Merge pull request #14 from hiker/mpi_omp_support

Add support for specifying MPI and OpenMP in the config file

.gitignore

@@ -4,9 +4,9 @@ __pycache__/
 *$py.class
 
 # Build directory for documentation
-docs/build
-docs/source/api
-docs/source/apidoc
+Documentation/build
+Documentation/source/api
+Documentation/source/apidoc
 
 # C extensions
 *.so

run_configs/gcom/build_gcom_ar.py

@@ -15,7 +15,7 @@
 if __name__ == '__main__':
 
     with BuildConfig(project_label='gcom object archive $compiler',
-                     tool_box=ToolBox()) as state:
+                     mpi=False, openmp=False, tool_box=ToolBox()) as state:
         common_build_steps(state)
         archive_objects(state, output_fpath='$output/libgcom.a')
         cleanup_prebuilds(state, all_unused=True)

run_configs/gcom/build_gcom_so.py

@@ -20,7 +20,7 @@
     parsed_args = arg_parser.parse_args()
 
     with BuildConfig(project_label='gcom shared library $compiler',
-                     tool_box=ToolBox()) as state:
+                     mpi=False, openmp=False, tool_box=ToolBox()) as state:
         common_build_steps(state, fpic=True)
-        link_shared_object(state, output_fpath='$output/libgcom.so'),
+        link_shared_object(state, output_fpath='$output/libgcom.so')
         cleanup_prebuilds(state, all_unused=True)

run_configs/gcom/grab_gcom.py

@@ -14,7 +14,7 @@
 
 # we put this here so the two build configs can read its source_root
 grab_config = BuildConfig(project_label=f'gcom_source {revision}',
-                          tool_box=ToolBox())
+                          mpi=False, openmp=False, tool_box=ToolBox())
 
 
 if __name__ == '__main__':

run_configs/jules/build_jules.py

@@ -42,12 +42,15 @@ def __init__(self):
     tool_box.add_tool(Linker(compiler=fc))
 
     with BuildConfig(project_label=f'jules {revision} $compiler',
-                     tool_box=tool_box) as state:
-        # grab the source. todo: use some checkouts instead of exports in these configs.
-        fcm_export(state, src='fcm:jules.xm_tr/src', revision=revision, dst_label='src')
-        fcm_export(state, src='fcm:jules.xm_tr/utils', revision=revision, dst_label='utils')
+                     mpi=False, openmp=False, tool_box=tool_box) as state:
+        # grab the source. todo: use some checkouts instead of exports
+        # in these configs.
+        fcm_export(state, src='fcm:jules.xm_tr/src', revision=revision,
+                   dst_label='src')
+        fcm_export(state, src='fcm:jules.xm_tr/utils', revision=revision,
+                   dst_label='utils')
 
-        grab_pre_build(state, path='/not/a/real/folder', allow_fail=True),
+        grab_pre_build(state, path='/not/a/real/folder', allow_fail=True)
 
         # find the source files
         find_source_files(state, path_filters=[
@@ -61,9 +64,11 @@ def __init__(self):
         # move inc files to the root for easy tool use
         root_inc_files(state)
 
-        preprocess_fortran(state, common_flags=['-P', '-DMPI_DUMMY', '-DNCDF_DUMMY', '-I$output'])
+        preprocess_fortran(state, common_flags=['-P', '-DMPI_DUMMY',
+                                                '-DNCDF_DUMMY', '-I$output'])
 
-        analyse(state, root_symbol='jules', unreferenced_deps=['imogen_update_carb'])
+        analyse(state, root_symbol='jules',
+                unreferenced_deps=['imogen_update_carb'])
 
         compile_fortran(state)
 

run_configs/lfric/atm.py

@@ -172,7 +172,7 @@ def file_filtering(config):
     gpl_utils_source = gpl_utils_source_config.source_root / 'gpl_utils'
 
     with BuildConfig(project_label='atm $compiler $two_stage',
-                     tool_box=ToolBox()) as state:
+                     mpi=False, openmp=False, tool_box=ToolBox()) as state:
 
