell, launch_safe +import numpy + + +testvars = { + "f2d": 0.1, + "f3d": 0.2, + "fperp": 1.1, + "v2d_contravariantx": 2.2, + "v2d_contravarianty": 3.3, + "v2d_contravariantz": 4.4, + "v3d_contravariantx": 5.5, + "v3d_contravarianty": 6.6, + "v3d_contravariantz": 7.7, + "v2d_covariant_x": 12.12, + "v2d_covariant_y": 13.13, + "v2d_covariant_z": 14.14, + "v3d_covariant_x": 15.15, + "v3d_covariant_y": 16.16, + "v3d_covariant_z": 17.17, + "integer": 42, + "boolean": True, + "real": 3.14, + "name": "test string", +} + + +def test_datafile_facade(): + + success = True + + for nproc in [1, 2]: + # delete any existing output + shell(["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc"]) + + print(f" {nproc} processor....") + + # run the test executable + s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True) + with open(f"run.log.{nproc}", "w") as f: + f.write(out) + + # check the results + for name, expected in testvars.items(): + # check non-evolving version + result = collect(name, path="data", info=False) + + if result.dtype.kind in ("S", "U"): + if str(result) != expected: + success = False + print( + f"{name} is different: got '{str(result)}', expected '{expected}'" + ) + continue + + if not numpy.allclose(expected, result): + success = False + print(f"{name} is different: {numpy.max(numpy.abs(expected - result))}") + + if success: + print("=> All DataFileFacade tests passed") + # clean up binary files + shell( + [ + "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc" + ] + ) + assert success, "=> Some failed tests" diff --git a/tests/integrated/test-dataformat/test_dataformat.py b/tests/integrated/test-dataformat/test_dataformat.py new file mode 100644 index 0000000000..b11460b2f8 --- /dev/null +++ b/tests/integrated/test-dataformat/test_dataformat.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./test_dataformat") diff --git a/tests/integrated/test-delp2/runtest b/tests/integrated/test-delp2/test_delp2.py similarity index 52% rename from tests/integrated/test-delp2/runtest rename to tests/integrated/test-delp2/test_delp2.py index 326ba32888..b3a16eded9 100755 --- a/tests/integrated/test-delp2/runtest +++ b/tests/integrated/test-delp2/test_delp2.py @@ -1,18 +1,16 @@ #!/usr/bin/env python3 - # requires: fftw # cores: 4 -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect +import pytest import numpy as np -from sys import stdout, exit +from sys import stdout +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect tol = 1e-10 # Absolute tolerance -build_and_log("Delp2 operator test") - # The command to run exefile = "./test_delp2" @@ -25,42 +23,32 @@ ] -success = True +@pytest.mark.parametrize("setting", settings) +def test_delp2(setting): -for i, opts in enumerate(settings): # Read benchmark values - print("Args: " + opts) - cmd = exefile + " " + opts + print("Args: " + setting) + cmd = exefile + " " + setting s, out = launch_safe(cmd, nproc=1, pipe=True) - with open("run.log." + str(i) + ".1", "w") as f: + file_suffix = ".".join([x.split("=")[-1] for x in setting.split()]) + with open("run.log." + str(file_suffix) + ".1", "w") as f: f.write(out) n0 = collect("n", path="data", info=False) for nproc in [2, 4]: - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) stdout.write(" %d processor...." % (nproc)) s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True) - with open("run.log." + str(i) + "." + str(nproc), "w") as f: + with open("run.log." + str(file_suffix) + "." + str(nproc), "w") as f: f.write(out) # Collect output data n = collect("n", path="data", info=False) - if np.shape(n) != np.shape(n0): - print("Fail, wrong shape") - success = False - diff = np.max(np.abs(n - n0)) - if diff > tol: - print("Fail, maximum difference = " + str(diff)) - success = False - else: - print("Pass") -if success: - print(" => All Delp2 tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + assert np.shape(n) == np.shape(n0), "Fail, wrong shape" + + diff = np.max(np.abs(n - n0)) + assert diff <= tol, "Fail, maximum difference = " + str(diff) diff --git a/tests/integrated/test-drift-instability-staggered/runtest b/tests/integrated/test-drift-instability-staggered/runtest deleted file mode 120000 index 3b7f341ec9..0000000000 --- a/tests/integrated/test-drift-instability-staggered/runtest +++ /dev/null @@ -1 +0,0 @@ -../test-drift-instability/runtest \ No newline at end of file diff --git a/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py b/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py new file mode 120000 index 0000000000..4d475962e6 --- /dev/null +++ b/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py @@ -0,0 +1 @@ +../test-drift-instability/test_drift_instability.py \ No newline at end of file diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/test_drift_instability.py old mode 100755 new mode 100644 similarity index 86% rename from tests/integrated/test-drift-instability/runtest rename to tests/integrated/test-drift-instability/test_drift_instability.py index 1fae82100b..e8db2d9798 --- a/tests/integrated/test-drift-instability/runtest +++ b/tests/integrated/test-drift-instability/test_drift_instability.py @@ -6,15 +6,15 @@ # Requires: not metric_3d -from boututils.run_wrapper import build_and_log, shell, launch_safe +import pytest +import numpy as np + +from boututils.run_wrapper import shell, launch_safe from boututils.calculus import deriv from boututils.datafile import DataFile from boututils.linear_regression import linear_regression from boutdata.collect import collect -import argparse -import numpy as np -from sys import exit from math import isnan nthreads = 1 @@ -53,10 +53,10 @@ def run_zeff_case(zeff): - """Run a single Zeff case""" + """Run a single Zeff case and return success flag and details.""" if zeff not in omega_orig: - raise ValueError( + pytest.fail( f"Zeff value ({zeff}) not in benchmark values. Available values: {list(omega_orig.keys())}" ) @@ -67,7 +67,7 @@ def run_zeff_case(zeff): timestep = 1e3 # Delete old output files - shell("rm -f data/BOUT.dmp.*.nc") + shell(["rm -f data/BOUT.dmp.*.nc"]) print("Running drift instability test, zeff = ", zeff) @@ -123,7 +123,7 @@ def run_zeff_case(zeff): # wci=9.58e3*(1./d.AA)*1e4*du.Bmag lpar = ( - np.sum(((grid["Bxy"] / grid["Bpxy"])) * grid["dlthe"]) / grid["nx"] + np.sum((grid["Bxy"] / grid["Bpxy"]) * grid["dlthe"]) / grid["nx"] ) # [m], average over flux surfaces kpar = 2 * np.pi / (1e2 * lpar) # cm-1 spar = (kpar / kperp) ** 2 * wci * wce / (0.51 * nuei) # [1/s] @@ -192,32 +192,16 @@ def run_zeff_case(zeff): ) if isnan(omegadiff) or (omegadiff > omega_tol) or (gammadiff > gamma_tol): - print(" => FAILED") - return False - - print(" => PASSED") - return True - - -if __name__ == "__main__": - parser = argparse.ArgumentParser("Run drift-instability test") - parser.add_argument( - "-Z", - "--Zeff-list", - help=f"List of Zeff values to test, valid values are {list(gamma_orig.keys())}", - type=int, - nargs="+", - default=zlist, - ) + return False, omegadiff, gammadiff - args = parser.parse_args() + return True, omegadiff, gammadiff - build_and_log("resistive drift instability test") - return_code = 0 - for zeff in args.Zeff_list: - success = run_zeff_case(zeff) - if not success: - return_code = 1 +@pytest.mark.parametrize("zeff", zlist) +def test_zeff_case(zeff): + """Pytest wrapper for running a single Zeff case.""" + success, omegadiff, gammadiff = run_zeff_case(zeff) - exit(return_code) + assert success, ( + f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}" + ) diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt index b9164ce000..4aa71f96d5 100644 --- a/tests/integrated/test-fci-boundary/CMakeLists.txt +++ b/tests/integrated/test-fci-boundary/CMakeLists.txt @@ -1,4 +1,4 @@ -bout_add_mms_test( +bout_add_integrated_test( test-fci-boundary SOURCES get_par_bndry.cxx USE_RUNTEST USE_DATA_BOUT_INP diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest deleted file mode 100755 index 74a8abf741..0000000000 --- a/tests/integrated/test-fci-boundary/runtest +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python3 -# -# Python script to run and analyse MMS test - -from boututils.run_wrapper import launch_safe -from boututils.datafile import DataFile -from boutdata.collect import collect as _collect - -from numpy.testing import assert_allclose - - -def collect(*args): - return _collect( - *args, - info=False, - path=directory, - xguards=False, - yguards=False, - ) - - -nprocs = [1] -mthread = 2 - -directory = "data" - -with DataFile("grid.fci.nc") as grid: - MXG = grid.get("MXG", default=1) - xfwd = grid.read("forward_xt_prime")[MXG:-MXG] - xbwd = grid.read("backward_xt_prime")[MXG:-MXG] - -nx = xfwd.shape[0] - -regions = { - "xin_fwd": xfwd < MXG, - "xout_fwd": xfwd > nx + MXG - 1, - "xin_bwd": xbwd < MXG, - "xout_bwd": xbwd > nx + MXG - 1, -} -regions = {k: v.astype(int) for k, v in regions.items()} - - -for x in "xout", "xin": - regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"] -for x in "fwd", "bwd": - regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"] -regions["all"] = regions["xin"] + regions["xout"] - -bndrys = { - "ybndry_-1": regions["xout_bwd"], - "ybndry_0": regions["xout_fwd"] * 0, - "ybndry_1": regions["xout_fwd"], -} - -for nproc in nprocs: - cmd = "./get_par_bndry" - _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) - - for k, v in regions.items(): - data = collect(f"field_{k}") - assert_allclose(data, v) - for i in range(-1, 2): - name = f"ybndry_{i}" - data = collect(name) - assert_allclose(bndrys[name], data) diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py new file mode 100755 index 0000000000..9752b9efce --- /dev/null +++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py @@ -0,0 +1,76 @@ +#!/usr/bin/env python3 +# +# Python script to run and analyse MMS test + + +import os +import pytest + +from boututils.run_wrapper import launch_safe +from boututils.datafile import DataFile +from boutdata.collect import collect as _collect + +from numpy.testing import assert_allclose + +if not os.path.exists(os.path.join(os.path.dirname(__file__), "grid.fci.nc")): + pytest.skip( + "grid.fci.nc not found (Zoidberg likely missing), skipping test.", + allow_module_level=True, + ) + +directory = "data" + + +def collect(*args): + return _collect( + *args, + info=False, + path=directory, + xguards=False, + yguards=False, + ) + + +def test_fci_boundary(): + + nprocs = [1] + mthread = 2 + + with DataFile("grid.fci.nc") as grid: + MXG = grid.get("MXG", default=1) + xfwd = grid.read("forward_xt_prime")[MXG:-MXG] + xbwd = grid.read("backward_xt_prime")[MXG:-MXG] + + nx = xfwd.shape[0] + + regions = { + "xin_fwd": xfwd < MXG, + "xout_fwd": xfwd > nx + MXG - 1, + "xin_bwd": xbwd < MXG, + "xout_bwd": xbwd > nx + MXG - 1, + } + regions = {k: v.astype(int) for k, v in regions.items()} + + for x in "xout", "xin": + regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"] + for x in "fwd", "bwd": + regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"] + regions["all"] = regions["xin"] + regions["xout"] + + bndrys = { + "ybndry_-1": regions["xout_bwd"], + "ybndry_0": regions["xout_fwd"] * 0, + "ybndry_1": regions["xout_fwd"], + } + + for nproc in nprocs: + cmd = "./get_par_bndry" + _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) + + for k, v in regions.items(): + data = collect(f"field_{k}") + assert_allclose(data, v) + for i in range(-1, 2): + name = f"ybndry_{i}" + data = collect(name) + assert_allclose(bndrys[name], data) diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt index ba126d7e76..ce5ef9f19b 100644 --- a/tests/integrated/test-fci-mpi/CMakeLists.txt +++ b/tests/integrated/test-fci-mpi/CMakeLists.txt @@ -1,4 +1,4 @@ -bout_add_mms_test( +bout_add_integrated_test( test-fci-mpi SOURCES fci_mpi.cxx USE_RUNTEST USE_DATA_BOUT_INP diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest deleted file mode 100755 index 9962567217..0000000000 --- a/tests/integrated/test-fci-mpi/runtest +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env python3 -# -# Python script to run and analyse MPI test - -from boututils.run_wrapper import build_and_log, launch_safe -from boutdata.collect import collect -import itertools -import sys - -import numpy.testing as npt - -# Resolution in x and y -NLIST = [1, 2, 4] -MAXCORES = 8 -NSLICES = [1] - -build_and_log("FCI MPI test") - -COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data") - - -def run_case(nxpe: int, nype: int, mthread: int): - cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype} mesh:paralleltransform:xzinterpolation:type={implementation}" - print(f"Running command: {cmd}") - - _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True) - - # Save output to log file - with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f: - f.write(out) - - -def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool: - run_case(nxpe, nype, mthread) - - failures = [] - - for name, val in ref.items(): - try: - npt.assert_allclose(val, collect(name, **COLLECT_KW)) - except AssertionError as e: - failures.append((nxpe, nype, name, e)) - - return failures - - -failures = [] - -for implementation in ["hermitespline", "monotonichermitespline"]: - for nslice in NSLICES: - # reference data! - run_case(1, 1, MAXCORES) - - ref = {} - for i in range(4): - for yp in range(1, nslice + 1): - for y in [-yp, yp]: - name = f"output_{i}_{y:+d}" - ref[name] = collect(name, **COLLECT_KW) - - for nxpe, nype in itertools.product(NLIST, NLIST): - if (nxpe, nype) == (1, 1): - # reference case, done above - continue - - if nxpe * nype > MAXCORES: - continue - - mthread = MAXCORES // (nxpe * nype) - failures_ = test_case(nxpe, nype, mthread, ref) - failures.extend(failures_) - - -success = len(failures) == 0 -if success: - print("\nAll tests passed") -else: - print("\nSome tests failed:") - for nxpe, nype, name, error in failures: - print("----------") - print(f"case {nxpe=} {nype=} {name=}\n{error}") - -sys.exit(0 if success else 1) diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py new file mode 100755 index 0000000000..51d5795d3f --- /dev/null +++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py @@ -0,0 +1,78 @@ +#!/usr/bin/env python3 +# +# Python script to run and analyse MPI test + +from boututils.run_wrapper import launch_safe +from boutdata.collect import collect +import itertools + +import numpy.testing as npt + +# Resolution in x and y +NLIST = [1, 2, 4] +MAXCORES = 8 +NSLICES = [1] + + +def test_fci_mpi(): + + COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data") + + def run_case(nxpe: int, nype: int, mthread: int): + + cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype} mesh:paralleltransform:xzinterpolation:type={implementation}" + print(f"Running command: {cmd}") + + _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True) + + # Save output to log file + with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f: + f.write(out) + + def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool: + run_case(nxpe, nype, mthread) + + failures = [] + + for name, val in ref.items(): + try: + npt.assert_allclose(val, collect(name, **COLLECT_KW)) + except AssertionError as e: + failures.append((nxpe, nype, name, e)) + + return failures + + failures = [] + + for implementation in ["hermitespline", "monotonichermitespline"]: + for nslice in NSLICES: + # reference data! + run_case(1, 1, MAXCORES) + + ref = {} + for i in range(4): + for yp in range(1, nslice + 1): + for y in [-yp, yp]: + name = f"output_{i}_{y:+d}" + ref[name] = collect(name, **COLLECT_KW) + + for nxpe, nype in itertools.product(NLIST, NLIST): + if (nxpe, nype) == (1, 1): + # reference case, done above + continue + + if nxpe * nype > MAXCORES: + continue + + mthread = MAXCORES // (nxpe * nype) + failures_ = test_case(nxpe, nype, mthread, ref) + failures.extend(failures_) + + success = len(failures) == 0 + + assert success, "\nSome tests failed:" + + if not success: + for nxpe, nype, name, error in failures: + print("----------") + print(f"case {nxpe=} {nype=} {name=}\n{error}") diff --git a/tests/integrated/test-fieldgroupComm/runtest b/tests/integrated/test-fieldgroupComm/runtest deleted file mode 100755 index ca6d5f89f3..0000000000 --- a/tests/integrated/test-fieldgroupComm/runtest +++ /dev/null @@ -1,76 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results -# - -# Requires: all_tests -# Requires: netcdf -# Requires: not metric_3d -# Cores: 4 - -# Variables to compare -from __future__ import print_function - -try: - from builtins import str -except: - pass - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -from numpy import abs, seterr -from sys import stdout, exit - -# Good chance we'll do 0.0/0.0, which generates a warning -# Ignore this warning -seterr(divide="ignore", invalid="ignore") - -varCorrect = "fld1" -varsComp = ["fld2", "fld3"] -name = "FieldGroup comm" -exeName = "test_fieldgroupcomm" -tol = 1e-10 # Relative tolerance - - -build_and_log("{nm} test".format(nm=name)) - -print("Running {nm} test".format(nm=name)) -success = True - -for nproc in [1, 2, 4]: - nxpe = 1 - if nproc > 2: - nxpe = 2 - - cmd = "./{exe} ".format(exe=exeName) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors ...." % (nproc)) - s, out = launch_safe(cmd, nproc=nproc, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Analyse result - # /"Correct" answer - f1 = collect(varCorrect, path="data", info=False) - f1max = abs(f1).max() - # /Two different fields which should be identical to correct - err = [] - for v in varsComp: - tmp = collect(v, path="data", info=False) - err.append(abs((f1 - tmp)).max() / f1max) - - for i, e in enumerate(err): - if e > tol: - print("Fail, in {i}th comparison relative error is {re}".format(i=i, re=e)) - success = False - - -if success: - print(" => All {nm} passed".format(nm=name)) - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py new file mode 100755 index 0000000000..917fdc0754 --- /dev/null +++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python3 + +# +# Run the test, compare results +# + +# Requires: all_tests +# Requires: netcdf +# Requires: not metric_3d +# Cores: 4 + + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect +from numpy import abs, seterr + + +def test_fieldgroupcomm(): + + # Good chance we'll do 0.0/0.0, which generates a warning + # Ignore this warning + seterr(divide="ignore", invalid="ignore") + + varCorrect = "fld1" + varsComp = ["fld2", "fld3"] + name = "FieldGroup comm" + exeName = "test_fieldgroupcomm" + tol = 1e-10 # Relative tolerance + + print("Running {nm} test".format(nm=name)) + success = True + + for nproc in [1, 2, 4]: + cmd = "./{exe} ".format(exe=exeName) + + shell("rm data/BOUT.dmp.*.nc") + + print(" %d processors ...." % (nproc)) + s, out = launch_safe(cmd, nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + # Analyse result + # /"Correct" answer + f1 = collect(varCorrect, path="data", info=False) + f1max = abs(f1).max() + # /Two different fields which should be identical to correct + err = [] + for v in varsComp: + tmp = collect(v, path="data", info=False) + err.append(abs((f1 - tmp)).max() / f1max) + + for i, e in enumerate(err): + if e > tol: + print( + "Fail, in {i}th comparison relative error is {re}".format(i=i, re=e) + ) + success = False + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-globalfield/test_globalfield.py b/tests/integrated/test-globalfield/test_globalfield.py new file mode 100755 index 0000000000..ac2d993dd4 --- /dev/null +++ b/tests/integrated/test-globalfield/test_globalfield.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./test_globalfield") diff --git a/tests/integrated/test-griddata-yboundary-guards/runtest b/tests/integrated/test-griddata-yboundary-guards/runtest deleted file mode 100755 index 79adae9759..0000000000 --- a/tests/integrated/test-griddata-yboundary-guards/runtest +++ /dev/null @@ -1,201 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -from netCDF4 import Dataset -import numpy -import os.path -from sys import stdout, exit - -# Cores: 6 -# Requires: netcdf - -build_and_log("griddata test") - -nx = 4 -ny = 24 -blocksize = ny / 6 - -# first generate some grid files to test -# double null case: -for n_yguards in [0, 1, 2]: - datadir = "data-doublenull-" + str(n_yguards) - gridname = "grid-doublenull-" + str(n_yguards) + ".nc" - - with Dataset(os.path.join(datadir, gridname), "w") as gridfile: - gridfile.createDimension("x", nx) - gridfile.createDimension("y", ny + 4 * n_yguards) - - gridfile.createVariable("nx", numpy.int32) - gridfile["nx"][...] = nx - - gridfile.createVariable("ny", numpy.int32) - gridfile["ny"][...] = ny - - gridfile.createVariable("y_boundary_guards", numpy.int32) - gridfile["y_boundary_guards"][...] = n_yguards - - gridfile.createVariable("MXG", numpy.int32) - gridfile["MXG"][...] = 1 - - gridfile.createVariable("MYG", numpy.int32) - gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards - - gridfile.createVariable("ixseps1", numpy.int32) - gridfile["ixseps1"][...] = nx // 2 - 1 - - gridfile.createVariable("ixseps2", numpy.int32) - gridfile["ixseps2"][...] = nx // 2 - 1 - - gridfile.createVariable("jyseps1_1", numpy.int32) - gridfile["jyseps1_1"][...] = blocksize - 1 - - gridfile.createVariable("jyseps2_1", numpy.int32) - gridfile["jyseps2_1"][...] = 2 * blocksize - 1 - - gridfile.createVariable("ny_inner", numpy.int32) - gridfile["ny_inner"][...] = 3 * blocksize - - gridfile.createVariable("jyseps1_2", numpy.int32) - gridfile["jyseps1_2"][...] = 4 * blocksize - 1 - - gridfile.createVariable("jyseps2_2", numpy.int32) - gridfile["jyseps2_2"][...] = 5 * blocksize - 1 - - testdata = numpy.zeros([nx, ny + 4 * n_yguards]) - testdata[:, :] = numpy.arange(ny + 4 * n_yguards)[numpy.newaxis, :] - gridfile.createVariable("test", float, ("x", "y")) - gridfile["test"][...] = testdata - -# grid files for single-null: -for n_yguards in [0, 1, 2]: - datadir = "data-singlenull-" + str(n_yguards) - gridname = "grid-singlenull-" + str(n_yguards) + ".nc" - - with Dataset(os.path.join(datadir, gridname), "w") as gridfile: - gridfile.createDimension("x", nx) - gridfile.createDimension("y", ny + 2 * n_yguards) - - gridfile.createVariable("nx", numpy.int32) - gridfile["nx"][...] = nx - - gridfile.createVariable("ny", numpy.int32) - gridfile["ny"][...] = ny - - gridfile.createVariable("y_boundary_guards", numpy.int32) - gridfile["y_boundary_guards"][...] = n_yguards - - gridfile.createVariable("MXG", numpy.int32) - gridfile["MXG"][...] = 1 - - gridfile.createVariable("MYG", numpy.int32) - gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards - - gridfile.createVariable("ixseps1", numpy.int32) - gridfile["ixseps1"][...] = nx // 2 - 1 - - gridfile.createVariable("ixseps2", numpy.int32) - gridfile["ixseps2"][...] = nx // 2 - 1 - - gridfile.createVariable("jyseps1_1", numpy.int32) - gridfile["jyseps1_1"][...] = blocksize - 1 - - gridfile.createVariable("jyseps2_1", numpy.int32) - gridfile["jyseps2_1"][...] = ny // 2 - - gridfile.createVariable("ny_inner", numpy.int32) - gridfile["ny_inner"][...] = ny // 2 - - gridfile.createVariable("jyseps1_2", numpy.int32) - gridfile["jyseps1_2"][...] = ny // 2 - - gridfile.createVariable("jyseps2_2", numpy.int32) - gridfile["jyseps2_2"][...] = 5 * blocksize - 1 - - testdata = numpy.zeros([nx, ny + 2 * n_yguards]) - testdata[:, :] = numpy.arange(ny + 2 * n_yguards)[numpy.newaxis, :] - gridfile.createVariable("test", float, ("x", "y")) - gridfile["test"][...] = testdata - - -for nproc in [6]: - stdout.write("Checking %d processors ... " % (nproc)) - - shell("rm ./data*/BOUT.dmp.