         # todo: use different dst_labels because they all go into the same folder,
         #       making it hard to see what came from where?

run_configs/lfric/grab_lfric.py

@@ -16,10 +16,12 @@
 # these configs are interrogated by the build scripts
 # todo: doesn't need two separate configs, they use the same project workspace
 tool_box = ToolBox()
-lfric_source_config = BuildConfig(project_label=f'lfric source {LFRIC_REVISION}',
-                                  tool_box=tool_box)
-gpl_utils_source_config = BuildConfig(project_label=f'lfric source {LFRIC_REVISION}',
-                                      tool_box=tool_box)
+lfric_source_config = BuildConfig(
+    project_label=f'lfric source {LFRIC_REVISION}',
+    mpi=False, openmp=False, tool_box=tool_box)
+gpl_utils_source_config = BuildConfig(
+    project_label=f'lfric source {LFRIC_REVISION}',
+    mpi=False, openmp=False, tool_box=tool_box)
 
 
 if __name__ == '__main__':

run_configs/lfric/gungho.py

@@ -33,7 +33,7 @@
     gpl_utils_source = gpl_utils_source_config.source_root / 'gpl_utils'
 
     with BuildConfig(project_label='gungho $compiler $two_stage',
-                     tool_box=ToolBox()) as state:
+                     mpi=False, openmp=False, tool_box=ToolBox()) as state:
         grab_folder(state, src=lfric_source / 'infrastructure/source/', dst_label='')
         grab_folder(state, src=lfric_source / 'components/driver/source/', dst_label='')
         grab_folder(state, src=lfric_source / 'components' / 'inventory' / 'source', dst_label='')

run_configs/lfric/mesh_tools.py

@@ -25,7 +25,7 @@
     psyclone_overrides = Path(__file__).parent / 'mesh_tools_overrides'
 
     with BuildConfig(project_label='mesh tools $compiler $two_stage',
-                     tool_box=ToolBox()) as state:
+                     mpi=False, openmp=False, tool_box=ToolBox()) as state:
         grab_folder(state, src=lfric_source / 'infrastructure/source/', dst_label='')
         grab_folder(state, src=lfric_source / 'mesh_tools/source/', dst_label='')
         grab_folder(state, src=lfric_source / 'components/science/source/', dst_label='')

run_configs/tiny_fortran/build_tiny_fortran.py

@@ -31,15 +31,15 @@ def __init__(self):
     tool_box.add_tool(Linker(compiler=fc))
 
     with BuildConfig(project_label='tiny_fortran $compiler',
-                     tool_box=tool_box) as state:
+                     mpi=False, openmp=False, tool_box=tool_box) as state:
         git_checkout(state, src='https://github.com/metomi/fab-test-data.git',
-                     revision='main', dst_label='src'),
+                     revision='main', dst_label='src')
 
-        find_source_files(state),
+        find_source_files(state)
 
-        preprocess_fortran(state),
+        preprocess_fortran(state)
 
-        analyse(state, root_symbol='my_prog'),
+        analyse(state, root_symbol='my_prog')
 
-        compile_fortran(state),
-        link_exe(state),
+        compile_fortran(state)
+        link_exe(state)

run_configs/um/build_um.py

@@ -124,8 +124,9 @@ def replace_in_file(inpath, outpath, find, replace):
     revision = 'vn12.1'
     um_revision = revision.replace('vn', 'um')
 
-    state = BuildConfig(project_label=f'um atmos safe {revision} $compiler $two_stage',
-                        tool_box=ToolBox())
+    state = BuildConfig(
+        project_label=f'um atmos safe {revision} $compiler $two_stage',
+        mpi=False, openmp=False, tool_box=ToolBox())
 