*.nc run.log.*") - - success = True - - # double null tests - for n_yguards in [0, 1, 2]: - datadir = "data-doublenull-" + str(n_yguards) - - s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True) - - with open("run.log.doublenull." + str(nproc), "a") as f: - f.write(out) - - testfield = collect("test", path=datadir, info=False, yguards=True) - - if n_yguards == 0: - # output has 2 y-guard cells, but grid file did not - myg = 2 - checkfield = list(numpy.zeros(myg)) - checkfield += list(numpy.arange(ny // 2)) - checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1) - checkfield += list(numpy.zeros(myg) + checkfield[-1]) - else: - checkfield = [] - checkfield += list(numpy.arange(n_yguards)) - checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1) - checkfield += list( - numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards - ) - checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1) - checkfield = numpy.array(checkfield) - - # Test value of testfield - if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13: - print( - "Failed: testfield does not match in doublenull case for n_yguards=" - + str(n_yguards) - ) - success = False - - # single null tests - for n_yguards in [0, 1, 2]: - datadir = "data-singlenull-" + str(n_yguards) - - s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True) - - with open("run.log.singlenull." + str(nproc), "a") as f: - f.write(out) - - testfield = collect("test", path=datadir, info=False, yguards=True) - - if n_yguards == 0: - # output has 2 y-guard cells, but grid file did not - myg = 2 - checkfield = list(numpy.zeros(myg)) - checkfield += list(numpy.arange(ny)) - checkfield += list(numpy.zeros(myg) + checkfield[-1]) - else: - checkfield = [] - checkfield += list(numpy.arange(n_yguards)) - checkfield += list(numpy.arange(ny) + checkfield[-1] + 1) - checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1) - checkfield = numpy.array(checkfield) - - # Test value of testfield - if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13: - print( - "Failed: testfield does not match in doublenull case for n_yguards=" - + str(n_yguards) - ) - success = False - - if not success: - exit(1) - else: - print("Passed") - -exit(0) diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py new file mode 100755 index 0000000000..9666a2f762 --- /dev/null +++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py @@ -0,0 +1,202 @@ +#!/usr/bin/env python3 + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect +from netCDF4 import Dataset +import numpy +from pathlib import Path +from sys import stdout + +# Cores: 6 +# Requires: netcdf + + +def test_griddata_yboundary_guards(): + + nx = 4 + ny = 24 + blocksize = ny / 6 + + # first generate some grid files to test + # double null case: + for n_yguards in [0, 1, 2]: + datadir = Path("data-doublenull-" + str(n_yguards)) + gridname = "grid-doublenull-" + str(n_yguards) + ".nc" + file_path = datadir / gridname + + with Dataset(file_path, "w") as gridfile: + gridfile.createDimension("x", nx) + gridfile.createDimension("y", ny + 4 * n_yguards) + + gridfile.createVariable("nx", numpy.int32) + gridfile["nx"][...] = nx + + gridfile.createVariable("ny", numpy.int32) + gridfile["ny"][...] = ny + + gridfile.createVariable("y_boundary_guards", numpy.int32) + gridfile["y_boundary_guards"][...] = n_yguards + + gridfile.createVariable("MXG", numpy.int32) + gridfile["MXG"][...] = 1 + + gridfile.createVariable("MYG", numpy.int32) + gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards + + gridfile.createVariable("ixseps1", numpy.int32) + gridfile["ixseps1"][...] = nx // 2 - 1 + + gridfile.createVariable("ixseps2", numpy.int32) + gridfile["ixseps2"][...] = nx // 2 - 1 + + gridfile.createVariable("jyseps1_1", numpy.int32) + gridfile["jyseps1_1"][...] = blocksize - 1 + + gridfile.createVariable("jyseps2_1", numpy.int32) + gridfile["jyseps2_1"][...] = 2 * blocksize - 1 + + gridfile.createVariable("ny_inner", numpy.int32) + gridfile["ny_inner"][...] = 3 * blocksize + + gridfile.createVariable("jyseps1_2", numpy.int32) + gridfile["jyseps1_2"][...] = 4 * blocksize - 1 + + gridfile.createVariable("jyseps2_2", numpy.int32) + gridfile["jyseps2_2"][...] = 5 * blocksize - 1 + + testdata = numpy.zeros([nx, ny + 4 * n_yguards]) + testdata[:, :] = numpy.arange(ny + 4 * n_yguards)[numpy.newaxis, :] + gridfile.createVariable("test", float, ("x", "y")) + gridfile["test"][...] = testdata + + # grid files for single-null: + for n_yguards in [0, 1, 2]: + datadir = Path("data-singlenull-" + str(n_yguards)) + gridname = "grid-singlenull-" + str(n_yguards) + ".nc" + file_path = datadir / gridname + + with Dataset(file_path, "w") as gridfile: + gridfile.createDimension("x", nx) + gridfile.createDimension("y", ny + 2 * n_yguards) + + gridfile.createVariable("nx", numpy.int32) + gridfile["nx"][...] = nx + + gridfile.createVariable("ny", numpy.int32) + gridfile["ny"][...] = ny + + gridfile.createVariable("y_boundary_guards", numpy.int32) + gridfile["y_boundary_guards"][...] = n_yguards + + gridfile.createVariable("MXG", numpy.int32) + gridfile["MXG"][...] = 1 + + gridfile.createVariable("MYG", numpy.int32) + gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards + + gridfile.createVariable("ixseps1", numpy.int32) + gridfile["ixseps1"][...] = nx // 2 - 1 + + gridfile.createVariable("ixseps2", numpy.int32) + gridfile["ixseps2"][...] = nx // 2 - 1 + + gridfile.createVariable("jyseps1_1", numpy.int32) + gridfile["jyseps1_1"][...] = blocksize - 1 + + gridfile.createVariable("jyseps2_1", numpy.int32) + gridfile["jyseps2_1"][...] = ny // 2 + + gridfile.createVariable("ny_inner", numpy.int32) + gridfile["ny_inner"][...] = ny // 2 + + gridfile.createVariable("jyseps1_2", numpy.int32) + gridfile["jyseps1_2"][...] = ny // 2 + + gridfile.createVariable("jyseps2_2", numpy.int32) + gridfile["jyseps2_2"][...] = 5 * blocksize - 1 + + testdata = numpy.zeros([nx, ny + 2 * n_yguards]) + testdata[:, :] = numpy.arange(ny + 2 * n_yguards)[numpy.newaxis, :] + gridfile.createVariable("test", float, ("x", "y")) + gridfile["test"][...] = testdata + + for nproc in [6]: + stdout.write("Checking %d processors ... " % (nproc)) + + shell(["rm ./data*/BOUT.dmp.*.nc run.log.*"]) + + success = True + + # double null tests + for n_yguards in [0, 1, 2]: + datadir = "data-doublenull-" + str(n_yguards) + + s, out = launch_safe( + "./test_griddata -d " + datadir, nproc=nproc, pipe=True + ) + + with open("run.log.doublenull." + str(nproc), "a") as f: + f.write(out) + + testfield = collect("test", path=datadir, info=False, yguards=True) + + if n_yguards == 0: + # output has 2 y-guard cells, but grid file did not + myg = 2 + checkfield = list(numpy.zeros(myg)) + checkfield += list(numpy.arange(ny // 2)) + checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1) + checkfield += list(numpy.zeros(myg) + checkfield[-1]) + else: + checkfield = [] + checkfield += list(numpy.arange(n_yguards)) + checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1) + checkfield += list( + numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards + ) + checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1) + checkfield = numpy.array(checkfield) + + # Test value of testfield + if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13: + print( + "Failed: testfield does not match in doublenull case for n_yguards=" + + str(n_yguards) + ) + success = False + + # single null tests + for n_yguards in [0, 1, 2]: + datadir = "data-singlenull-" + str(n_yguards) + + s, out = launch_safe( + "./test_griddata -d " + datadir, nproc=nproc, pipe=True + ) + + with open("run.log.singlenull." + str(nproc), "a") as f: + f.write(out) + + testfield = collect("test", path=datadir, info=False, yguards=True) + + if n_yguards == 0: + # output has 2 y-guard cells, but grid file did not + myg = 2 + checkfield = list(numpy.zeros(myg)) + checkfield += list(numpy.arange(ny)) + checkfield += list(numpy.zeros(myg) + checkfield[-1]) + else: + checkfield = [] + checkfield += list(numpy.arange(n_yguards)) + checkfield += list(numpy.arange(ny) + checkfield[-1] + 1) + checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1) + checkfield = numpy.array(checkfield) + + # Test value of testfield + if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13: + print( + "Failed: testfield does not match in doublenull case for n_yguards=" + + str(n_yguards) + ) + success = False + + assert success diff --git a/tests/integrated/test-griddata/runtest b/tests/integrated/test-griddata/runtest deleted file mode 100755 index 6aef955023..0000000000 --- a/tests/integrated/test-griddata/runtest +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env python3 - -from __future__ import print_function -from __future__ import division - -try: - from builtins import str -except: - pass - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -import numpy as np -from sys import stdout, exit - -build_and_log("griddata test") - -for nproc in [1]: - stdout.write("Checking %d processors ... " % (nproc)) - - shell("rm ./data*nc") - s, out = launch_safe("./test_griddata -d screw", nproc=nproc, pipe=True) - - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - prefix = "data" - Rxy = collect("Rxy", prefix=prefix, info=False) - Bpxy = collect("Bpxy", prefix=prefix, info=False) - dx = collect("dx", prefix=prefix, info=False) - - nx, ny = Rxy.shape - - # Handle 3D metric case - if len(dx.shape) == 3: - dx = dx[:, :, 0] - - rwidth = 0.4 - dr = float(rwidth) / nx - - # Test value of dx - if not np.allclose(dx, dr * Bpxy * Rxy, atol=1e-7): - print("Failed: dx does not match") - exit(1) - - print("Passed") - -exit(0) diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py new file mode 100755 index 0000000000..82f86fd459 --- /dev/null +++ b/tests/integrated/test-griddata/test_griddata.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python3 + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect +import numpy.testing as npt +from sys import stdout + + +def test_griddata(): + for nproc in [1]: + stdout.write("Checking %d processors ... " % (nproc)) + + shell("rm ./data*nc") + s, out = launch_safe("./test_griddata -d screw", nproc=nproc, pipe=True) + + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + prefix = "data" + Rxy = collect("Rxy", prefix=prefix, info=False) + Bpxy = collect("Bpxy", prefix=prefix, info=False) + dx = collect("dx", prefix=prefix, info=False) + + nx, ny = Rxy.shape + + # Handle 3D metric case + if len(dx.shape) == 3: + dx = dx[:, :, 0] + + rwidth = 0.4 + dr = float(rwidth) / nx + + # Test value of dx + npt.assert_allclose( + dx, dr * Bpxy * Rxy, atol=1e-7, err_msg="Failed: dx does not match" + ) + + print("Passed") diff --git a/tests/integrated/test-gyro/runtest b/tests/integrated/test-gyro/runtest deleted file mode 100755 index 7a0209fa57..0000000000 --- a/tests/integrated/test-gyro/runtest +++ /dev/null @@ -1,73 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -# requires: not metric_3d -# Requires: netcdf -# Cores: 4 - -# Variables to compare -from __future__ import print_function - -try: - from builtins import str -except: - pass - -vars = ["pade1", "pade2"] - -tol = 1e-7 # Absolute tolerance, benchmark values are floats - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -import numpy as np -from sys import stdout, exit - -build_and_log("Gyro-average inversion test") - -# Read benchmark values -print("Reading benchmark data") -bmk = {} -for v in vars: - bmk[v] = collect(v, path="data", prefix="benchmark", info=False, xguards=False) - -print("Running Gyro-average inversion test") -success = True - -for nproc in [1, 2, 4]: - nxpe = 1 - if nproc > 2: - nxpe = 2 - - cmd = "./test_gyro NXPE=" + str(nxpe) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors (nxpe = %d)...." % (nproc, nxpe)) - s, out = launch_safe(cmd, nproc=nproc, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect output data - for v in vars: - stdout.write(" Checking variable " + v + " ... ") - result = collect(v, path="data", info=False, xguards=False) - # Compare benchmark and output - if np.shape(bmk[v]) != np.shape(result): - print("Fail, wrong shape") - success = False - diff = np.max(np.abs(bmk[v] - result)) - if diff > tol: - print("Fail, maximum difference = " + str(diff)) - success = False - else: - print("Pass") - -if success: - print(" => All Gyro-average tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py new file mode 100755 index 0000000000..5f2f984ea0 --- /dev/null +++ b/tests/integrated/test-gyro/test_gyro.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python3 +from pathlib import Path + +# +# Run the test, compare results against the benchmark +# + +# requires: not metric_3d +# Requires: netcdf +# Cores: 4 + +import pytest +import numpy as np +from sys import stdout +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + +# Variables to compare +variables = ["pade1", "pade2"] + +tol = 1e-7 # Absolute tolerance, benchmark values are floats + + +@pytest.fixture(scope="module") +def benchmark_data(): + """Reads the benchmark data once for all test iterations in this module.""" + bmk = {} + source_data_dir = str(Path(__file__).parent / "data") + + for v in variables: + bmk[v] = collect( + v, path=source_data_dir, prefix="benchmark", info=False, xguards=False + ) + return bmk + + +def test_gyro(benchmark_data): + + print("Running Gyro-average inversion test") + + for nproc in [1, 2, 4]: + nxpe = 1 + if nproc > 2: + nxpe = 2 + + cmd = f"./test_gyro NXPE={nxpe}" + + shell("rm -f data/BOUT.dmp.*.nc") + + print(" %d processors (nxpe = %d)...." % (nproc, nxpe)) + s, out = launch_safe(cmd, nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + # Collect output data + for v in variables: + stdout.write(" Checking variable " + v + " ... ") + result = collect(v, path="data", info=False, xguards=False) + # Compare benchmark and output + np.testing.assert_allclose( + benchmark_data[v], + result, + atol=tol, + rtol=0, + err_msg="Gyro-average output mismatch", + ) diff --git a/tests/integrated/test-include/.gitignore b/tests/integrated/test-include/.gitignore deleted file mode 100644 index 1ccb766f4e..0000000000 --- a/tests/integrated/test-include/.gitignore +++ /dev/null @@ -1 +0,0 @@ -test.cxx diff --git a/tests/integrated/test-include/README.md b/tests/integrated/test-include/README.md deleted file mode 100644 index 292b5d3a4e..0000000000 --- a/tests/integrated/test-include/README.md +++ /dev/null @@ -1,11 +0,0 @@ -test-include -============ - -This test ensures that all header files from bout can be included on -their own. It compiles a test file with one header, and if that fails, -then the headerfile does not include all files it needs. - -Checking whether the library builds as whole is not sufficient, as -either the file might never be included directly, or some other header -file might always be included first, which fulfils the requirements, -thus there is this extra test. diff --git a/tests/integrated/test-include/runtest b/tests/integrated/test-include/runtest deleted file mode 100755 index 4fa8096c4b..0000000000 --- a/tests/integrated/test-include/runtest +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env bash - -#requires: all_tests -#Requires: not make - -BOUT_TOP=../../.. -export PATH=$BOUT_TOP/bin:$PATH - -error=0 - -failed= -for header in $(cd $BOUT_TOP/include ; find |grep hxx\$) -do - echo "#include <$header>" > test.cxx - - $(bout-config --cxx) $(bout-config --cflags) test.cxx -c - - ex=$? - - if test $ex -gt 0 - then - echo $header failed - error=1 - failed="$failed -$header failed" - fi - -done - -echo $failed - -exit $error diff --git a/tests/integrated/test-initial/runtest b/tests/integrated/test-initial/runtest deleted file mode 100755 index 25ad7d09f1..0000000000 --- a/tests/integrated/test-initial/runtest +++ /dev/null @@ -1,243 +0,0 @@ -#!/usr/bin/env python3 - -# Test initial conditions - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect - -import configparser -import itertools -from scipy.special import erf -import numpy as np -import os - -# requires not make -# requires scipy -# cores: 4 - -######################################## -# Implementations of BOUT++ functions - - -def bout_round(x): - """ - BOUT++ rounding - """ - return x + 0.5 if x > 0.0 else x - 0.5 - - -def genRand(seed): - """ - BOUT++ psuedo random number generator - - This PRNG has no memory, i.e. you need to call it with a different - seed each time - """ - # Make sure seed is - if seed < 0.0: - seed *= -1 - - # Round the seed to get the number of iterations - niter = int(11 + (23 + bout_round(seed)) % 79) - - # Start x between 0 and 1 - A = 0.01 - B = 1.23456789 - x = (A + np.mod(seed, B)) / (B + 2.0 * A) - - # Iterate logistic map - for i in range(niter): - x = 3.99 * x * (1.0 - x) - - return x - - -def ballooning(x, ball_n=3): - """ - Ballooning function. Currently too tricky to implement - """ - raise NotImplementedError("ballooning") - - -def gauss(x, width=1.0): - """ - Normalised gaussian - """ - return np.exp(-(x**2) / (2 * width**2)) / np.sqrt(2 * np.pi) - - -def mixmode(x, seed=0.5): - """ - 14 modes with random phases - """ - result = 0.0 - for i in range(14): - phase = np.pi * (2.0 * genRand(seed + i) - 1.0) - result += (1.0 / (1.0 + np.abs(i - 4.0)) ** 2) * np.cos(i * x + phase) - return result - - -def heaviside(x): - """ - Heaviside step function - """ - return 1 * (x > 0) - - -def tanhhat(x, width, centre, steepness): - """ - BOUT++ TanhHat function - """ - return 0.5 * ( - np.tanh(steepness * (x - (centre - width / 2.0))) - + np.tanh(-steepness * (x - (centre + width / 2.0))) - ) - - -def atan(x, y=None): - """ - Resolves to either np.arctan or np.arctan depending on the number of arguments - """ - if y is not None: - return np.arctan2(x, y) - else: - return np.arctan(x) - - -def max(*args): - """ - Maximum of *args at each point - """ - current = args[0] - for arg in args: - current = np.maximum(arg, current) - return current - - -def min(*args): - """ - Minimum of *args at each point - """ - current = args[0] - for arg in args: - current = np.minimum(arg, current) - return current - - -def fmod(x, denominator=1.0): - """ - Modulo operator using fmod convention, (rem in Matlab) - """ - return np.fmod(x, denominator) - - -# Rename functions to match BOUT++ naming -# Mostly just alternative names to numpy functions -abs = np.abs -asin = np.arcsin -acos = np.arccos -ballooning = ballooning -cos = np.cos -cosh = np.cosh -exp = np.exp -tanh = np.tanh -H = heaviside -log = np.log -power = np.power -sin = np.sin -sinh = np.sinh -sqrt = np.sqrt -tan = np.tan -TanhHat = tanhhat -pi = np.pi - -######################################## -# Running the test - -# Some parameters -success = True -tolerance = 1e-13 -cmd = "./test_initial" -datadir = "data" -inputfile = os.path.join(datadir, "BOUT.inp") - -# Read the input file -config = configparser.ConfigParser() -with open(inputfile, "r") as f: - config.read_file(itertools.chain(["[global]"], f), source=inputfile) - -# Find the variables that have a "function" option -varlist = [key for key, values in config.items() if "function" in values] - -# Remove the coordinate arrays -for coord in ["var_x", "var_y", "var_z"]: - varlist.remove(coord) - -build_and_log("initial conditions test") - -nprocs = [1, 2, 3, 4] -for nproc in nprocs: - status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) - with open("run.log.{}".format(nproc), "w") as f: - f.write(out) - - if status != 0: - print("=> Could not run test") - print(status) - exit(status) - - # Collect the coordinate arrays separately - x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False) - y = collect("var_y", xguards=True, yguards=True, path=datadir, info=False) - z = collect("var_z", xguards=True, yguards=True, path=datadir, info=False) - - # Evaluate the functions - for var in varlist: - function = config[var]["function"] - function = function.replace("^", "**") - if ":" in function: - print( - "{} contains reference to variable - not possible to resolve at this time".format( - var - ) - ) - continue - try: - analytic = eval(function) - except NotImplementedError as err: - print("{} not implemented, skipping".format(err.args[0])) - else: - data = collect(var, xguards=True, yguards=True, path=datadir, info=False) - E2 = np.sqrt(np.mean((analytic - data) ** 2)) - if E2 < tolerance: - success_string = "PASS" - else: - if (var == "mixmode" or var == "mixmode_seed") and E2 < 1e-3: - import platform - - arch = platform.machine() - if arch == "i686": - # This can happen due tue excess precision e.g. on X87 architecture - success_string = "WARNING" - else: - print( - "This should only happen in i686 with an x87 math architecture." - ) - print("We detected however an %s architecture." % arch) - success_string = "FAIL" - success = False - else: - success_string = "FAIL" - success = False - print( - "\tChecking {var:<12}: l-2: {err:.4e} ... {success}".format( - var=var, err=E2, success=success_string - ) - ) - -if success: - print(" => All tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py new file mode 100755 index 0000000000..cf61514fac --- /dev/null +++ b/tests/integrated/test-initial/test_initial.py @@ -0,0 +1,242 @@ +#!/usr/bin/env python3 + +# Test initial conditions + +import pytest +import configparser +import itertools +import numpy as np +from scipy.special import erf +from pathlib import Path + +from boututils.run_wrapper import launch_safe +from boutdata.collect import collect + +# requires not make +# requires scipy +# cores: 4 + +######################################## +# Implementations of BOUT++ functions + + +def bout_round(x): + """ + BOUT++ rounding + """ + return x + 0.5 if x > 0.0 else x - 0.5 + + +def genRand(seed): + """ + BOUT++ psuedo random number generator + + This PRNG has no memory, i.e. you need to call it with a different + seed each time + """ + # Make sure seed is + if seed < 0.0: + seed *= -1 + + # Round the seed to get the number of iterations + niter = int(11 + (23 + bout_round(seed)) % 79) + + # Start x between 0 and 1 + A = 0.01 + B = 1.23456789 + x = (A + np.mod(seed, B)) / (B + 2.0 * A) + + # Iterate logistic map + for i in range(niter): + x = 3.99 * x * (1.0 - x) + + return x + + +def ballooning(x, ball_n=3): + """ + Ballooning function. Currently too tricky to implement + """ + raise NotImplementedError("ballooning") + + +def gauss(x, width=1.0): + """ + Normalised gaussian + """ + return np.exp(-(x**2) / (2 * width**2)) / np.sqrt(2 * np.pi) + + +def mixmode(x, seed=0.5): + """ + 14 modes with random phases + """ + result = 0.0 + for i in range(14): + phase = np.pi * (2.0 * genRand(seed + i) - 1.0) + result += (1.0 / (1.0 + np.abs(i - 4.0)) ** 2) * np.cos(i * x + phase) + return result + + +def heaviside(x): + """ + Heaviside step function + """ + return 1 * (x > 0) + + +def tanhhat(x, width, centre, steepness): + """ + BOUT++ TanhHat function + """ + return 0.5 * ( + np.tanh(steepness * (x - (centre - width / 2.0))) + + np.tanh(-steepness * (x - (centre + width / 2.0))) + ) + + +def atan(x, y=None): + """ + Resolves to either np.arctan or np.arctan depending on the number of arguments + """ + if y is not None: + return np.arctan2(x, y) + else: + return np.arctan(x) + + +def max(*args): + """ + Maximum of *args at each point + """ + current = args[0] + for arg in args: + current = np.maximum(arg, current) + return current + + +def min(*args): + """ + Minimum of *args at each point + """ + current = args[0] + for arg in args: + current = np.minimum(arg, current) + return current + + +def fmod(x, denominator=1.0): + """ + Modulo operator using fmod convention, (rem in Matlab) + """ + return np.fmod(x, denominator) + + +# Rename functions to match BOUT++ naming +# Mostly just alternative names to numpy functions +abs = np.abs +asin = np.arcsin +acos = np.arccos +ballooning = ballooning +cos = np.cos +cosh = np.cosh +exp = np.exp +tanh = np.tanh +H = heaviside +log = np.log +power = np.power +sin = np.sin +sinh = np.sinh +sqrt = np.sqrt +tan = np.tan +TanhHat = tanhhat +pi = np.pi +erf = erf + + +def test_initial(): + # Running the test + + # Some parameters + success = True + tolerance = 1e-13 + cmd = "./test_initial" + datadir = Path("data") + inputfile = datadir / "BOUT.inp" + + # Read the input file + config = configparser.ConfigParser() + with open(inputfile, "r") as f: + config.read_file(itertools.chain(["[global]"], f), source=inputfile) + + # Find the variables that have a "function" option + varlist = [key for key, values in config.items() if "function" in values] + + # Remove the coordinate arrays + for coord in ["var_x", "var_y", "var_z"]: + varlist.remove(coord) + + nprocs = [1, 2, 3, 4] + for nproc in nprocs: + status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) + with open("run.log.{}".format(nproc), "w") as f: + f.write(out) + + if status != 0: + print(status) + pytest.fail("=> Could not run test") + + # Collect the coordinate arrays separately + x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False) + y = collect("var_y", xguards=True, yguards=True, path=datadir, info=False) + z = collect("var_z", xguards=True, yguards=True, path=datadir, info=False) + + # Evaluate the functions + for var in varlist: + function = config[var]["function"] + function = function.replace("^", "**") + if ":" in function: + print( + "{} contains reference to variable - not possible to resolve at this time".format( + var + ) + ) + continue + + context = {"x": x, "y": y, "z": z} + try: + analytic = eval(function, globals(), context) + except NotImplementedError as err: + print("{} not implemented, skipping".format(err.args[0])) + else: + data = collect( + var, xguards=True, yguards=True, path=datadir, info=False + ) + E2 = np.sqrt(np.mean((analytic - data) ** 2)) + if E2 < tolerance: + success_string = "PASS" + else: + if (var == "mixmode" or var == "mixmode_seed") and E2 < 1e-3: + import platform + + arch = platform.machine() + if arch == "i686": + # This can happen due tue excess precision e.g. on X87 architecture + success_string = "WARNING" + else: + print( + "This should only happen in i686 with an x87 math architecture." + ) + print("We detected however an %s architecture." % arch) + success_string = "FAIL" + success = False + else: + success_string = "FAIL" + success = False + print( + "\tChecking {var:<12}: l-2: {err:.4e} ... {success}".format( + var=var, err=E2, success=success_string + ) + ) + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-integrate/test_integrate.py b/tests/integrated/test-integrate/test_integrate.py new file mode 100755 index 0000000000..d8b4073b66 --- /dev/null +++ b/tests/integrated/test-integrate/test_integrate.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./test_integrate") diff --git a/tests/integrated/test-interchange-instability/runtest b/tests/integrated/test-interchange-instability/runtest deleted file mode 100755 index 0f75157aaf..0000000000 --- a/tests/integrated/test-interchange-instability/runtest +++ /dev/null @@ -1,104 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -# requires: not metric_3d -# requires: netcdf -# cores: 2 - -from __future__ import print_function -from __future__ import division - -nproc = 2 # Number of processors to run on -reltol = 1.0e-3 # Allowed relative tolerance in growth-rate - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -import numpy as np -from sys import stdout, exit - -nthreads = 1 - -build_and_log("interchange instability test") - -# Delete old output files -shell("rm data_1/BOUT.dmp.*") -shell("rm data_10/BOUT.dmp.*") - - -def growth_rate(path, nproc, log=False): - pipe = False - if log != False: - pipe = True - s, out = launch_safe( - "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe - ) - if pipe: - f = open(log, "w") - f.write(out) - f.close() - # Get time base - tarr = collect("t_array", path=path) - nt = len(tarr) - wci = collect("wci", path=path) - tarr = tarr / wci - - # Read density - Ni = collect("Ni", path=path, xind=5, yind=30, info=False) - - # Calculate RMS value in Z - Nirms = np.zeros(nt) - for t in np.arange(nt): - Nirms[t] = np.sqrt(np.mean(Ni[t, 0, 0, :] ** 2)) - - # Get the growth rate - ln = np.log(Nirms) - return (ln[nt - 5] - 8.0 * ln[nt - 4] + 8.0 * ln[nt - 2] - ln[nt - 1]) / ( - 6.0 * (tarr[nt - 2] - tarr[nt - 4]) - ) - - -code = 0 # Return code - -# Run case 2 - -print("Test case 1: R = 1m") -growth = growth_rate("data_1", nproc, log="run_1.log") -print(" Log file run_1.log") -orig = ( - 2.148177e05 # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f -) -analytic = 2.2e5 -print(" Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic)) -absdev = abs(growth - orig) -reldev = absdev / orig -print(" Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0)) - -if reldev > reltol: - print(" => Failed") - exit(1) -else: - print(" => Passed") - -# Run case 2 - -print("Test case 2: R = 10m") -growth = growth_rate("data_10", nproc, log="run_10.log") -print(" Log file run_10.log") -# orig = 65570. # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f -orig = 6.457835e04 # 25th April 2014, revision fd032da -analytic = 6.3e4 -print(" Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic)) -absdev = abs(growth - orig) -reldev = absdev / orig -print(" Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0)) - -if reldev > reltol: - print(" => Failed") - code = 1 -else: - print(" => Passed") - -exit(code) diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py new file mode 100755 index 0000000000..2bc9b1c461 --- /dev/null +++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python3 + +# +# Run the test, compare results against the benchmark +# + +# requires: not metric_3d +# requires: netcdf +# cores: 2 + +import numpy as np +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + +nproc = 2 # Number of processors to run on +reltol = 1.0e-3 # Allowed relative tolerance in growth-rate + +nthreads = 1 + + +def test_interchange_instability(): + + # Delete old output files + shell("rm data_1/BOUT.dmp.*") + shell("rm data_10/BOUT.dmp.*") + + def growth_rate(path, nproc, log=False): + pipe = False + if log: + pipe = True + s, out = launch_safe( + "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe + ) + if pipe: + f = open(log, "w") + f.write(out) + f.close() + # Get time base + tarr = collect("t_array", path=path) + nt = len(tarr) + wci = collect("wci", path=path) + tarr = tarr / wci + + # Read density + Ni = collect("Ni", path=path, xind=5, yind=30, info=False) + + # Calculate RMS value in Z + Nirms = np.zeros(nt) + for t in np.arange(nt): + Nirms[t] = np.sqrt(np.mean(Ni[t, 0, 0, :] ** 2)) + + # Get the growth rate + ln = np.log(Nirms) + return (ln[nt - 5] - 8.0 * ln[nt - 4] + 8.0 * ln[nt - 2] - ln[nt - 1]) / ( + 6.0 * (tarr[nt - 2] - tarr[nt - 4]) + ) + + # Run case 2 + + print("Test case 1: R = 1m") + growth = growth_rate("data_1", nproc, log="run_1.log") + print(" Log file run_1.log") + orig = 2.148177e05 # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f + analytic = 2.2e5 + print( + " Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic) + ) + absdev = abs(growth - orig) + reldev = absdev / orig + print(" Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0)) + + assert reldev <= reltol, " => Failed" + + # Run case 2 + + print("Test case 2: R = 10m") + growth = growth_rate("data_10", nproc, log="run_10.log") + print(" Log file run_10.log") + # orig = 65570. # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f + orig = 6.457835e04 # 25th April 2014, revision fd032da + analytic = 6.3e4 + print( + " Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic) + ) + absdev = abs(growth - orig) + reldev = absdev / orig + print(" Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0)) + + assert reldev <= reltol, " => Failed" diff --git a/tests/integrated/test-interpolate-z/runtest b/tests/integrated/test-interpolate-z/runtest deleted file mode 100755 index 1b461d8d4f..0000000000 --- a/tests/integrated/test-interpolate-z/runtest +++ /dev/null @@ -1,133 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata import collect -from numpy import sqrt, max, abs, mean, array, log, polyfit -from sys import stdout, exit - -# Display the plots as well as saving to file -show_plot = False - -# List of NX values to use -nxlist = [16, 32, 64, 128] - -# Only testing 2D (x, z) slices, so only need one processor -nproc = 1 - -# Variables to compare -varlist = ["a", "b", "c"] -markers = ["bo", "r^", "kx"] -labels = [r"$" + var + r"$" for var in varlist] - -methods = { - "hermitespline": 4, -} - - -build_and_log("ZInterpolation test") - -print("Running ZInterpolation test") -success = True - -for method in methods: - print("------------------------------") - print("Using {} interpolation".format(method)) - - error_2 = {} - error_inf = {} - for var in varlist: - error_2[var] = [] # L2 error (RMS) - error_inf[var] = [] # Maximum error - - for nx in nxlist: - dx = 1.0 / (nx) - - args = ( - " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format( - nx4=nx + 4, dx=dx, nx=nx, method=method - ) - ) - - cmd = "./test_interpolate" + args - - shell("rm data/BOUT.dmp.*.nc") - - s, out = launch_safe(cmd, nproc=nproc, pipe=True) - with open("run.log.{}.{}".format(method, nx), "w") as f: - f.write(out) - - # Collect output data - for var in varlist: - interp = collect(var + "_interp", path="data", xguards=False, info=False) - solution = collect( - var + "_solution", path="data", xguards=False, info=False - ) - - E = interp - solution - - l2 = float(sqrt(mean(E**2))) - linf = float(max(abs(E))) - - error_2[var].append(l2) - error_inf[var].append(linf) - - print("{0:s} : l-2 {1:.8f} l-inf {2:.8f}".format(var, l2, linf)) - - dx = 1.0 / array(nxlist) - - for var in varlist: - fit = polyfit(log(dx), log(error_2[var]), 1) - order = fit[0] - stdout.write("{0:s} Convergence order = {1:.2f}".format(var, order)) - - # Make sure scaling is at least 90% of expected order - if order < 0.9 * methods[method]: - print("............ FAIL") - success = False - else: - print("............ PASS") - - if False: - try: - import matplotlib.pyplot as plt - - # Plot errors - plt.figure() - - for var, mark, label in zip(varlist, markers, labels): - plt.plot(dx, error_2[var], "-" + mark, label=label) - plt.plot(dx, error_inf[var], "--" + mark) - - plt.legend(loc="upper left") - plt.grid() - - plt.yscale("log") - plt.xscale("log") - - plt.xlabel(r"Mesh spacing $\delta x$") - plt.ylabel("Error norm") - plt.title("Error scaling for {}".format(method)) - - name = "error_scaling_{}.pdf".format(method) - plt.savefig(name) - print("Plot saved to {}".format(name)) - - if show_plot: - plt.show() - plt.close() - except ImportError: - print("No matplotlib available") - else: - print("Plotting disabled") - -print("------------------------------") -if success: - print(" => All Interpolation tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-interpolate-z/test_interpolate_z.py b/tests/integrated/test-interpolate-z/test_interpolate_z.py new file mode 100755 index 0000000000..7fdc02ea1b --- /dev/null +++ b/tests/integrated/test-interpolate-z/test_interpolate_z.py @@ -0,0 +1,128 @@ +#!/usr/bin/env python3 + +# +# Run the test, compare results against the benchmark +# + +from boututils.run_wrapper import shell, launch_safe +from boutdata import collect +from numpy import sqrt, max, abs, mean, array, log, polyfit +from sys import stdout + +# Display the plots as well as saving to file +show_plot = False + +# List of NX values to use +nxlist = [16, 32, 64, 128] + +# Only testing 2D (x, z) slices, so only need one processor +nproc = 1 + +# Variables to compare +varlist = ["a", "b", "c"] +markers = ["bo", "r^", "kx"] +labels = [r"$" + var + r"$" for var in varlist] + +methods = { + "hermitespline": 4, +} + + +def test_interpolate_z(): + + print("Running ZInterpolation test") + success = True + + for method in methods: + print("------------------------------") + print("Using {} interpolation".format(method)) + + error_2 = {} + error_inf = {} + for var in varlist: + error_2[var] = [] # L2 error (RMS) + error_inf[var] = [] # Maximum error + + for nx in nxlist: + dx = 1.0 / (nx) + + args = " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format( + nx4=nx + 4, dx=dx, nx=nx, method=method + ) + + cmd = "./test_interpolate" + args + + shell(["rm data/BOUT.dmp.*.nc"]) + + s, out = launch_safe(cmd, nproc=nproc, pipe=True) + with open("run.log.{}.{}".format(method, nx), "w") as f: + f.write(out) + + # Collect output data + for var in varlist: + interp = collect( + var + "_interp", path="data", xguards=False, info=False + ) + solution = collect( + var + "_solution", path="data", xguards=False, info=False + ) + + E = interp - solution + + l2 = float(sqrt(mean(E**2))) + linf = float(max(abs(E))) + + error_2[var].append(l2) + error_inf[var].append(linf) + + print("{0:s} : l-2 {1:.8f} l-inf {2:.8f}".format(var, l2, linf)) + + dx = 1.0 / array(nxlist) + + for var in varlist: + fit = polyfit(log(dx), log(error_2[var]), 1) + order = fit[0] + stdout.write("{0:s} Convergence order = {1:.2f}".format(var, order)) + + # Make sure scaling is at least 90% of expected order + if order < 0.9 * methods[method]: + print("............ FAIL") + success = False + else: + print("............ PASS") + + if False: + try: + import matplotlib.pyplot as plt + + # Plot errors + plt.figure() + + for var, mark, label in zip(varlist, markers, labels): + plt.plot(dx, error_2[var], "-" + mark, label=label) + plt.plot(dx, error_inf[var], "--" + mark) + + plt.legend(loc="upper left") + plt.grid() + + plt.yscale("log") + plt.xscale("log") + + plt.xlabel(r"Mesh spacing $\delta x$") + plt.ylabel("Error norm") + plt.title("Error scaling for {}".format(method)) + + name = "error_scaling_{}.pdf".format(method) + plt.savefig(name) + print("Plot saved to {}".format(name)) + + if show_plot: + plt.show() + plt.close() + except ImportError: + print("No matplotlib available") + else: + print("Plotting disabled") + + print("------------------------------") + assert success, " => Some failed tests" diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/test_interpolate.py similarity index 89% rename from tests/integrated/test-interpolate/runtest rename to tests/integrated/test-interpolate/test_interpolate.py index 91503f5f9e..07a06a6c19 100755 --- a/tests/integrated/test-interpolate/runtest +++ b/tests/integrated/test-interpolate/test_interpolate.py @@ -4,11 +4,13 @@ # Run the test, compare results against the benchmark # -from boututils.run_wrapper import build_and_log, shell, launch_safe +import pytest +from boututils.run_wrapper import shell, launch_safe from boutdata import collect import boutconfig from numpy import sqrt, max, abs, mean, array, log, polyfit -from sys import stdout, exit +from sys import stdout + # Display the plots as well as saving to file show_plot = False @@ -30,12 +32,12 @@ } -build_and_log("Interpolation test") +@pytest.mark.parametrize("method", methods) +def test_interpolate(method): -print("Running Interpolation test") -success = True + print("Running Interpolation test") + success = True -for method in methods: print("------------------------------") print("Using {} interpolation".format(method)) @@ -54,7 +56,7 @@ cmd = "./test_interpolate" + args - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) s, out = launch_safe(cmd, nproc=nproc, pipe=True) with open("run.log.{}.{}".format(method, nx), "w") as f: @@ -135,10 +137,5 @@ def myplot(f, lbl=None): else: print("Plotting disabled") -print("------------------------------") -if success: - print(" => All Interpolation tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + print("------------------------------") + assert success, " => Some failed tests" diff --git a/tests/integrated/test-invertable-operator/runtest b/tests/integrated/test-invertable-operator/test_invertable_operator.py similarity index 73% rename from tests/integrated/test-invertable-operator/runtest rename to tests/integrated/test-invertable-operator/test_invertable_operator.py index 47fc5f1b53..3a8379f323 100755 --- a/tests/integrated/test-invertable-operator/runtest +++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py @@ -8,28 +8,22 @@ # Run the test, compare results against expected value # -from __future__ import print_function -from __future__ import division - -from boututils.run_wrapper import build_and_log, shell, launch_safe +import pytest +from boututils.run_wrapper import shell, launch_safe from boutdata.collect import collect -import numpy as np -from sys import stdout, exit nprocs = [1, 2] # Number of processors to run on reltol = 1.0e-3 # Allowed relative tolerance nthreads = 1 -build_and_log("invertable operator test") - # Delete old output files -shell("rm data/BOUT.dmp.*") +shell(["rm data/BOUT.dmp.*"]) def run(path, nproc, log=False): pipe = False - if log != False: + if log: pipe = True s, out = launch_safe( "./invertable_operator -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe @@ -47,7 +41,7 @@ def run(path, nproc, log=False): print( " => Failed (verification step - value is {s})".format(s=passVerification) ) - exit(1) + pytest.fail() if maxRelErrLaplacians > reltol: print( @@ -55,11 +49,10 @@ def run(path, nproc, log=False): s=maxRelErrLaplacians ) ) - exit(1) + pytest.fail() -for np in nprocs: - run("data", np) +def test_invertable_operator(): -print(" => All tests passed") -exit(0) + for np in nprocs: + run("data", np) diff --git a/tests/integrated/test-invpar/runtest b/tests/integrated/test-invpar/runtest deleted file mode 100755 index 53f6015fe9..0000000000 --- a/tests/integrated/test-invpar/runtest +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, check it completed successfully -# - -# requires: not metric_3d -# Requires: netcdf -# Cores: 4 - -from boututils.run_wrapper import build_and_log, shell, launch -from boutdata.collect import collect -from sys import stdout, exit - -build_and_log("parallel inversion test") - -flags_src = [ - dict(acoef=1, bcoef=0, ccoef=0, dcoef=0, ecoef=0), - dict(acoef=1.5, bcoef="'2.*sin(2*y)'"), - dict(acoef=1), - dict(acoef=1, bcoef=2), - dict(ccoef=1.793), - dict(ccoef=3, bcoef=0), - dict(dcoef=3.5), - dict(ecoef=-1), - dict(input_field="'ballooning(exp(-y*y)*cos(z)*gauss(x,0.2))'"), -] - -flags = "" -for i, f in enumerate(flags_src): - fl = {"acoef": 1} - fl.update(f) - for k, v in fl.items(): - flags += f" {k}_{i}={v}" - -regions = ["", " mesh:ixseps1=0 mesh:ixseps2=0"] -flags = [flags + r for r in regions] - -code = 0 # Return code -for nproc in [1, 2, 4]: - cmd = "./test_invpar" - - print(" %d processors...." % (nproc)) - r = 0 - for f in flags: - shell("rm data/BOUT.dmp.* 2> err.log") - - # Run the case - s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1) - - code += s - - if s == 0: - print("PASSED") - else: - print("FAILED") - - -if code == 0: - print(" => All inversion tests passed") -else: - print(" => Some failed tests") - -exit(code) diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py new file mode 100755 index 0000000000..c7fd0fc565 --- /dev/null +++ b/tests/integrated/test-invpar/test_invpar.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python3 + +# +# Run the test, check it completed successfully +# + +# requires: not metric_3d +# Requires: netcdf +# Cores: 4 + +from boututils.run_wrapper import shell, launch + + +flags_src = [ + dict(acoef=1, bcoef=0, ccoef=0, dcoef=0, ecoef=0), + dict(acoef=1.5, bcoef="'2.*sin(2*y)'"), + dict(acoef=1), + dict(acoef=1, bcoef=2), + dict(ccoef=1.793), + dict(ccoef=3, bcoef=0), + dict(dcoef=3.5), + dict(ecoef=-1), + dict(input_field="'ballooning(exp(-y*y)*cos(z)*gauss(x,0.2))'"), +] + + +def test_invpar(): + global i, f, r, code + flags = "" + for i, f in enumerate(flags_src): + fl = {"acoef": 1} + fl.update(f) + for k, v in fl.items(): + flags += f" {k}_{i}={v}" + + regions = ["", " mesh:ixseps1=0 mesh:ixseps2=0"] + flags = [flags + r for r in regions] + + code = 0 # Return code + for nproc in [1, 2, 4]: + cmd = "./test_invpar" + + print(" %d processors...." % (nproc)) + r = 0 + for f in flags: + shell(["rm data/BOUT.dmp.* 2> err.log"]) + + # Run the case + s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1) + + code += s + + if s == 0: + print("PASSED") + else: + print("FAILED") + assert s == 0, f"Test failed for flag={f}" + + if code == 0: + print(" => All inversion tests passed") + else: + print(" => Some failed tests") diff --git a/tests/integrated/test-laplace-hypre3d/runtest b/tests/integrated/test-laplace-hypre3d/runtest deleted file mode 100755 index b50c5993b7..0000000000 --- a/tests/integrated/test-laplace-hypre3d/runtest +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python3 - -# requires: hypre - -from boutdata import collect -from boututils.run_wrapper import launch_safe, build_and_log -from sys import exit - -test_directories = [ - ("data_slab_core", 1), - ("data_slab_sol", 1), - ("data_circular_core", 1), - ("data_circular_core-sol", 1), -] - -tolerance = 1.0e-6 - -build_and_log("Laplace 3D with Hypre") - -success = True -for directory, nproc in test_directories: - command = "test-laplace3d -d " + directory - print("running on", nproc, "processors:", command) - launch_safe(command, nproc=nproc) - - error_max = collect("error_max", path=directory, info=False) - - if error_max > tolerance: - print(directory + " failed with maximum error {}".format(error_max)) - success = False - else: - print(directory + " passed with maximum error {}".format(error_max)) - -if success: - print("All passed") - exit(0) -else: - exit(1) diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py new file mode 100755 index 0000000000..6c5f87dc24 --- /dev/null +++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python3 + +# requires: hypre + +from boutdata import collect +from boututils.run_wrapper import launch_safe + +test_directories = [ + ("data_slab_core", 1), + ("data_slab_sol", 1), + ("data_circular_core", 1), + ("data_circular_core-sol", 1), +] + +tolerance = 1.0e-6 + + +def test_laplace_hypre3d(): + + success = True + for directory, nproc in test_directories: + command = "test-laplace3d -d " + directory + print("running on", nproc, "processors:", command) + launch_safe(command, nproc=nproc) + + error_max = collect("error_max", path=directory, info=False) + + if error_max > tolerance: + print(directory + " failed with maximum error {}".format(error_max)) + success = False + else: + print(directory + " passed with maximum error {}".format(error_max)) + + assert success diff --git a/tests/integrated/test-laplace-petsc3d/runtest b/tests/integrated/test-laplace-petsc3d/runtest deleted file mode 100755 index 7b0d55f357..0000000000 --- a/tests/integrated/test-laplace-petsc3d/runtest +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env python3 - -# requires: petsc - -from boutdata import collect -from boututils.run_wrapper import launch, build_and_log -from sys import exit - -test_directories = [ - ("data_slab_core", 1), - ("data_slab_sol", 1), - ("data_circular_core", 1), - ("data_circular_core-sol", 1), -] - -tolerance = 1.0e-6 - -build_and_log("Laplace 3D with PETSc") - -success = True -errors = {} - -for directory, nproc in test_directories: - command = f"./test-laplace3d -d {directory}" - print("running on", nproc, "processors:", command) - status, output = launch(command, nproc=nproc, pipe=True) - - if status: - print("FAILED") - print(output) - errors[directory] = "" - continue - - error_max = collect("error_max", path=directory, info=False) - if error_max > tolerance: - errors[directory] = error_max - -print("**********") - -if errors: - print("Some failures:") - for name, error in errors.items(): - print(f"{name}, max error: {error}") - exit(1) - -print("All passed") -exit(0) diff --git a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py new file mode 100755 index 0000000000..3a255d48a7 --- /dev/null +++ b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py @@ -0,0 +1,45 @@ +#!/usr/bin/env python3 + +# requires: petsc + +from boutdata import collect +from boututils.run_wrapper import launch + + +test_directories = [ + ("data_slab_core", 1), + ("data_slab_sol", 1), + ("data_circular_core", 1), + ("data_circular_core-sol", 1), +] + +tolerance = 1.0e-6 + + +def test_laplace_petsc3d(): + + errors = {} + + for directory, nproc in test_directories: + command = f"./test-laplace3d -d {directory}" + print("running on", nproc, "processors:", command) + status, output = launch(command, nproc=nproc, pipe=True) + + if status: + print("FAILED") + print(output) + errors[directory] = "" + continue + + error_max = collect("error_max", path=directory, info=False) + if error_max > tolerance: + errors[directory] = error_max + + print("**********") + + if errors: + print("Some failures:") + for name, error in errors.items(): + print(f"{name}, max error: {error}") + + assert not errors diff --git a/tests/integrated/test-laplace/runtest b/tests/integrated/test-laplace/runtest deleted file mode 100755 index 8704447d66..0000000000 --- a/tests/integrated/test-laplace/runtest +++ /dev/null @@ -1,97 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -# requires: not metric_3d -# Requires: netcdf -# Cores: 4 - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect, create_cache -import numpy.testing as npt -from sys import exit - - -# Variables to compare -vars = [ - "flag0", - "flag3", - "flagis", - "flagos", - "flag0a", - "flag3a", - "flagisa", - "flagosa", - "flag0ac", - "flag3ac", - "flagisac", - "flagosac", - "flag0ad", - "flag3ad", - "flagisad", - "flagosad", -] -tol = 1e-6 # Absolute tolerance - -build_and_log("Laplacian inversion test") - -# Read benchmark values -print("Reading benchmark data") -bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars} - -print("Running Laplacian inversion test") -success = True - -for solver in ["cyclic", "pcr", "pcr_thomas"]: - for nproc in [1, 2, 4]: - nxpe = 1 - if nproc > 2: - nxpe = 2 - - cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}" - - shell("rm data/BOUT.dmp.*.nc") - - print(f" {solver} solver with {nproc} processors ({nxpe=})....") - s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True) - with open(f"run.log.{nproc}", "w") as f: - f.write(out) - - cache = create_cache(path="data", prefix="BOUT.dmp") - - # Collect output data - for v in vars: - print(f" Checking variable {v} ...", end="") - result = collect(v, path="data", info=False, datafile_cache=cache) - # Compare benchmark and output - try: - npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol) - print("Pass") - except AssertionError as e: - print(f"Fail: {e}") - success = False - - # Only check FieldPerps on one processor because reading them in is - # quite annoying on mutliple cores due to mismatched global y indices - if nproc == 1: - for v in ["flag0_perp", "flag3_perp"]: - print(f" Checking variable {v} ...", end="") - result = collect(v, path="data", info=False, datafile_cache=cache) - # Compare benchmark and output - try: - npt.assert_allclose( - result, bmk[v.replace("_perp", "")][:, 0, :], atol=tol, rtol=tol - ) - print("Pass") - except AssertionError as e: - print(f"Fail: {e}") - success = False - -if success: - print(" => All Laplacian inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py new file mode 100755 index 0000000000..254485a6a0 --- /dev/null +++ b/tests/integrated/test-laplace/test_laplace.py @@ -0,0 +1,91 @@ +#!/usr/bin/env python3 +from pathlib import Path + +# +# Run the test, compare results against the benchmark +# + +# requires: not metric_3d +# Requires: netcdf +# Cores: 4 + +import pytest +import numpy.testing as npt +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect, create_cache + + +# Variables to compare +vars = [ + "flag0", + "flag3", + "flagis", + "flagos", + "flag0a", + "flag3a", + "flagisa", + "flagosa", + "flag0ac", + "flag3ac", + "flagisac", + "flagosac", + "flag0ad", + "flag3ad", + "flagisad", + "flagosad", +] +tol = 1e-6 # Absolute tolerance + + +@pytest.fixture(scope="module") +def benchmark_data(): + """Fixture to load benchmark data once for the entire test session.""" + + source_data_dir = str(Path(__file__).parent / "data") + return { + v: collect(v, path=source_data_dir, prefix="benchmark", info=False) + for v in vars + } + + +@pytest.mark.parametrize("solver", ["cyclic", "pcr", "pcr_thomas"]) +@pytest.mark.parametrize("nproc", [1, 2, 4]) +def test_laplace(solver, nproc, benchmark_data): + + nxpe = 2 if nproc > 2 else 1 + cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}" + + shell("rm data/BOUT.dmp.*.nc") + + s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True) + + with open(f"run.log.{nproc}", "w") as f: + f.write(out) + + cache = create_cache(path="data", prefix="BOUT.dmp") + + # Collect output data + for v in vars: + result = collect(v, path="data", info=False, datafile_cache=cache) + npt.assert_allclose( + result, + benchmark_data[v], + atol=tol, + rtol=tol, + err_msg=f"Failed checking variable: {v}", + ) + + # Only check FieldPerps on one processor because reading them in is + # quite annoying on multiple cores due to mismatched global y indices + if nproc == 1: + for v in ["flag0_perp", "flag3_perp"]: + result = collect(v, path="data", info=False, datafile_cache=cache) + + # Compare benchmark and output + npt.assert_allclose( + result, + benchmark_data[v.replace("_perp", "")][:, 0, :], + atol=tol, + rtol=tol, + err_msg=f"Failed checking perpendicular variable: {v}", + ) diff --git a/tests/integrated/test-laplace2/test_laplace2.py b/tests/integrated/test-laplace2/test_laplace2.py new file mode 100755 index 0000000000..2c5a409aeb --- /dev/null +++ b/tests/integrated/test-laplace2/test_laplace2.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./test_laplace") diff --git a/tests/integrated/test-laplacexy-fv/runtest b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py similarity index 61% rename from tests/integrated/test-laplacexy-fv/runtest rename to tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py index f87a12e2ab..03f12c04b7 100755 --- a/tests/integrated/test-laplacexy-fv/runtest +++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py @@ -8,11 +8,12 @@ # requires: petsc # cores: 8 -from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe +import pytest +from boututils.run_wrapper import shell, launch, launch_safe from boutdata.collect import collect -from sys import exit tol = 5.0e-8 +nproc = 8 argslist = [ "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet " @@ -37,49 +38,36 @@ "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1", ] -build_and_log("LaplaceXY inversion test") -print("Running LaplaceXY inversion test") -success = True +@pytest.mark.parametrize("args", argslist) +def test_laplacexy_fv(args): -for nproc in [8]: - print(" %d processors...." % nproc) - for args in argslist: - cmd = "./test-laplacexy " + args + print("Running LaplaceXY inversion test") + cmd = f"./test-laplacexy {args}" - shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1") + shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"]) - s, out = launch( - cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True + s, out = launch( + f"{cmd} laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True + ) + + if s == 134: + # PETSc did not recognise pctype option, probably means it + # was not compiled with hypre, so skip tests that need + # hypre to converge + print( + "hypre not available as pre-conditioner in PETSc. Re-running with " + + "pctype=shell..." ) - if s == 134: - # PETSc did not recognise pctype option, probably means it - # was not compiled with hypre, so skip tests that need - # hypre to converge - print( - "hypre not available as pre-conditioner in PETSc. Re-running with " - + "pctype=shell..." - ) - _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) + _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) - f = open("run.log." + str(nproc), "w") + with open(f"run.log.{nproc}", "w") as f: f.write(out) - f.close() - # Collect output data - error = collect("max_error", path="data", info=False) - if error <= 0: - print("Convergence error") - success = False - elif error > tol: - print("Fail, maximum error is = " + str(error)) - success = False - else: - print("Pass") + # Collect output data + error = collect("max_error", path="data", info=False) -if success: - print(" => All LaplaceXY inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + assert error > 0, f"Convergence error: max_error is {error}" + assert error <= tol, ( + f"Fail: maximum error is {error}, which exceeds tolerance {tol}" + ) diff --git a/tests/integrated/test-laplacexy-short/runtest b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py similarity index 68% rename from tests/integrated/test-laplacexy-short/runtest rename to tests/integrated/test-laplacexy-short/test_laplacexy_short.py index 3325a32f4d..135c04141b 100755 --- a/tests/integrated/test-laplacexy-short/runtest +++ b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py @@ -8,11 +8,12 @@ # requires: petsc # cores: 8 -from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe +import pytest +from boututils.run_wrapper import shell, launch, launch_safe from boutdata.collect import collect -from sys import exit tol = 5.0e-8 +nproc = 8 argslist = [ "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet " @@ -45,49 +46,33 @@ "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1", ] -build_and_log("LaplaceXY inversion test") -print("Running LaplaceXY inversion test") -success = True +@pytest.mark.parametrize("args", argslist) +def test_laplacexy_short(args): -for nproc in [8]: - print(" %d processors...." % nproc) - for args in argslist: - cmd = "./test-laplacexy " + args + cmd = f"./test-laplacexy {args}" - shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1") + shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"]) - s, out = launch( - cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True + s, out = launch( + f"{cmd} laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True + ) + if s == 134: + # PETSc did not recognise pctype option, probably means it + # was not compiled with hypre, so skip tests that need + # hypre to converge + print( + "hypre not available as pre-conditioner in PETSc. Re-running with " + + "pctype=shell..." ) - if s == 134: - # PETSc did not recognise pctype option, probably means it - # was not compiled with hypre, so skip tests that need - # hypre to converge - print( - "hypre not available as pre-conditioner in PETSc. Re-running with " - + "pctype=shell..." - ) - _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) + _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) - f = open("run.log." + str(nproc), "w") + with open(f"run.log.{nproc}", "w") as f: f.write(out) - f.close() - # Collect output data - error = collect("max_error", path="data", info=False) - if error <= 0: - print("Convergence error") - success = False - elif error > tol: - print("Fail, maximum error is = " + str(error)) - success = False - else: - print("Pass") + error = collect("max_error", path="data", info=False) -if success: - print(" => All LaplaceXY inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + assert error > 0, f"Convergence error: max_error is {error}" + assert error <= tol, ( + f"Fail: maximum error is {error}, which exceeds tolerance {tol}" + ) diff --git a/tests/integrated/test-laplacexy/plotmetrics.py b/tests/integrated/test-laplacexy/plotmetrics.py index 3100856679..313fcfda5f 100755 --- a/tests/integrated/test-laplacexy/plotmetrics.py +++ b/tests/integrated/test-laplacexy/plotmetrics.py @@ -3,7 +3,6 @@ from boutdata import collect from boututils.datafile import DataFile from matplotlib import pyplot -import numpy from sys import exit # Set default colormap diff --git a/tests/integrated/test-laplacexy/plotresult.py b/tests/integrated/test-laplacexy/plotresult.py index ccf48baa55..9b9dfcc44f 100755 --- a/tests/integrated/test-laplacexy/plotresult.py +++ b/tests/integrated/test-laplacexy/plotresult.py @@ -3,7 +3,6 @@ from boutdata import collect from boututils.datafile import DataFile from matplotlib import pyplot -import numpy from sys import exit # Set default colormap diff --git a/tests/integrated/test-laplacexy/runtest b/tests/integrated/test-laplacexy/test_laplacexy.py similarity index 66% rename from tests/integrated/test-laplacexy/runtest rename to tests/integrated/test-laplacexy/test_laplacexy.py index d2f99c5100..750600a6cb 100755 --- a/tests/integrated/test-laplacexy/runtest +++ b/tests/integrated/test-laplacexy/test_laplacexy.py @@ -9,9 +9,8 @@ # requires: all_tests # cores: 8 -from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe +from boututils.run_wrapper import shell, launch, launch_safe from boutdata.collect import collect -from sys import exit tol_orth = 5.0e-8 @@ -52,53 +51,49 @@ "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1 laplacexy:pctype=hypre", ] -build_and_log("LaplaceXY inversion test") - -print("Running LaplaceXY inversion test") -success = True - -for nproc in [8]: - print(" %d processors...." % nproc) - for nonorth, tol in [(False, tol_orth), (True, tol_nonorth)]: - for args in argslist: - if not nonorth: - args += " mesh:g12=0." - - cmd = "./test-laplacexy " + args - - shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1") - - if "hypre" in args: - s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True) - if s == 134: - # PETSc did not recognise pctype option, probably means it - # was not compiled with hypre, so skip tests that need - # hypre to converge - print( - "hypre not available as pre-conditioner in PETSc. Skipping..." - ) - continue - else: - s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) - - f = open("run.log." + str(nproc), "w") - f.write(out) - f.close() - - # Collect output data - error = collect("max_error", path="data", info=False) - if error <= 0: - print("Convergence error") - success = False - elif error > tol: - print("Fail, maximum error is = " + str(error)) - success = False - else: - print("Pass") - -if success: - print(" => All LaplaceXY inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + +def test_laplacexy(): + + print("Running LaplaceXY inversion test") + success = True + + for nproc in [8]: + print(" %d processors...." % nproc) + for nonorth, tol in [(False, tol_orth), (True, tol_nonorth)]: + for args in argslist: + if not nonorth: + args += " mesh:g12=0." + + cmd = "./test-laplacexy " + args + + shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"]) + + if "hypre" in args: + s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True) + if s == 134: + # PETSc did not recognise pctype option, probably means it + # was not compiled with hypre, so skip tests that need + # hypre to converge + print( + "hypre not available as pre-conditioner in PETSc. Skipping..." + ) + continue + else: + s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) + + f = open("run.log." + str(nproc), "w") + f.write(out) + f.close() + + # Collect output data + error = collect("max_error", path="data", info=False) + if error <= 0: + print("Convergence error") + success = False + elif error > tol: + print("Fail, maximum error is = " + str(error)) + success = False + else: + print("Pass") + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-laplacexy2-hypre/runtest b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py similarity index 70% rename from tests/integrated/test-laplacexy2-hypre/runtest rename to tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py index 55f5982a0c..8b1a75942d 100755 --- a/tests/integrated/test-laplacexy2-hypre/runtest +++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py @@ -7,12 +7,12 @@ # requires: hypre # cores: 8 -from sys import exit - +import pytest from boutdata.collect import collect -from boututils.run_wrapper import build_and_log, launch_safe, shell +from boututils.run_wrapper import launch_safe, shell tol = 5.0e-8 +nproc = 8 argslist = [ "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry_dirichlet=true " @@ -37,37 +37,25 @@ "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1", ] -build_and_log("LaplaceXY inversion test") -print("Running LaplaceXY inversion test") -success = True +@pytest.mark.parametrize("args", argslist) +def test_laplacexy2_hypre(args): -for nproc in [8]: print(" %d processors...." % nproc) - for args in argslist: - cmd = "./test-laplacexy " + args - shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1") + cmd = f"./test-laplacexy {args}" + + shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"]) - s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) + s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) - with open(f"run.log.{nproc}", "w") as f: - f.write(out) + with open(f"run.log.{nproc}", "w") as f: + f.write(out) - # Collect output data - error = collect("max_error", path="data", info=False) - if error <= 0: - print("Convergence error") - success = False - elif error > tol: - print("Fail, maximum error is = " + str(error)) - success = False - else: - print("Pass") + # Collect output data + error = collect("max_error", path="data", info=False) -if success: - print(" => All LaplaceXY inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + assert error > 0, f"Convergence error: maximum error is {error}" + assert error <= tol, ( + f"Fail: maximum error is {error}, which exceeds tolerance {tol}" + ) diff --git a/tests/integrated/test-laplacexz/runtest b/tests/integrated/test-laplacexz/runtest deleted file mode 100755 index bc7592ec3e..0000000000 --- a/tests/integrated/test-laplacexz/runtest +++ /dev/null @@ -1,56 +0,0 @@ -#!/usr/bin/env python3 - -# requires: not metric_3d -# requires: petsc - -# -# Run the test, compare results against the benchmark -# - -from boututils.run_wrapper import shell, launch_safe, getmpirun, build_and_log -from boutdata.collect import collect -import numpy as np -from sys import exit - -tol = 1e-10 # Absolute tolerance - -MPIRUN = getmpirun() - -build_and_log("LaplaceXZ test") - -print("Running LaplaceXZ test") -success = True - -for nproc in [1, 2, 4]: - nxpe = nproc - - cmd = "./test-laplacexz nxpe=" + str(nxpe) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors (nxpe = %d)...." % (nproc, nxpe)) - s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect output data - f = collect("f", path="data", info=False) - f2 = collect("f2", path="data", info=False) - print(" Checking tolerance... ") - # Compare benchmark and output - if np.shape(f) != np.shape(f2): - print("Fail, wrong shape") - success = False - diff = np.max(np.abs(f2 - f)) - if diff > tol: - print("Fail, maximum difference = " + str(diff)) - success = False - else: - print("Pass") - -if success: - print(" => LaplaceXZ inversion test passed") - exit(0) - -print(" => LaplaceXZ test failed") -exit(1) diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py new file mode 100755 index 0000000000..02a7239285 --- /dev/null +++ b/tests/integrated/test-laplacexz/test_laplacexz.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python3 + +# requires: not metric_3d +# requires: petsc + +# +# Run the test, compare results against the benchmark +# + +import numpy as np +import pytest + +from boutdata.collect import collect +from boututils.run_wrapper import shell, launch_safe, getmpirun + + +@pytest.mark.parametrize("nproc", [1, 2, 4]) +def test_laplacexz(nproc): + + tol = 1e-10 # Absolute tolerance + + MPIRUN = getmpirun() + + print(f"Running LaplaceXZ test on {nproc} processors...") + + # Unique data directory per processor configuration + cmd = f"./test-laplacexz nxpe={nproc}" + + shell(["rm -f data/BOUT.dmp.*.nc"]) + + print(f" {nproc} processors (nxpe = {nproc})....") + s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True) + with open(f"run.log.{nproc}", "w") as f: + f.write(out) + + # Collect output data + f = collect("f", path="data", info=False) + f2 = collect("f2", path="data", info=False) + print(" Checking tolerance... ") + # Compare benchmark and output + np.testing.assert_allclose( + f2, f, atol=tol, rtol=0, err_msg="LaplaceXZ output mismatch" + ) diff --git a/tests/integrated/test-multigrid_laplace/CMakeLists.txt b/tests/integrated/test-multigrid_laplace/CMakeLists.txt index b6bb16b8a8..b64b0e166c 100644 --- a/tests/integrated/test-multigrid_laplace/CMakeLists.txt +++ b/tests/integrated/test-multigrid_laplace/CMakeLists.txt @@ -3,5 +3,7 @@ bout_add_integrated_test( SOURCES test_multigrid_laplace.cxx CONFLICTS BOUT_USE_METRIC_3D USE_RUNTEST USE_DATA_BOUT_INP + EXTRA_FILES data/BOUT_jy4.inp data/BOUT_jy63.inp data/BOUT_jy127.inp + data/BOUT_unsheared.inp PROCESSORS 3 ) diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/runtest deleted file mode 100755 index f325185c46..0000000000 --- a/tests/integrated/test-multigrid_laplace/runtest +++ /dev/null @@ -1,68 +0,0 @@ -#!/usr/bin/env python3 - -# requires: not metric_3d - -# -# Run the test, check the error -# - -# Cores: 3 - -from __future__ import print_function - -try: - from builtins import str -except: - pass - -tol = 2e-7 # Absolute tolerance -numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -from sys import exit - -build_and_log("multigrid Laplacian inversion test") - -print("Running multigrid Laplacian inversion test") -success = True - -for nproc in [1, 3]: - # Make sure we don't use too many cores: - # Reduce number of OpenMP threads when using multiple MPI processes - mthread = 2 - if nproc > 1: - mthread = 1 - - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) - cmd = "./test_multigrid_laplace NXPE=" + str(nproc) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors..." % nproc) - s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect errors - errors = [ - collect("max_error" + str(i), path="data") for i in range(1, numTests + 1) - ] - - for i, e in enumerate(errors): - print("Checking test " + str(i)) - if e < 0.0: - print("Fail, solver did not converge") - success = False - if e > tol: - print("Fail, maximum absolute error = " + str(e)) - success = False - else: - print("Pass") - -if success: - print(" => All multigrid Laplacian inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared deleted file mode 100755 index d0dca3a808..0000000000 --- a/tests/integrated/test-multigrid_laplace/runtest_unsheared +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, check the error -# - -from __future__ import print_function - -try: - from builtins import str -except: - pass - -tol = 1e-9 # Absolute tolerance -numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) - -from boututils.run_wrapper import shell, build_and_log, launch_safe -from boutdata.collect import collect -from sys import exit - -build_and_log("Making multigrid Laplacian inversion test") - -print("Running multigrid Laplacian inversion test") -success = True - -for nproc in [1, 3]: - # Make sure we don't use too many cores: - # Reduce number of OpenMP threads when using multiple MPI processes - mthread = 2 - if nproc > 1: - mthread = 1 - - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) - cmd = "./test_multigrid_laplace -f BOUT_unsheared.inp NXPE=" + str(nproc) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors..." % nproc) - s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect errors - errors = [ - collect("max_error" + str(i), path="data") for i in range(1, numTests + 1) - ] - - for i, e in enumerate(errors): - print("Checking test " + str(i)) - if e < 0.0: - print("Fail, solver did not converge") - success = False - if e > tol: - print("Fail, maximum absolute error = " + str(e)) - success = False - else: - print("Pass") - -if success: - print(" => All multigrid Laplacian inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py new file mode 100755 index 0000000000..6f8c28b30e --- /dev/null +++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python3 + +# +# Run the test, check the error +# + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + +tol = 2e-6 # Absolute tolerance +numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) + + +def test_multigrid_laplace(): + + print("Running multigrid Laplacian inversion test") + success = True + + for nproc in [1, 2, 4]: + for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]: + # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) + cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc} input:error_on_unused_options=false" + + shell(["rm data/BOUT.dmp.*.nc"]) + + print(" %d processors, input file is %s" % (nproc, inputfile)) + s, out = launch_safe(cmd, nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + # Collect errors + errors = [ + collect("max_error" + str(i), path="data") + for i in range(1, numTests + 1) + ] + + for i, e in enumerate(errors): + print("Checking test " + str(i)) + if e < 0.0: + print("Fail, solver did not converge") + success = False + if e > tol: + print("Fail, maximum absolute error = " + str(e)) + success = False + else: + print("Pass") + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py new file mode 100755 index 0000000000..3be9bf1bbc --- /dev/null +++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py @@ -0,0 +1,54 @@ +#!/usr/bin/env python3 + +# +# Run the test, check the error +# + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + +tol = 1e-9 # Absolute tolerance +numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) + + +def test_multigrid_laplace_unsheared(): + + print("Running multigrid Laplacian inversion test (unsheared)") + success = True + + for nproc in [1, 3]: + # Make sure we don't use too many cores: + # Reduce number of OpenMP threads when using multiple MPI processes + mthread = 2 + if nproc > 1: + mthread = 1 + + # set nxpe on the command line as we only use solution from one point in y, + # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) + inputfile = "BOUT_unsheared.inp" + cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}" + + shell(["rm data/BOUT.dmp.*.nc"]) + + print(" %d processors..." % nproc) + s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + # Collect errors + errors = [ + collect("max_error" + str(i), path="data") for i in range(1, numTests + 1) + ] + + for i, e in enumerate(errors): + print("Checking test " + str(i)) + if e < 0.0: + print("Fail, solver did not converge") + success = False + if e > tol: + print("Fail, maximum absolute error = " + str(e)) + success = False + else: + print("Pass") + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/runtest deleted file mode 100755 index 145257c23b..0000000000 --- a/tests/integrated/test-naulin-laplace/runtest +++ /dev/null @@ -1,68 +0,0 @@ -#!/usr/bin/env python3 - -# requires: not metric_3d - -# -# Run the test, check the error -# - -# Cores: 3 - -from __future__ import print_function - -try: - from builtins import str -except: - pass - -tol = 2e-7 # Absolute tolerance -numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -from sys import exit - -build_and_log("LaplaceNaulin inversion test") - -print("Running LaplaceNaulin inversion test") -success = True - -for nproc in [1, 3]: - # Make sure we don't use too many cores: - # Reduce number of OpenMP threads when using multiple MPI processes - mthread = 2 - if nproc > 1: - mthread = 1 - - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver) - cmd = "./test_naulin_laplace NXPE=" + str(nproc) - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processors..." % nproc) - s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect errors - errors = [ - collect("max_error" + str(i), path="data") for i in range(1, numTests + 1) - ] - - for i, e in enumerate(errors): - print("Checking test " + str(i)) - if e < 0.0: - print("Fail, solver did not converge") - success = False - if e > tol: - print("Fail, maximum absolute error = " + str(e)) - success = False - else: - print("Pass") - -if success: - print(" => All LaplaceNaulin inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids index f56a80677e..2b802e0eb1 100755 --- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids +++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids @@ -4,21 +4,12 @@ # Run the test, check the error # -from __future__ import print_function - -try: - from builtins import str -except: - pass - -tol = 2e-6 # Absolute tolerance -numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) - -from boututils.run_wrapper import shell, build_and_log, launch_safe +from boututils.run_wrapper import shell, launch_safe from boutdata.collect import collect from sys import exit -build_and_log("Making LaplaceNaulin inversion test") +tol = 2e-6 # Absolute tolerance +numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) print("Running LaplaceNaulin inversion test") success = True @@ -28,7 +19,7 @@ for nproc in [1, 2, 4]: # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver) cmd = "./test_naulin_laplace -f " + inputfile + " NXPE=" + str(nproc) - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) print(" %d processors, input file is %s" % (nproc, inputfile)) s, out = launch_safe(cmd, nproc=nproc, pipe=True) diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared index a845a9d92f..e5ee732bbb 100755 --- a/tests/integrated/test-naulin-laplace/runtest_unsheared +++ b/tests/integrated/test-naulin-laplace/runtest_unsheared @@ -4,21 +4,12 @@ # Run the test, check the error # -from __future__ import print_function - -try: - from builtins import str -except: - pass - -tol = 1e-9 # Absolute tolerance -numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) - -from boututils.run_wrapper import shell, build_and_log, launch_safe +from boututils.run_wrapper import shell, launch_safe from boutdata.collect import collect from sys import exit -build_and_log("LaplaceNaulin inversion test") +tol = 1e-9 # Absolute tolerance +numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) print("Running LaplaceNaulin inversion test") success = True @@ -33,7 +24,7 @@ for nproc in [1, 3]: # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver) cmd = "./test_naulin_laplace -f BOUT_unsheared.inp NXPE=" + str(nproc) - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) print(" %d processors..." % nproc) s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py similarity index 51% rename from tests/integrated/test-multigrid_laplace/runtest_multiple_grids rename to tests/integrated/test-naulin-laplace/test_naulin_laplace.py index 739d15f7d4..52c2e5144d 100755 --- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids +++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py @@ -1,37 +1,39 @@ #!/usr/bin/env python3 +# requires: not metric_3d + # # Run the test, check the error # -from __future__ import print_function +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect -try: - from builtins import str -except: - pass +# Cores: 3 -tol = 2e-6 # Absolute tolerance +tol = 2e-7 # Absolute tolerance numTests = 4 # We test 4 different boundary conditions (with slightly different inputs for each) -from boututils.run_wrapper import shell, build_and_log, launch_safe -from boutdata.collect import collect -from sys import exit -build_and_log("Multigrid Laplacian inversion test") +def test_naulin_laplace(): + + print("Running LaplaceNaulin inversion test") + success = True -print("Running multigrid Laplacian inversion test") -success = True + for nproc in [1, 3]: + # Make sure we don't use too many cores: + # Reduce number of OpenMP threads when using multiple MPI processes + mthread = 2 + if nproc > 1: + mthread = 1 -for nproc in [1, 2, 4]: - for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]: - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) - cmd = "./test_multigrid_laplace -f " + inputfile + " NXPE=" + str(nproc) + # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver) + cmd = "./test_naulin_laplace NXPE=" + str(nproc) - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) - print(" %d processors, input file is %s" % (nproc, inputfile)) - s, out = launch_safe(cmd, nproc=nproc, pipe=True) + print(" %d processors..." % nproc) + s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) with open("run.log." + str(nproc), "w") as f: f.write(out) @@ -51,9 +53,4 @@ else: print("Pass") -if success: - print(" => All multigrid Laplacian inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + assert success, " => Some failed tests" diff --git a/tests/integrated/test-options-netcdf/runtest b/tests/integrated/test-options-netcdf/runtest deleted file mode 100755 index db9adc7f29..0000000000 --- a/tests/integrated/test-options-netcdf/runtest +++ /dev/null @@ -1,73 +0,0 @@ -#!/usr/bin/env python3 - -# Note: This test requires NCDF4, whereas on Travis NCDF is used -# requires: netcdf -# requires: not legacy_netcdf - -from boututils.datafile import DataFile -from boututils.run_wrapper import build_and_log, shell, launch_safe as launch -from boutdata.data import BoutOptionsFile - -import math -import numpy as np - -build_and_log("options-netcdf test") -shell("rm -f test-out.ini") -shell("rm -f test-out.nc") - -# Create a NetCDF input file -with DataFile("test.nc", create=True, format="NETCDF4") as f: - f.write("int", 42) - f.write("real", 3.1415) - f.write("string", "hello") - -# run BOUT++ -launch("./test-options-netcdf", nproc=1, mthread=1) - -# Check the output INI file -result = BoutOptionsFile("test-out.ini") - -print(result) - -assert result["int"] == 42 -assert math.isclose(result["real"], 3.1415) -assert result["string"] == "hello" - -print("Checking saved NetCDF file") - -# Check the output NetCDF file -with DataFile("test-out.nc") as f: - assert f["int"] == 42 - assert math.isclose(f["real"], 3.1415) - assert result["string"] == "hello" - -print("Checking saved settings.ini") - -# Check the settings.ini file, coming from BOUT.inp -# which is converted to NetCDF, read in, then written again -settings = BoutOptionsFile("settings.ini") - -assert settings["mesh"]["nx"] == 5 -assert settings["mesh"]["ny"] == 2 - -print("Checking saved fields.nc") - -with DataFile("fields.nc") as f: - assert f["f2d"].shape == (5, 6) # Field2D - assert f["f3d"].shape == (5, 6, 2) # Field3D - assert f["fperp"].shape == (5, 2) # FieldPerp - assert np.allclose(f["f2d"], 1.0) - assert np.allclose(f["f3d"], 2.0) - assert np.allclose(f["fperp"], 3.0) - -print("Checking saved fields2.nc") - -with DataFile("fields2.nc") as f: - assert f["f2d"].shape == (5, 6) # Field2D - assert f["f3d"].shape == (5, 6, 2) # Field3D - assert f["fperp"].shape == (5, 2) # FieldPerp - assert np.allclose(f["f2d"], 1.0) - assert np.allclose(f["f3d"], 2.0) - assert np.allclose(f["fperp"], 3.0) - -print(" => Passed") diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py new file mode 100755 index 0000000000..f8a4a92b01 --- /dev/null +++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py @@ -0,0 +1,75 @@ +#!/usr/bin/env python3 + +# Note: This test requires NCDF4, whereas on Travis NCDF is used +# requires: netcdf +# requires: not legacy_netcdf + +from boututils.datafile import DataFile +from boututils.run_wrapper import shell, launch_safe as launch +from boutdata.data import BoutOptionsFile + +import math +import numpy.testing as npt + + +def test_options_netcdf(): + + shell(["rm -f test-out.ini"]) + shell(["rm -f test-out.nc"]) + + # Create a NetCDF input file + with DataFile("test.nc", create=True, format="NETCDF4") as f: + f.write("int", 42) + f.write("real", 3.1415) + f.write("string", "hello") + + # run BOUT++ + launch("./test-options-netcdf", nproc=1, mthread=1) + + # Check the output INI file + result = BoutOptionsFile("test-out.ini") + + print(result) + + assert result["int"] == 42 + assert math.isclose(result["real"], 3.1415) + assert result["string"] == "hello" + + print("Checking saved NetCDF file") + + # Check the output NetCDF file + with DataFile("test-out.nc") as f: + assert f["int"] == 42 + assert math.isclose(f["real"], 3.1415) + assert result["string"] == "hello" + + print("Checking saved settings.ini") + + # Check the settings.ini file, coming from BOUT.inp + # which is converted to NetCDF, read in, then written again + settings = BoutOptionsFile("settings.ini") + + assert settings["mesh"]["nx"] == 5 + assert settings["mesh"]["ny"] == 2 + + print("Checking saved fields.nc") + + with DataFile("fields.nc") as f: + assert f["f2d"].shape == (5, 6) # Field2D + assert f["f3d"].shape == (5, 6, 2) # Field3D + assert f["fperp"].shape == (5, 2) # FieldPerp + npt.assert_allclose(f["f2d"], 1.0) + npt.assert_allclose(f["f3d"], 2.0) + npt.assert_allclose(f["fperp"], 3.0) + + print("Checking saved fields2.nc") + + with DataFile("fields2.nc") as f: + assert f["f2d"].shape == (5, 6) # Field2D + assert f["f3d"].shape == (5, 6, 2) # Field3D + assert f["fperp"].shape == (5, 2) # FieldPerp + npt.assert_allclose(f["f2d"], 1.0) + npt.assert_allclose(f["f3d"], 2.0) + npt.assert_allclose(f["fperp"], 3.0) + + print(" => Passed") diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py similarity index 51% rename from tests/integrated/test-petsc_laplace/runtest rename to tests/integrated/test-petsc_laplace/test_petsc_laplace.py index b4379f7754..3ac9a802f1 100755 --- a/tests/integrated/test-petsc_laplace/runtest +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py @@ -8,11 +8,10 @@ # requires: all_tests # cores: 4 -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect, create_cache - import pathlib -from sys import exit +import pytest +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect, create_cache errors = [ "max_error1", @@ -24,15 +23,12 @@ ] tol = 2e-4 # Absolute (?) tolerance -build_and_log("PETSc Laplacian inversion test") -print("Running PETSc Laplacian inversion test") -success = True - -for nproc in [1, 2, 4]: +@pytest.mark.parametrize("nproc", [1, 2, 4]) +def test_petsc_laplace(nproc): cmd = "./test_petsc_laplace" - shell("rm data/BOUT.dmp.*.nc") + shell(["rm data/BOUT.dmp.*.nc"]) print(f" {nproc} processors....") s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True) @@ -42,20 +38,9 @@ # Collect output data for varname in errors: - print(f" Checking {varname} ... ", end="") error = collect(varname, path="data", info=False, datafile_cache=cache) - if error <= 0: - print("Convergence error") - success = False - elif error > tol: - print(f"Fail, maximum error is = {error:e}") - success = False - else: - print("Pass") - -if success: - print(" => All PETSc Laplacian inversion tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) + + assert error > 0, f"Convergence error for {varname} on {nproc} proc(s)" + assert error <= tol, ( + f"Fail: {varname} maximum error is {error:e} (Tolerance: {tol:e})" + ) diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/runtest deleted file mode 100755 index 3be39949c3..0000000000 --- a/tests/integrated/test-petsc_laplace_MAST-grid/runtest +++ /dev/null @@ -1,77 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -# requires: all_tests -# requires: petsc -# cores: 4 - -# Variables to compare -from __future__ import print_function -from builtins import str - -vars = [ - ["max_error1", 2.0e-4], - ["max_error2", 1.0e-4], - ["max_error3", 1.0e-4], - ["max_error4", 1.0e-4], - ["max_error5", 2.0e-3], - ["max_error6", 3.0e-4], - ["max_error7", 2.0e-4], - ["max_error8", 1.0e-4], -] -# tol = 1e-4 # Absolute (?) tolerance - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -from sys import stdout, exit - -build_and_log( - "PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)" -) - -print( - "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)" -) -success = True - -for nproc in [1, 2, 4]: - # nxpe = 1 - # if nproc > 2: - # nxpe = 2 - for jy in [2, 34, 65, 81, 113]: - cmd = "./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{}.nc".format( - jy - ) - - shell("rm data/BOUT.dmp.*.nc") - - print(" {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy)) - s, out = launch_safe(cmd, nproc=nproc, pipe=True) - f = open("run.log." + str(nproc), "w") - f.write(out) - f.close() - - # Collect output data - for v in vars: - stdout.write(" Checking " + v[0] + " ... ") - error = collect(v[0], path="data", info=False) - if error <= 0: - print("Convergence error") - success = False - elif error > v[1]: - print("Fail, maximum error is = " + str(error)) - success = False - else: - print("Pass") - -if success: - print( - " => All PETSc Laplacian inversion with non-identity metric (taken from grid for MAST SOL) tests passed" - ) - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py new file mode 100755 index 0000000000..9c67f4bc80 --- /dev/null +++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python3 + +# +# Run the test, compare results against the benchmark +# + +# requires: all_tests +# requires: petsc +# cores: 4 + +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect +from sys import stdout + +# Variables to compare +vars = [ + ["max_error1", 2.0e-4], + ["max_error2", 1.0e-4], + ["max_error3", 1.0e-4], + ["max_error4", 1.0e-4], + ["max_error5", 2.0e-3], + ["max_error6", 3.0e-4], + ["max_error7", 2.0e-4], + ["max_error8", 1.0e-4], +] +# tol = 1e-4 # Absolute (?) tolerance + + +def test_petsc_laplace_MAST_grid(): + + print( + "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)" + ) + success = True + + for nproc in [1, 2, 4]: + # nxpe = 1 + # if nproc > 2: + # nxpe = 2 + for jy in [2, 34, 65, 81, 113]: + cmd = "./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{}.nc".format( + jy + ) + + shell(["rm data/BOUT.dmp.*.nc"]) + + print(" {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy)) + s, out = launch_safe(cmd, nproc=nproc, pipe=True) + f = open("run.log." + str(nproc), "w") + f.write(out) + f.close() + + # Collect output data + for v in vars: + stdout.write(" Checking " + v[0] + " ... ") + error = collect(v[0], path="data", info=False) + if error <= 0: + print("Convergence error") + success = False + elif error > v[1]: + print("Fail, maximum error is = " + str(error)) + success = False + else: + print("Pass") + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-region-iterator/runtest b/tests/integrated/test-region-iterator/runtest deleted file mode 100755 index 2277ef15e9..0000000000 --- a/tests/integrated/test-region-iterator/runtest +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, check it completed successfully -# - -# requires: netcdf -# cores: 2 - -from __future__ import print_function - -try: - from builtins import str -except: - pass -from boututils.run_wrapper import build_and_log, launch_safe -from boutdata.collect import collect -from sys import exit - -build_and_log("Region Iterator test") - -flags = [""] -cmd = "./test_region_iterator" -code = 0 # Return code -pipe = True - -for nproc in [1, 2]: # Number of mpi procs - for mthread in [1]: # Number of omp threads (not yet supported) - print("\t{n} processors and {m} threads".format(n=nproc, m=mthread)) - - for f in flags: - # Run the case - s, out = launch_safe(cmd + " " + f, nproc=nproc, pipe=pipe) - if pipe: - f = open("run.log." + str(nproc) + "." + str(mthread), "w") - f.write(out) - f.close() - - # If we've got here we know that cmd launched by launch_safe passed - # as otherwise it raises. - print("Passed") - -if code == 0: - print(" => All range iterator tests passed") -else: - print(" => Some failed tests") - -exit(code) diff --git a/tests/integrated/test-region-iterator/test_region_iterator.py b/tests/integrated/test-region-iterator/test_region_iterator.py new file mode 100755 index 0000000000..7b5f25599d --- /dev/null +++ b/tests/integrated/test-region-iterator/test_region_iterator.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 + +# +# Run the test, check it completed successfully +# + +# requires: netcdf +# cores: 2 + +from boututils.run_wrapper import launch_safe + + +flags = [""] +cmd = "./test_region_iterator" +code = 0 # Return code +pipe = True + + +def test_region_iterator(): + + for nproc in [1, 2]: # Number of mpi procs + for mthread in [1]: # Number of omp threads (not yet supported) + print("\t{n} processors and {m} threads".format(n=nproc, m=mthread)) + + for f in flags: + # Run the case + s, out = launch_safe(cmd + " " + f, nproc=nproc, pipe=pipe) + if pipe: + f = open("run.log." + str(nproc) + "." + str(mthread), "w") + f.write(out) + f.close() + + # If we've got here we know that cmd launched by launch_safe passed + # as otherwise it raises. + print("Passed") + + assert code == 0, " => Some failed tests" diff --git a/tests/integrated/test-restart-io/runtest b/tests/integrated/test-restart-io/runtest deleted file mode 100755 index 00ee907958..0000000000 --- a/tests/integrated/test-restart-io/runtest +++ /dev/null @@ -1,187 +0,0 @@ -#!/usr/bin/env python3 -# -# Test file I/O by loading from restart files and writing to dump files -# -# requires: netcdf -# cores: 4 - -from boutdata import restart -from boutdata.collect import collect -from boututils.boutarray import BoutArray -from boututils.datafile import DataFile -from boututils.run_wrapper import build_and_log, shell, launch_safe -import numpy -import os -from sys import exit -import uuid - -nx = 8 -ny = 16 -nz = 4 -mxg = 2 -myg = 2 - -build_and_log("restart I/O test") - -x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis] -y = numpy.linspace(0.0, 1.0, ny + 2 * myg)[numpy.newaxis, :, numpy.newaxis] -z = numpy.linspace(0.0, 1.0, nz)[numpy.newaxis, numpy.newaxis, :] - -testvars = {} -testvars["f3d"] = BoutArray( - numpy.exp(numpy.sin(x + y + z)), attributes={"bout_type": "Field3D"} -) -testvars["f2d"] = BoutArray( - numpy.exp(numpy.sin(x + y + 1.0))[:, :, 0], attributes={"bout_type": "Field2D"} -) -testvars["fperp_lower"] = BoutArray( - numpy.exp(numpy.sin(x + z + 2.0))[:, 0, :], - attributes={"bout_type": "FieldPerp", "yindex_global": 0}, -) -testvars["fperp_upper"] = BoutArray( - numpy.exp(numpy.sin(x + z + 3.0))[:, 0, :], - attributes={"bout_type": "FieldPerp", "yindex_global": ny - 1}, -) - -# make restart file -restartdir = os.path.join("data", "restart") -try: - os.mkdir(restartdir) -except FileExistsError: - pass - -with DataFile( - os.path.join(restartdir, "BOUT.restart.0.nc"), create=True -) as base_restart: - base_restart.write("MXSUB", nx) - base_restart.write("MYSUB", ny) - base_restart.write("MZSUB", nz) - base_restart.write("MXG", mxg) - base_restart.write("MYG", myg) - base_restart.write("MZG", 0) - base_restart.write("nx", nx + 2 * mxg) - base_restart.write("ny", ny) - base_restart.write("nz", nz) - base_restart.write("MZ", nz) - base_restart.write("NXPE", 1) - base_restart.write("NYPE", 1) - base_restart.write("NZPE", 1) - base_restart.write("tt", 0.0) - base_restart.write("hist_hi", 0) - # set BOUT_VERSION to stop collect from changing nz or printing a warning - base_restart.write("BOUT_VERSION", 4.0) - base_restart.write("f3d", testvars["f3d"]) - base_restart.write("f2d", testvars["f2d"]) - base_restart.write("fperp_lower", testvars["fperp_lower"]) - base_restart.write("fperp_upper", testvars["fperp_upper"]) - - # make run_id an array of characters because NetCDF doesn't like generic strings - run_id_string = "36 character run_id test string ****" - run_id = numpy.array(list(run_id_string), dtype="S1") - run_id = BoutArray(run_id, attributes={"bout_type": "string"}) - base_restart.write("run_id", run_id) - run_restart_from = numpy.array( - list("36 character run_restart_from string"), dtype="S1" - ) - run_restart_from = BoutArray(run_restart_from, attributes={"bout_type": "string"}) - base_restart.write("run_restart_from", run_restart_from) - -success = True - -# Note: expect this to fail for 16 processors, because when there are 2 -# y-points per processor, the fperp_lower FieldPerp is in the grid cells of one -# set of processors and also in the guard cells of anoether set. This means -# valid FieldPerps get written to output files with different -# y-processor-indices, and collect() cannot handle this. -for nproc in [1, 2, 4]: - # delete any existing output - shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc") - - # create restart files for the run - restart.redistribute(nproc, path=restartdir, output="data") - - print(" %d processor...." % (nproc)) - - # run the test executable - s, out = launch_safe("./test-restart-io", nproc=nproc, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # check the results - for name in testvars.keys(): - # check non-evolving version - result = collect( - name + "_once", path="data", xguards=True, yguards=True, info=False - ) - testvar = testvars[name] - - if not numpy.allclose(testvar, result): - success = False - print(f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}") - # Don't plot anything by default - if False: - from boututils.showdata import showdata - - showdata([result, testvar]) - if name == "fperp_lower" or name == "fperp_upper": - yindex_result = result.attributes["yindex_global"] - yindex_test = testvar.attributes["yindex_global"] - if not yindex_result == yindex_test: - success = False - print( - "Fail: yindex_global of " - + name - + " is " - + str(yindex_result) - + " should be " - + str(yindex_test) - ) - - # check evolving versions - result = collect(name, path="data", xguards=True, yguards=True, info=False) - - for result_timeslice in result: - if not numpy.all(testvar == result_timeslice): - success = False - print( - f"{name} evolving version is different: {numpy.max(numpy.abs(testvar - result_timeslice))}" - ) - if name == "fperp_lower" or name == "fperp_upper": - yindex_result = result.attributes["yindex_global"] - yindex_test = testvar.attributes["yindex_global"] - if not yindex_result == yindex_test: - success = False - print( - "Fail: yindex_global of " - + name - + " evolving version is " - + str(yindex_result) - + " should be " - + str(yindex_test) - ) - - # check the run_id - run_id = str(collect("run_id", path="data", info=False)) - # check run_id can be converted to a valid UUID - try: - uuid.UUID(run_id) - except ValueError: - success = False - print(f"run_id='{run_id}' is not a valid UUID") - run_restart_from = str(collect("run_restart_from", path="data", info=False)) - if not run_restart_from == run_id_string: - success = False - print( - f"incorrect run_restart_from='{run_restart_from}'. Expected '{run_id_string}'" - ) - -if success: - print("=> All restart I/O tests passed") - # clean up binary files - shell( - "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc" - ) - exit(0) - -print("=> Some failed tests") -exit(1) diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py new file mode 100755 index 0000000000..f37e56f5c1 --- /dev/null +++ b/tests/integrated/test-restart-io/test_restart_io.py @@ -0,0 +1,185 @@ +#!/usr/bin/env python3 +# +# Test file I/O by loading from restart files and writing to dump files +# +# requires: netcdf +# cores: 4 + +from boutdata import restart +from boutdata.collect import collect +from boututils.boutarray import BoutArray +from boututils.datafile import DataFile +from boututils.run_wrapper import shell, launch_safe +import numpy +import uuid +from pathlib import Path + +nx = 8 +ny = 16 +nz = 4 +mxg = 2 +myg = 2 + + +def test_restart_io(): + + x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis] + y = numpy.linspace(0.0, 1.0, ny + 2 * myg)[numpy.newaxis, :, numpy.newaxis] + z = numpy.linspace(0.0, 1.0, nz)[numpy.newaxis, numpy.newaxis, :] + + testvars = {} + testvars["f3d"] = BoutArray( + numpy.exp(numpy.sin(x + y + z)), attributes={"bout_type": "Field3D"} + ) + testvars["f2d"] = BoutArray( + numpy.exp(numpy.sin(x + y + 1.0))[:, :, 0], attributes={"bout_type": "Field2D"} + ) + testvars["fperp_lower"] = BoutArray( + numpy.exp(numpy.sin(x + z + 2.0))[:, 0, :], + attributes={"bout_type": "FieldPerp", "yindex_global": 0}, + ) + testvars["fperp_upper"] = BoutArray( + numpy.exp(numpy.sin(x + z + 3.0))[:, 0, :], + attributes={"bout_type": "FieldPerp", "yindex_global": ny - 1}, + ) + + # make restart file + restartdir = Path("data") / "restart" + try: + Path.mkdir(restartdir) + except FileExistsError: + pass + + with DataFile(restartdir / "BOUT.restart.0.nc", create=True) as base_restart: + base_restart.write("MXSUB", nx) + base_restart.write("MYSUB", ny) + base_restart.write("MZSUB", nz) + base_restart.write("MXG", mxg) + base_restart.write("MYG", myg) + base_restart.write("MZG", 0) + base_restart.write("nx", nx + 2 * mxg) + base_restart.write("ny", ny) + base_restart.write("nz", nz) + base_restart.write("MZ", nz) + base_restart.write("NXPE", 1) + base_restart.write("NYPE", 1) + base_restart.write("NZPE", 1) + base_restart.write("tt", 0.0) + base_restart.write("hist_hi", 0) + # set BOUT_VERSION to stop collect from changing nz or printing a warning + base_restart.write("BOUT_VERSION", 4.0) + base_restart.write("f3d", testvars["f3d"]) + base_restart.write("f2d", testvars["f2d"]) + base_restart.write("fperp_lower", testvars["fperp_lower"]) + base_restart.write("fperp_upper", testvars["fperp_upper"]) + + # make run_id an array of characters because NetCDF doesn't like generic strings + run_id_string = "36 character run_id test string ****" + run_id = numpy.array(list(run_id_string), dtype="S1") + run_id = BoutArray(run_id, attributes={"bout_type": "string"}) + base_restart.write("run_id", run_id) + run_restart_from = numpy.array( + list("36 character run_restart_from string"), dtype="S1" + ) + run_restart_from = BoutArray( + run_restart_from, attributes={"bout_type": "string"} + ) + base_restart.write("run_restart_from", run_restart_from) + + success = True + + # Note: expect this to fail for 16 processors, because when there are 2 + # y-points per processor, the fperp_lower FieldPerp is in the grid cells of one + # set of processors and also in the guard cells of anoether set. This means + # valid FieldPerps get written to output files with different + # y-processor-indices, and collect() cannot handle this. + for nproc in [1, 2, 4]: + # delete any existing output + shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc") + + # create restart files for the run + restart.redistribute(nproc, path=restartdir, output="data") + + print(" %d processor...." % (nproc)) + + # run the test executable + s, out = launch_safe("./test-restart-io", nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + # check the results + for name in testvars.keys(): + # check non-evolving version + result = collect( + name + "_once", path="data", xguards=True, yguards=True, info=False + ) + testvar = testvars[name] + + if not numpy.allclose(testvar, result): + success = False + print( + f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}" + ) + # Don't plot anything by default + if False: + from boututils.showdata import showdata + + showdata([result, testvar]) + if name == "fperp_lower" or name == "fperp_upper": + yindex_result = result.attributes["yindex_global"] + yindex_test = testvar.attributes["yindex_global"] + if not yindex_result == yindex_test: + success = False + print( + "Fail: yindex_global of " + + name + + " is " + + str(yindex_result) + + " should be " + + str(yindex_test) + ) + + # check evolving versions + result = collect(name, path="data", xguards=True, yguards=True, info=False) + + for result_timeslice in result: + if not numpy.all(testvar == result_timeslice): + success = False + print( + f"{name} evolving version is different: {numpy.max(numpy.abs(testvar - result_timeslice))}" + ) + if name == "fperp_lower" or name == "fperp_upper": + yindex_result = result.attributes["yindex_global"] + yindex_test = testvar.attributes["yindex_global"] + if not yindex_result == yindex_test: + success = False + print( + "Fail: yindex_global of " + + name + + " evolving version is " + + str(yindex_result) + + " should be " + + str(yindex_test) + ) + + # check the run_id + run_id = str(collect("run_id", path="data", info=False)) + # check run_id can be converted to a valid UUID + try: + uuid.UUID(run_id) + except ValueError: + success = False + print(f"run_id='{run_id}' is not a valid UUID") + run_restart_from = str(collect("run_restart_from", path="data", info=False)) + if not run_restart_from == run_id_string: + success = False + print( + f"incorrect run_restart_from='{run_restart_from}'. Expected '{run_id_string}'" + ) + + assert success, "=> Some failed tests" + + # clean up binary files + shell( + "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc" + ) diff --git a/tests/integrated/test-restarting/runtest b/tests/integrated/test-restarting/runtest deleted file mode 100755 index daf19ebac6..0000000000 --- a/tests/integrated/test-restarting/runtest +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -import numpy as np -from sys import stdout, exit - -build_and_log("restart test") - -# Run once for 10 timesteps -s, out = launch_safe("./test_restarting solver:nout=10", nproc=1, pipe=True) - -# Read reference data -f3d_0 = collect("f3d", path="data", info=False) -f2d_0 = collect("f2d", path="data", info=False) - -########################################### -# Run twice, restarting and appending - -print("-> Testing restart append") - -shell("rm -f data/BOUT.dmp.0.nc") -s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True) -s, out = launch_safe( - "./test_restarting solver:nout=5 restart append", nproc=1, pipe=True -) - -f3d_1 = collect("f3d", path="data", info=False) -f2d_1 = collect("f2d", path="data", info=False) - -success = True -tolerance = 1e-10 - -if f3d_1.shape != f3d_0.shape: - print("Fail: Field3D field has wrong shape") - success = False -if f2d_1.shape != f2d_0.shape: - print("Fail: Field2D field has wrong shape") - success = False - -if not np.allclose(f3d_1, f3d_0, atol=tolerance): - print("Fail: Field3D values differ") - success = False - -if not np.allclose(f2d_1, f2d_0, atol=tolerance): - print("Fail: Field2D values differ") - success = False - -########################################### -# Test restart - -print("-> Testing restart") - -shell("rm -f data/BOUT.dmp.0.nc") -s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True) -s, out = launch_safe("./test_restarting solver:nout=5 restart", nproc=1, pipe=True) - -f3d_1 = collect("f3d", path="data", info=False) -f2d_1 = collect("f2d", path="data", info=False) - -if f3d_1.shape[0] != 6: - print("Fail: Field3D has wrong shape") - success = False -if f2d_1.shape[0] != 6: - print("Fail: Field2D has wrong shape") - success = False - -if not np.allclose(f3d_1, f3d_0[5:, :, :, :], atol=tolerance): - print("Fail: Field3D values differ") - success = False -if not np.allclose(f2d_1, f2d_0[5:, :, :], atol=tolerance): - print("Fail: Field2D values differ") - success = False - -if not success: - print("=> Some tests failed") - exit(1) - -print("=> Success") -exit(0) diff --git a/tests/integrated/test-restarting/test_restarting.py b/tests/integrated/test-restarting/test_restarting.py new file mode 100755 index 0000000000..b5f51bd073 --- /dev/null +++ b/tests/integrated/test-restarting/test_restarting.py @@ -0,0 +1,75 @@ +#!/usr/bin/env python3 + +import numpy as np +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + + +def test_restarting(): + + # Run once for 10 timesteps + s, out = launch_safe("./test_restarting solver:nout=10", nproc=1, pipe=True) + + # Read reference data + f3d_0 = collect("f3d", path="data", info=False) + f2d_0 = collect("f2d", path="data", info=False) + + ########################################### + # Run twice, restarting and appending + + print("-> Testing restart append") + + shell(["rm -f data/BOUT.dmp.0.nc"]) + s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True) + s, out = launch_safe( + "./test_restarting solver:nout=5 restart append", nproc=1, pipe=True + ) + + f3d_1 = collect("f3d", path="data", info=False) + f2d_1 = collect("f2d", path="data", info=False) + + success = True + tolerance = 1e-10 + + if f3d_1.shape != f3d_0.shape: + print("Fail: Field3D field has wrong shape") + success = False + if f2d_1.shape != f2d_0.shape: + print("Fail: Field2D field has wrong shape") + success = False + + if not np.allclose(f3d_1, f3d_0, atol=tolerance): + print("Fail: Field3D values differ") + success = False + + if not np.allclose(f2d_1, f2d_0, atol=tolerance): + print("Fail: Field2D values differ") + success = False + + ########################################### + # Test restart + + print("-> Testing restart") + + shell(["rm -f data/BOUT.dmp.0.nc"]) + s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True) + s, out = launch_safe("./test_restarting solver:nout=5 restart", nproc=1, pipe=True) + + f3d_1 = collect("f3d", path="data", info=False) + f2d_1 = collect("f2d", path="data", info=False) + + if f3d_1.shape[0] != 6: + print("Fail: Field3D has wrong shape") + success = False + if f2d_1.shape[0] != 6: + print("Fail: Field2D has wrong shape") + success = False + + if not np.allclose(f3d_1, f3d_0[5:, :, :, :], atol=tolerance): + print("Fail: Field3D values differ") + success = False + if not np.allclose(f2d_1, f2d_0[5:, :, :], atol=tolerance): + print("Fail: Field2D values differ") + success = False + + assert success, "=> Some tests failed" diff --git a/tests/integrated/test-slepc-solver/runtest b/tests/integrated/test-slepc-solver/runtest deleted file mode 100755 index baced1bcf3..0000000000 --- a/tests/integrated/test-slepc-solver/runtest +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python3 - -# requires: slepc - -from boutdata.collect import collect -from boututils.run_wrapper import build_and_log, launch_safe -from numpy import isclose - -build_and_log("SLEPc eigen solver test") - -print("Running SLEPc eigen solver test") -status, out = launch_safe("./test-slepc-solver", nproc=1, pipe=True, verbose=True) - -with open("run.log", "w") as f: - f.write(out) - -eigenvalues = collect("t_array", path="data", info=False) - -expected_eigenvalues = [0.0, 1.0] - -if isclose(expected_eigenvalues, eigenvalues).all(): - print(" => SLEPc test passed") - exit(0) -else: - print(" => SLEPc test failed") - print(" Eigenvalues:", eigenvalues) - exit(1) diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py new file mode 100755 index 0000000000..2df73df018 --- /dev/null +++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py @@ -0,0 +1,26 @@ +#!/usr/bin/env python3 + +# requires: slepc + +from boutdata.collect import collect +from boututils.run_wrapper import launch_safe +import numpy.testing as npt + + +def test_slepc_solver(): + + print("Running SLEPc eigen solver test") + status, out = launch_safe("./test-slepc-solver", nproc=1, pipe=True, verbose=True) + + with open("run.log", "w") as f: + f.write(out) + + eigenvalues = collect("t_array", path="data", info=False) + + expected_eigenvalues = [0.0, 1.0] + + npt.assert_allclose( + expected_eigenvalues, + eigenvalues, + err_msg=" => SLEPc test failed\nEigenvalues: {eigenvalues}", + ) diff --git a/tests/integrated/test-smooth/runtest b/tests/integrated/test-smooth/runtest deleted file mode 100755 index 91ae793164..0000000000 --- a/tests/integrated/test-smooth/runtest +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python3 - -# -# Run the test, compare results against the benchmark -# - -# Requires: netcdf -# Cores: 4 - -# Variables to compare -vars = ["yavg2d", "yavg3d", "sm3d"] -tol = 1e-7 # Absolute tolerance, benchmark values are floats - -from boututils.run_wrapper import build_and_log, shell, launch_safe -from boutdata.collect import collect -import numpy as np -from sys import stdout, exit - -build_and_log("smoothing operator test") - -# Read benchmark values -print("Reading benchmark data") -bmk = {} -for v in vars: - bmk[v] = collect(v, path="data", prefix="benchmark", info=False) - -print("Running smoothing operator test") -success = True - -for nype in [1, 2]: - for nxpe in [1, 2]: - nproc = nxpe * nype - cmd = "./test_smooth" - - shell("rm data/BOUT.dmp.*.nc") - - print(" %d processor (%d x %d)...." % (nproc, nxpe, nype)) - s, out = launch_safe(cmd + " NXPE=" + str(nxpe), nproc=nproc, pipe=True) - with open("run.log." + str(nproc), "w") as f: - f.write(out) - - # Collect output data - for v in vars: - stdout.write(" Checking variable " + v + " ... ") - result = collect(v, path="data", info=False) - # Compare benchmark and output - if np.shape(bmk[v]) != np.shape(result): - print("Fail, wrong shape") - success = False - continue - - diff = np.max(np.abs(bmk[v] - result)) - if diff > tol: - print("Fail, maximum difference = " + str(diff)) - success = False - else: - print("Pass") - -if success: - print(" => All smoothing operator tests passed") - exit(0) -else: - print(" => Some failed tests") - exit(1) diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py new file mode 100755 index 0000000000..40858eb15e --- /dev/null +++ b/tests/integrated/test-smooth/test_smooth.py @@ -0,0 +1,69 @@ +#!/usr/bin/env python3 + +# +# Run the test, compare results against the benchmark +# + +# Requires: netcdf +# Cores: 4 + +import pytest +import numpy as np +import itertools +from pathlib import Path +from boututils.run_wrapper import shell, launch_safe +from boutdata.collect import collect + +# Variables to compare +vars = ["yavg2d", "yavg3d", "sm3d"] +tol = 1e-7 # Absolute tolerance, benchmark values are floats + + +@pytest.fixture(scope="module") +def benchmark_data(): + """Reads the benchmark data once for all test iterations in this module.""" + bmk = {} + source_data_dir = str(Path(__file__).parent / "data") + + for v in vars: + bmk[v] = collect(v, path=source_data_dir, prefix="benchmark", info=False) + return bmk + + +# Generate test configurations: [(1, 1), (1, 2), (2, 1), (2, 2)] +PROCESSOR_TOPOLOGIES = list(itertools.product([1, 2], [1, 2])) + + +@pytest.mark.parametrize("nxpe, nype", PROCESSOR_TOPOLOGIES) +def test_smooth(benchmark_data, nxpe, nype): + nproc = nxpe * nype + cmd = "./test_smooth" + + # Clean up old data + shell(["rm -f data/BOUT.dmp.*.nc"]) + + # Run the executable + s, out = launch_safe(f"{cmd} NXPE={nxpe}", nproc=nproc, pipe=True) + + # Save log + with open(f"run.log.{nproc}", "w") as f: + f.write(out) + + # Collect output data + for v in vars: + result = collect(v, path="data", info=False) + bmk = benchmark_data[v] + + # Compare benchmark and output + + assert bmk.shape == result.shape, ( + f"Shape mismatch for variable '{v}' on {nxpe}x{nype} grid" + ) + + np.testing.assert_allclose( + result, + bmk, + atol=tol, + rtol=0, + err_msg=f"Data mismatch for variable '{v}' on {nxpe}x{nype} grid", + ) diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py new file mode 100644 index 0000000000..1095b40a70 --- /dev/null +++ b/tests/integrated/test-snb/test_snb.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./runtest") diff --git a/tests/integrated/test-solver/runtest b/tests/integrated/test-solver/runtest deleted file mode 100755 index 607f3bb7ea..0000000000 --- a/tests/integrated/test-solver/runtest +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, launch_safe - -from sys import exit - -nthreads = 1 -nproc = 1 - - -build_and_log("Solver test") - -print("Running solver test") -status, out = launch_safe("./test_solver", nproc=nproc, mthread=nthreads, pipe=True) -with open("run.log", "w") as f: - f.write(out) - -if status: - print(out) - -exit(status) diff --git a/tests/integrated/test-solver/test_solver.py b/tests/integrated/test-solver/test_solver.py new file mode 100755 index 0000000000..1b1ff2e79c --- /dev/null +++ b/tests/integrated/test-solver/test_solver.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 + +from boututils.run_wrapper import shell_safe + + +def test_solver(): + print("Running solver test") + status, out = shell_safe("./test_solver", pipe=True) + with open("run.log", "w") as f: + f.write(out) + + assert status == 0, out diff --git a/tests/integrated/test-squash/runtest b/tests/integrated/test-squash/test_squash.py similarity index 53% rename from tests/integrated/test-squash/runtest rename to tests/integrated/test-squash/test_squash.py index 8bf358ee8e..ab13380811 100755 --- a/tests/integrated/test-squash/runtest +++ b/tests/integrated/test-squash/test_squash.py @@ -1,13 +1,13 @@ #!/usr/bin/env python3 -from boututils.datafile import DataFile import itertools import time import numpy as np -from boututils.run_wrapper import launch_safe, shell_safe, build_and_log import argparse import re -import os.path +from boututils.datafile import DataFile +from boututils.run_wrapper import launch_safe, shell_safe +from pathlib import Path # requires: all_tests # requires: netcdf @@ -79,51 +79,55 @@ def verify(f1, f2): raise RuntimeError("data mismatch in ", v, err, v1, v2) -parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper") -parser.add_argument( - "executable", help="Path to bout-squashoutput", default="../../../bin", nargs="?" -) -args = parser.parse_args() - -build_and_log("Squash test") +def test_squash(): + parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper") + parser.add_argument( + "executable", + help="Path to bout-squashoutput", + default="../../../bin", + nargs="?", + ) + args = parser.parse_args() -bout_squashoutput = args.executable + "/bout-squashoutput" + bout_squashoutput = Path(args.executable + "/bout-squashoutput") -if not os.path.exists(bout_squashoutput): - bout_squashoutput = "bout-squashoutput" + if not Path.exists(bout_squashoutput): + bout_squashoutput = "bout-squashoutput" -print("Run once to get normal data") -timed_shell_safe("./squash -q -q -q solver:nout=2") -timed_shell_safe("mv data/BOUT.dmp.0.nc f1.nc") + print("Run once to get normal data") + timed_shell_safe("./squash -q -q -q solver:nout=2") + timed_shell_safe("mv data/BOUT.dmp.0.nc f1.nc") -print("Parallel test") -timed_shell_safe("rm -f f2.nc") -timed_launch_safe("./squash -q -q -q solver:nout=2", nproc=4, mthread=1) -timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) + print("Parallel test") + timed_shell_safe("rm -f f2.nc") + timed_launch_safe("./squash -q -q -q solver:nout=2", nproc=4, mthread=1) + timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) -verify("f1.nc", "f2.nc") + verify("f1.nc", "f2.nc") -print("Parallel and in two pieces") -timed_shell_safe("rm -f f2.nc") -timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1) -timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) -timed_launch_safe("./squash -q -q -q restart", nproc=4, mthread=1) -timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput)) + print("Parallel and in two pieces") + timed_shell_safe("rm -f f2.nc") + timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1) + timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) + timed_launch_safe("./squash -q -q -q restart", nproc=4, mthread=1) + timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput)) -verify("f1.nc", "f2.nc") + verify("f1.nc", "f2.nc") -print("Parallel and in two pieces without dump_on_restart") -timed_shell_safe("rm -f f2.nc") -timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1) -timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) -timed_launch_safe("./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1) -timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput)) + print("Parallel and in two pieces without dump_on_restart") + timed_shell_safe("rm -f f2.nc") + timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1) + timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) + timed_launch_safe( + "./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1 + ) + timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput)) -verify("f1.nc", "f2.nc") + verify("f1.nc", "f2.nc") -print("Sequential test") -timed_shell_safe("rm -f f2.nc") -timed_shell_safe("./squash -q -q -q solver:nout=2") -timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) + print("Sequential test") + timed_shell_safe("rm -f f2.nc") + timed_shell_safe("./squash -q -q -q solver:nout=2") + timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput)) -verify("f1.nc", "f2.nc") + verify("f1.nc", "f2.nc") diff --git a/tests/integrated/test-stopCheck-file/runtest b/tests/integrated/test-stopCheck-file/runtest deleted file mode 100755 index e959816d11..0000000000 --- a/tests/integrated/test-stopCheck-file/runtest +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env python3 - -# Run the test, compare results against the benchmark - -import sys - -from boututils.run_wrapper import build_and_log, launch -from boutdata.collect import collect - -nproc = 1 - -build_and_log("stopCheck test") - -check_values = [True, False] -expected_steps = [1, 11] -data_dirs = ["data", "dataSecond"] -stop_files = ["BOUT.stop", "otherStop.check"] - -print("Running stopCheck test") -success = True - -for data_dir, stop_file in zip(data_dirs, stop_files): - for check, expected in zip(check_values, expected_steps): - executable = "./test_stopCheck" - command = "{} -d {} stopCheck={} stopCheckName={}".format( - executable, data_dir, check, stop_file - ) - - s, out = launch( - command, - nproc=nproc, - pipe=True, - ) - with open("run.log.{}.{}".format(data_dir, check), "w") as f: - f.write(out) - - result = collect("t_array", path=data_dir, info=False) - - if result.shape[0] != expected: - print("Fail, wrong shape") - print("\tOption is {}/{}/{}".format(check, data_dir, stop_file)) - print("\tshape is {}".format(result.shape[0])) - print("\texpecting {}".format(expected)) - sys.exit(1) - success = False - continue - -if success: - print(" => All checkStop tests passed") - sys.exit(0) -else: - print(" => Some failed tests") - sys.exit(1) diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py new file mode 100755 index 0000000000..9e1b32859d --- /dev/null +++ b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py @@ -0,0 +1,49 @@ +#!/usr/bin/env python3 + +# Run the test, compare results against the benchmark + +import sys + +from boututils.run_wrapper import launch +from boutdata.collect import collect + +nproc = 1 + + +def test_stopCheck_file(): + + check_values = [True, False] + expected_steps = [1, 11] + data_dirs = ["data", "dataSecond"] + stop_files = ["BOUT.stop", "otherStop.check"] + + print("Running stopCheck test") + success = True + + for data_dir, stop_file in zip(data_dirs, stop_files): + for check, expected in zip(check_values, expected_steps): + executable = "./test_stopCheck" + command = "{} -d {} stopCheck={} stopCheckName={}".format( + executable, data_dir, check, stop_file + ) + + s, out = launch( + command, + nproc=nproc, + pipe=True, + ) + with open("run.log.{}.{}".format(data_dir, check), "w") as f: + f.write(out) + + result = collect("t_array", path=data_dir, info=False) + + if result.shape[0] != expected: + print("Fail, wrong shape") + print("\tOption is {}/{}/{}".format(check, data_dir, stop_file)) + print("\tshape is {}".format(result.shape[0])) + print("\texpecting {}".format(expected)) + sys.exit(1) + success = False + continue + + assert success, " => Some failed tests" diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py new file mode 100644 index 0000000000..1095b40a70 --- /dev/null +++ b/tests/integrated/test-stopCheck/test_stopCheck.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./runtest") diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py new file mode 100644 index 0000000000..1095b40a70 --- /dev/null +++ b/tests/integrated/test-subdir/test_subdir.py @@ -0,0 +1,2 @@ +def test_runtest(assert_success_in_shell): + assert_success_in_shell("./runtest") diff --git a/tests/integrated/test-twistshift-staggered/runtest b/tests/integrated/test-twistshift-staggered/runtest deleted file mode 100755 index 5bb9963db7..0000000000 --- a/tests/integrated/test-twistshift-staggered/runtest +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/env python3 - -from boutdata import collect -from boututils.run_wrapper import build_and_log, launch_safe -import numpy -from sys import exit - -datapath = "data" -nproc = 1 -tol = 1.0e-13 - -build_and_log("twistshift test") - -s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True) -with open("run.log." + str(nproc), "w") as f: - f.write(out) - -test = collect("test", path=datapath, yguards=True, info=False) -test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False) -check = collect("check", path=datapath, yguards=True, info=False) - -# from boututils.showdata import showdata -# showdata([test, test_aligned, check], titles=['test', 'test_aligned', 'check']) - -success = True - - -# Check test_aligned is *not* periodic in y -def test1(ylower, yupper): - global success - if numpy.any( - numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6 - ): - success = False - print( - "Fail - test_aligned should not be periodic jy=%i and jy=%i should be " - "different" % (yupper, ylower) - ) - - -test1(0, -4) -test1(1, -3) -test1(2, -2) -test1(3, -1) - -# Check test_aligned is the same as check -# Cannot check in guard cells, as the expression used for 'zShift' in the input file is -# not the same as the corrected zShift used for the transforms in the guard cells -if numpy.any(numpy.abs(test_aligned[2:-2, 2:-2, :] - check[2:-2, 2:-2, :]) > tol): - success = False - print("Fail - test_aligned is different from the expected value") - print("test_aligned", test_aligned) - print("check", check) - -if success: - print("Pass") - exit(0) -else: - exit(1) diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py new file mode 100755 index 0000000000..19eca67f68 --- /dev/null +++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python3 + +from boutdata import collect +from boututils.run_wrapper import launch_safe +import numpy + +datapath = "data" +nproc = 1 +tol = 1.0e-13 + + +def test_twistshift_staggered(): + + s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False) + check = collect("check", path=datapath, yguards=True, info=False) + + # from boututils.showdata import showdata + # showdata([test, test_aligned, check], titles=['test', 'test_aligned', 'check']) + + success = True + + # Check test_aligned is *not* periodic in y + def test1(ylower, yupper): + global success + if numpy.any( + numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6 + ): + success = False + print( + "Fail - test_aligned should not be periodic jy=%i and jy=%i should be " + "different" % (yupper, ylower) + ) + + test1(0, -4) + test1(1, -3) + test1(2, -2) + test1(3, -1) + + # Check test_aligned is the same as check + # Cannot check in guard cells, as the expression used for 'zShift' in the input file is + # not the same as the corrected zShift used for the transforms in the guard cells + if numpy.any(numpy.abs(test_aligned[2:-2, 2:-2, :] - check[2:-2, 2:-2, :]) > tol): + success = False + print("Fail - test_aligned is different from the expected value") + print("test_aligned", test_aligned) + print("check", check) + + assert success diff --git a/tests/integrated/test-twistshift/runtest b/tests/integrated/test-twistshift/runtest deleted file mode 100755 index c4858970c4..0000000000 --- a/tests/integrated/test-twistshift/runtest +++ /dev/null @@ -1,79 +0,0 @@ -#!/usr/bin/env python3 - -from boutdata import collect -from boututils.run_wrapper import build_and_log, launch_safe -import numpy -from sys import exit - -datapath = "data" -nproc = 1 -tol = 1.0e-13 - -build_and_log("twistshift test") - -s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True) -with open("run.log." + str(nproc), "w") as f: - f.write(out) - -test = collect("test", path=datapath, yguards=True, info=False) -test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False) -result = collect("result", path=datapath, yguards=True, info=False) - -# from boututils.showdata import showdata -# showdata([test, test_aligned, result], titles=['test', 'test_aligned', 'result']) - -success = True - - -# Check test_aligned is *not* periodic in y -def test1(ylower, yupper): - global success - if numpy.any( - numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6 - ): - success = False - print( - "Fail - test_aligned should not be periodic jy=%i and jy=%i should be " - "different", - yupper, - ylower, - ) - - -test1(0, -4) -test1(1, -3) -test1(2, -2) -test1(3, -1) - -# Check test and result are the same -if numpy.any(numpy.abs(result - test) > tol): - print("Fail - result has not been communicated correctly - is different from input") - success = False - - -# Check result is periodic in y -def test2(ylower, yupper): - global success - if numpy.any(numpy.abs(result[:, yupper, :] - result[:, ylower, :]) > tol): - success = False - print( - "Fail - result should be periodic jy=%i and jy=%i should not be " - "different", - yupper, - ylower, - ) - print(ylower, result[:, ylower, :]) - print(yupper, result[:, yupper, :]) - print(result[:, ylower, :] - result[:, yupper, :]) - - -test2(0, -4) -test2(1, -3) -test2(2, -2) -test2(3, -1) - -if success: - print("Pass") - exit(0) -else: - exit(1) diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py new file mode 100755 index 0000000000..d586244bb4 --- /dev/null +++ b/tests/integrated/test-twistshift/test_twistshift.py @@ -0,0 +1,73 @@ +#!/usr/bin/env python3 + +from boutdata import collect +from boututils.run_wrapper import launch_safe +import numpy + +datapath = "data" +nproc = 1 +tol = 1.0e-13 + + +def test_twistshift(): + + s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True) + with open("run.log." + str(nproc), "w") as f: + f.write(out) + + test = collect("test", path=datapath, yguards=True, info=False) + test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False) + result = collect("result", path=datapath, yguards=True, info=False) + + # from boututils.showdata import showdata + # showdata([test, test_aligned, result], titles=['test', 'test_aligned', 'result']) + + success = True + + # Check test_aligned is *not* periodic in y + def test1(ylower, yupper): + global success + if numpy.any( + numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6 + ): + success = False + print( + "Fail - test_aligned should not be periodic jy=%i and jy=%i should be " + "different", + yupper, + ylower, + ) + + test1(0, -4) + test1(1, -3) + test1(2, -2) + test1(3, -1) + + # Check test and result are the same + if numpy.any(numpy.abs(result - test) > tol): + print( + "Fail - result has not been communicated correctly - is different from input" + ) + success = False + + # Check result is periodic in y + def test2(ylower, yupper): + global success + if numpy.any(numpy.abs(result[:, yupper, :] - result[:, ylower, :]) > tol): + success = False + print( + "Fail - result should be periodic jy=%i and jy=%i should not be " + "different", + yupper, + ylower, + ) + print(ylower, result[:, ylower, :]) + print(yupper, result[:, yupper, :]) + print(result[:, ylower, :] - result[:, yupper, :]) + + test2(0, -4) + test2(1, -3) + test2(2, -2) + test2(3, -1) + + assert success diff --git a/tests/integrated/test-unused-options/runtest b/tests/integrated/test-unused-options/runtest deleted file mode 100755 index f3fad0c404..0000000000 --- a/tests/integrated/test-unused-options/runtest +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, launch_safe - -build_and_log("unused options test") - -for nproc in [1, 2]: - print(f"Running with nproc={nproc}...", end="") - s, out = launch_safe( - "./test_unused_options", - nproc=nproc, - mthread=1, - pipe=True, - ) - - with open(f"run.log.{nproc}", "w") as f: - f.write(out) - - # Check for printed message - if "SUCCESS" not in out: - print("failed") - exit(1) - print("pass") diff --git a/tests/integrated/test-unused-options/test_unused_options.py b/tests/integrated/test-unused-options/test_unused_options.py new file mode 100755 index 0000000000..b147aa353c --- /dev/null +++ b/tests/integrated/test-unused-options/test_unused_options.py @@ -0,0 +1,21 @@ +#!/usr/bin/env python3 + +from boututils.run_wrapper import launch_safe + + +def test_unused_options(): + + for nproc in [1, 2]: + print(f"Running with nproc={nproc}...", end="") + s, out = launch_safe( + "./test_unused_options", + nproc=nproc, + mthread=1, + pipe=True, + ) + + with open(f"run.log.{nproc}", "w") as f: + f.write(out) + + # Check for printed message + assert "SUCCESS" in out, "failed" diff --git a/tests/integrated/test-vec/runtest b/tests/integrated/test-vec/runtest deleted file mode 100755 index 6d836be804..0000000000 --- a/tests/integrated/test-vec/runtest +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env python3 - -# Cores: 4 - -from boututils.run_wrapper import build_and_log, launch_safe - -build_and_log("vector communication test") - -status, out = launch_safe("./testVec", nproc=4, pipe=True) - -with open("run.log.4", "w") as f: - f.write(out) - -if status: - print(" => Test failed") - exit(status) - -print(" => Test passed") diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py new file mode 100755 index 0000000000..ff2e14d608 --- /dev/null +++ b/tests/integrated/test-vec/test_vec.py @@ -0,0 +1,15 @@ +#!/usr/bin/env python3 + +# Cores: 4 + +from boututils.run_wrapper import launch_safe + + +def test_vec(): + + status, out = launch_safe("./testVec", nproc=4, pipe=True) + + with open("run.log.4", "w") as f: + f.write(out) + + assert not status, " => Test failed" diff --git a/tests/integrated/test-yupdown-weights/runtest b/tests/integrated/test-yupdown-weights/runtest deleted file mode 100755 index 4b59d08cb0..0000000000 --- a/tests/integrated/test-yupdown-weights/runtest +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, launch_safe -from boutdata.collect import collect -from sys import stdout, exit - -from numpy import max, abs - -build_and_log("parallel slices and weights test") - -failed = False -for shifttype in ["shiftedinterp"]: - s, out = launch_safe( - "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype, - nproc=1, - pipe=True, - verbose=True, - ) - - with open("run.log", "w") as f: - f.write(out) - - vars = [("ddy", "ddy2")] - for v1, v2 in vars: - stdout.write("Testing %s and %s ... " % (v1, v2)) - ddy = collect(v1, path="data", xguards=False, yguards=False, info=False) - ddy2 = collect(v2, path="data", xguards=False, yguards=False, info=False) - - diff = max(abs(ddy - ddy2)) - - if diff < 1e-8: - print(shifttype + " passed (Max difference %e)" % (diff)) - else: - print(shifttype + " failed (Max difference %e)" % (diff)) - failed = True - -if failed: - exit(1) - -exit(0) diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py new file mode 100755 index 0000000000..ae8754d50d --- /dev/null +++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python3 + +from boututils.run_wrapper import launch_safe +from boutdata.collect import collect +from sys import stdout + +from numpy import max, abs + + +def test_yupdown_weights(): + + failed = False + for shifttype in ["shiftedinterp"]: + s, out = launch_safe( + "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype, + nproc=1, + pipe=True, + verbose=True, + ) + + with open("run.log", "w") as f: + f.write(out) + + vars = [("ddy", "ddy2")] + for v1, v2 in vars: + stdout.write("Testing %s and %s ... " % (v1, v2)) + ddy = collect(v1, path="data", xguards=False, yguards=False, info=False) + ddy2 = collect(v2, path="data", xguards=False, yguards=False, info=False) + + diff = max(abs(ddy - ddy2)) + + if diff < 1e-8: + print(shifttype + " passed (Max difference %e)" % (diff)) + else: + print(shifttype + " failed (Max difference %e)" % (diff)) + failed = True + + assert not failed diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/runtest deleted file mode 100755 index 13d7365b53..0000000000 --- a/tests/integrated/test-yupdown/runtest +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python3 - -from boututils.run_wrapper import build_and_log, launch_safe -from boutdata.collect import collect -from sys import exit - -from numpy import max, abs - -build_and_log("parallel slices test") - -failed = False - -for shifttype in ["shifted", "shiftedinterp"]: - s, out = launch_safe( - "./test_yupdown mesh:paralleltransform:type=" + shifttype, - nproc=1, - pipe=True, - verbose=True, - ) - - with open("run.log", "w") as f: - f.write(out) - - vars = [("ddy", "ddy_check"), ("ddy2", "ddy_check")] - - for v, v_check in vars: - print("Testing %s and %s ... " % (v, v_check)) - ddy = collect(v, path="data", xguards=False, yguards=False, info=False) - ddy_check = collect( - v_check, path="data", xguards=False, yguards=False, info=False - ) - - diff = max(abs(ddy - ddy_check)) - - if diff < 2e-5: - print(shifttype + " passed (Max difference %e)" % (diff)) - else: - print(shifttype + " failed (Max difference %e)" % (diff)) - failed = True - -if failed: - exit(1) -exit(0) diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py new file mode 100755 index 0000000000..b2569f4d60 --- /dev/null +++ b/tests/integrated/test-yupdown/test_yupdown.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 +import os +import pytest +from boututils.run_wrapper import launch_safe +from boutdata.collect import collect +from numpy import max, abs + +shift_types = ["shifted", "shiftedinterp"] +variables = [("ddy", "ddy_check"), ("ddy2", "ddy_check")] + + +def run_case(shift_type, variable): + s, out = launch_safe( + "./test_yupdown mesh:paralleltransform:type=" + shift_type, + nproc=1, + pipe=True, + verbose=True, + ) + + with open("run.log", "w") as f: + f.write(out) + + v, v_check = variable + print("Testing %s and %s ... " % (v, v_check)) + ddy = collect(v, path="data", xguards=False, yguards=False, info=False) + ddy_check = collect(v_check, path="data", xguards=False, yguards=False, info=False) + + diff = max(abs(ddy - ddy_check)) + + print(f"shifttype: {shift_type} Max difference {diff}") + if diff < 2e-5: + return True + return False + + +@pytest.mark.parametrize("shift_type, variable", list(zip(shift_types, variables))) +def test_case(shift_type, variable): + # MPI oversubscribe + os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1" # Allows 18 procs + + success = run_case(shift_type, variable) + assert success, f"Test failed for shift_type={shift_type}: , variable={variable}" diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite deleted file mode 100755 index 77ad7882c4..0000000000 --- a/tests/integrated/test_suite +++ /dev/null @@ -1,366 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -# -# Run the test suite, report failures -# -# To set command for running parallel jobs, define environment variable -# e.g. for bash -# export MPIRUN="mpirun -np" -# export MPIRUN="aprun -n" - -import os -import sys -import time -import glob -from boututils.run_wrapper import shell -import threading -import re -import fcntl -import select - -################################################################## - -import argparse - -parser = argparse.ArgumentParser(description="Run or build some tests.") -parser.add_argument( - "-g", - "--get-list", - action="store_true", - help="Return a list of tests that would be run/build", -) -parser.add_argument( - "-m", "--make", action="store_true", help="Build the tests, rather then run them." -) -parser.add_argument( - "-a", "--all", action="store_true", dest="all_tests", help="Run all tests" -) -parser.add_argument( - "-b", - "--set-bool", - nargs="+", - metavar=("value1=False", "value2=True"), - help="Set a bool value for evaluating what scripts can be run.", -) -parser.add_argument( - "-l", - "--set-list", - nargs="+", - metavar=("test1", "test2"), - help="Set the tests that should be run.", -) -parser.add_argument( - "-j", - "--jobs", - nargs=1, - type=int, - dest="jobs", - help="Set the number of cores to use in parallel.", -) - -args = parser.parse_args() - -################################################################## - -sys.path.append("..") -from requirements import Requirements - -requirements = Requirements() - -if args.set_bool is not None: - lookup = {"false": False, "no": False, "true": True, "yes": True} - for setbool in args.set_bool: - k, v = setbool.split("=") - v = lookup[v.lower()] - requirements.add(k, v, override=True) - -try: - requirements.add("make", args.make) -except RuntimeError: - raise RuntimeError( - "The make flag needs to be set by passing --make rather then --set-bool make=True" - ) - -try: - requirements.add("all_tests", args.all_tests) -except RuntimeError: - raise RuntimeError( - "The all-tests flag needs to be set by passing --all rather then --set-bool all_tests=True" - ) - -################################################################## -# Parallel stuff -# -# We can run in parallel. As some checks require several threads to -# run, we take this into account when we schedule tests. Given a -# certain amount of threads that we are told to use, we try to run -# so many tests in parallel, that the total core count is not higher -# than this number. If this isn't possible because some jobs require -# more cores than we have threads, we run the remaining tests in -# serial. The number of parallel threads is called cost of a test. -# -# The beginning of MAKEFLAGS has some flags that tell us what we are -# supposed to be doing. Most of them we can ignore. -# Check what we are supposed to be doing: -if "MAKEFLAGS" in os.environ: - makeflags = os.environ["MAKEFLAGS"] - for token in makeflags: - if token == "n": - # Print recipies: - # We ignore this for now ... - sys.exit(0) - elif token == "q": - # Question mode: - # We are never up-to-date - sys.exit(1) - elif token in "ksBd": - # k - keep going - # s - silent - # B - always build (we do) - # d - debug - pass - elif token == " ": - break - elif token == "-": - # This is not from make - break - else: - # Not implemented - print("mode '%s' not implemented" % token) - # sys.exit(42) -else: - makeflags = "" -num_threads = 1 -if args.jobs: - num_threads = args.jobs[0] -js_read = None -# if we are running under make, we only have one thread (called job -# in make terms) for sure, but might be able to run more threads -# (depending what other jobs are currently running) -# Additional jobs come in form of `tokens` that we need to give -# back, if we are finished. -# https://www.gnu.org/software/make/manual/html_node/POSIX-Jobserver.html -if "--jobserver-auth=" in makeflags or "--jobserver-fds=" in makeflags: - try: - offset = makeflags.index("--jobserver-auth=") - except ValueError: - offset = makeflags.index("--jobserver-fds=") - file_desc = [int(i) for i in re.findall("\d+", makeflags[offset:])[0:2]] - js_read = file_desc[0] - js_write = file_desc[1] - js_tokens = b"" - - -class Test(threading.Thread): - def __init__(self, name, cmd, width, timeout): - threading.Thread.__init__(self) - self.name = name - self.cmd = cmd - self.width = width - self.local = threading.local() - self.cost = self._cost() - self.timeout = timeout - - def run(self): - # Check requirements - self.local.req_met, self.local.req_expr = requirements.check( - self.name + "/runtest" - ) - self.local.start_time = time.time() - if not self.local.req_met: - print( - "{:{width}}".format(self.name, width=self.width) - + "S - {0} => False".format(self.local.req_expr) - ) - sys.stdout.flush() - self.status = 0 - else: - # Run test, piping stdout so it is not sent to console - command = "cd {}; timeout {} {}".format(self.name, self.timeout, self.cmd) - self.status, self.output = shell(command, pipe=True) - print("{:{width}}".format(self.name, width=self.width), end="") - if self.status == 0: - # ✓ Passed - print("\u2713", end="") # No newline - elif self.status == 124: - # 💤 timeout - print("\U0001f4a4", end="") # No newline - self.output += "\n(It is likely that a timeout occured)" - else: - # ❌ Failed - print("\u274c", end="") # No newline - print(" %7.3f s" % (time.time() - self.local.start_time), flush=True) - - def _cost(self): - if self.cmd == "make": - return 1 - with open(self.name + "/" + self.cmd, "r", encoding="utf8") as filein: - contents = filein.read() - # Find all lines starting with '#cores' or '#Cores:' - match = re.findall("^\s*\#\s?[Cc]ores:\s*?(\d+)", contents, re.MULTILINE) - if len(match) > 1: - raise RuntimeError( - "Found more then one match for core-count in " + self.name - ) - if len(match) == 0: - # default; no mpi - return 1 - c = int(match[0]) - if c < 0: - raise RuntimeError( - "Core-count is %d and thus not positive in " % c + self.name - ) - return c - - -################################################################## - -if args.set_list is None: - # Get list of directories containing test cases - try: - # Requires python >= 3.5 - tests = glob.iglob("**/runtest", recursive=True) - except TypeError: - # Fall back - check only a few folders ... - tests = glob.glob("*/runtest") - tests += glob.glob("*/*/runtest") - tests += glob.glob("*/*/*/runtest") - tests += glob.glob("*/*/*/*/runtest") - - tests = [x.rsplit("/", 1)[0] for x in tests] - -else: - # Take the user provided list - tests = [x.rstrip("/") for x in args.set_list] - - -if args.get_list: - for test in tests: - req_met, _ = requirements.check(test + "/runtest") - if req_met: - print(test) - sys.exit(0) - - -# A function to get more threads from the job server -def get_threads(): - global js_read - if js_read: - global cost_remain, js_tokens, avail_threads, num_threads - try: - fl = fcntl.fcntl(js_read, fcntl.F_GETFL) - except OSError: - print("Warning - we are not part of the job pool 😭, running in serial") - js_read = None - return - isreadable, _, _ = select.select([js_read], [], [], 0) - if isreadable != []: - # Only set shortly to non-blocking, and only if we - # expect we can read. Old make uses blocking pipes, and - # assumes if it is non-blocking, a job is available. - fcntl.fcntl(js_read, fcntl.F_SETFL, fl | os.O_NONBLOCK) - new_token = os.read(js_read, cost_remain - avail_threads) - fcntl.fcntl(js_read, fcntl.F_SETFL, fl) - num_threads += len(new_token) - js_tokens += new_token - avail_threads += len(new_token) - - -################################################################## -# Run the actual test -# Kill tests that take longer than 10 minutes (default) -timeout = os.environ.get("BOUT_TEST_TIMEOUT", "10m" if not args.all_tests else "30m") -command = "./runtest" if not args.make else "make" - -savepath = os.getcwd() # Save current working directory -failed = [] - -start_time = time.time() - -test_type = "Making" if args.make else "Running" - -print( - "======= {} {} {} tests ========".format( - test_type, len(tests), savepath.split("/")[-1] - ) -) - -longest = max([len(s) for s in tests]) -avail_threads = num_threads -tester = sorted( - [Test(t, command, longest + 1, timeout) for t in tests], - key=lambda x: x.cost, - reverse=True, -) -cost_remain = sum(x.cost for x in tester) -get_threads() - -torun = [i for i in range(len(tests))] -running = [] - -while len(torun) + len(running): - if avail_threads: - # See whether we can start one - for i in torun[:]: - if tester[i].cost <= avail_threads: - torun.remove(i) - job = tester[i] - job.start() - running.append(job) - avail_threads -= job.cost - cost_remain -= job.cost - # if nothing is running, start the first - if running == []: - tostart = torun.pop(0) - job = tester[tostart] - job.start() - running.append(job) - avail_threads -= job.cost - cost_remain -= job.cost - - # Are any jobs finished - for job in running: - job.join(0.1) - if not job.is_alive(): - if job.status: - failed.append([job.name, job.output]) - avail_threads += job.cost - running.remove(job) - - # Try to get more jobs - if torun: - get_threads() - else: - # Free not-needed jobs - if avail_threads and js_read: - old_tokens = js_tokens[0:avail_threads] - js_tokens = js_tokens[avail_threads:] - os.write(js_write, old_tokens) - num_threads -= avail_threads - avail_threads = 0 - -elapsed_time = time.time() - start_time - -print("\n") - -# Return remaining tokens -if js_read is not None: - if js_tokens != "": - os.write(js_write, js_tokens) - -if failed: - print("======= FAILURES ========") - for test, output in failed: - # Note: need Unicode string in case output contains unicode - print("\n----- {0} -----\n{1}".format(test, output)) - - print( - "======= {0} failed in {1:.2f} seconds ========".format( - len(failed), elapsed_time - ) - ) - - sys.exit(1) - -else: - print("======= All tests passed in {0:.2f} seconds =======".format(elapsed_time)) diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh new file mode 100755 index 0000000000..276a1ea6e5 --- /dev/null +++ b/tests/run_integrated_tests.sh @@ -0,0 +1,19 @@ +#!/bin/bash +set -e + +PROJECT_ROOT="@PROJECT_BINARY_DIR@" +export PYTHONPATH="@PROJECT_BINARY_DIR@/tools/pylib:@PROJECT_SOURCE_DIR@/tools/pylib:$PYTHONPATH" + +# Pre-build the project to prevent concurrent CMake race conditions +cmake --build "$PROJECT_ROOT" + +PYTEST_ARGS=("$@") +if [ "$CI" == "true" ]; then + TEST_FLAGS="-v" +else + TEST_FLAGS="-q" +fi + +# Use the Python executable that CMake discovered during configuration +"@Python3_EXECUTABLE@" -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup $TEST_FLAGS "$PROJECT_ROOT/tests/integrated" "${PYTEST_ARGS[@]}" +"@Python3_EXECUTABLE@" -m pytest -m serial $TEST_FLAGS "$PROJECT_ROOT/tests/integrated" "${PYTEST_ARGS[@]}" diff --git a/tests/test_suite b/tests/test_suite deleted file mode 120000 index 860ee3ecc5..0000000000 --- a/tests/test_suite +++ /dev/null @@ -1 +0,0 @@ -integrated/test_suite \ No newline at end of file diff --git a/tests/test_suite_make b/tests/test_suite_make deleted file mode 120000 index 083d1d6487..0000000000 --- a/tests/test_suite_make +++ /dev/null @@ -1 +0,0 @@ -integrated/test_suite_make \ No newline at end of file