     # compiler-specific flags
     compiler = state.tool_box[Category.FORTRAN_COMPILER]

source/fab/build_config.py

@@ -22,7 +22,8 @@
 
 from fab.artefacts import ArtefactSet, ArtefactStore
 from fab.constants import BUILD_OUTPUT, SOURCE_ROOT, PREBUILD
-from fab.metrics import send_metric, init_metrics, stop_metrics, metrics_summary
+from fab.metrics import (send_metric, init_metrics, stop_metrics,
+                         metrics_summary)
 from fab.tools.category import Category
 from fab.tools.tool_box import ToolBox
 from fab.steps.cleanup_prebuilds import CLEANUP_COUNT, cleanup_prebuilds
@@ -41,36 +42,50 @@ class BuildConfig():
     """
     def __init__(self, project_label: str,
                  tool_box: ToolBox,
-                 multiprocessing: bool = True, n_procs: Optional[int] = None,
+                 mpi: bool,
+                 openmp: bool,
+                 multiprocessing: bool = True,
+                 n_procs: Optional[int] = None,
                  reuse_artefacts: bool = False,
-                 fab_workspace: Optional[Path] = None, two_stage=False,
-                 verbose=False):
+                 fab_workspace: Optional[Path] = None,
+                 two_stage: bool = False,
+                 verbose: bool = False):
         """
         :param project_label:
-            Name of the build project. The project workspace folder is created from this name, with spaces replaced
-            by underscores.
+            Name of the build project. The project workspace folder is
+            created from this name, with spaces replaced by underscores.
         :param tool_box: The ToolBox with all tools to use in the build.
+        :param mpi: whether the project uses MPI or not. This is used to
+            pick a default compiler (if not explicitly set in the ToolBox),
+            and controls PSyclone parameters.
+        :param openmp: whether the project should use OpenMP or not.
         :param multiprocessing:
             An option to disable multiprocessing to aid debugging.
         :param n_procs:
-            The number of cores to use for multiprocessing operations. Defaults to the number of available cores.
+            The number of cores to use for multiprocessing operations.
+            Defaults to the number of available cores.
         :param reuse_artefacts:
             A flag to avoid reprocessing certain files on subsequent runs.
-            WARNING: Currently unsophisticated, this flag should only be used by Fab developers.
-            The logic behind flag will soon be improved, in a work package called "incremental build".
+            WARNING: Currently unsophisticated, this flag should only be
+            used by Fab developers. The logic behind flag will soon be
+            improved, in a work package called "incremental build".
         :param fab_workspace:
             Overrides the FAB_WORKSPACE environment variable.
-            If not set, and FAB_WORKSPACE is not set, the fab workspace defaults to *~/fab-workspace*.
+            If not set, and FAB_WORKSPACE is not set, the fab workspace
+            defaults to *~/fab-workspace*.
         :param two_stage:
-            Compile .mod files first in a separate pass. Theoretically faster in some projects..
+            Compile .mod files first in a separate pass. Theoretically faster
+            in some projects.
         :param verbose:
             DEBUG level logging.
 
         """
         self._tool_box = tool_box
+        self._mpi = mpi
+        self._openmp = openmp
         self.two_stage = two_stage
         self.verbose = verbose
-        compiler = tool_box[Category.FORTRAN_COMPILER]
+        compiler = tool_box.get_tool(Category.FORTRAN_COMPILER, mpi=mpi)
         project_label = Template(project_label).safe_substitute(
             compiler=compiler.name,
             two_stage=f'{int(two_stage)+1}stage')
@@ -83,7 +98,8 @@ def __init__(self, project_label: str,
         logger.info(f"fab workspace is {fab_workspace}")
 
         self.project_workspace: Path = fab_workspace / self.project_label
-        self.metrics_folder: Path = self.project_workspace / 'metrics' / self.project_label
+        self.metrics_folder: Path = (self.project_workspace / 'metrics' /
+                                     self.project_label)
 
         # source config
         self.source_root: Path = self.project_workspace / SOURCE_ROOT
@@ -93,7 +109,8 @@ def __init__(self, project_label: str,
         self.multiprocessing = multiprocessing
 
         # turn off multiprocessing when debugging
-        # todo: turn off multiprocessing when running tests, as a good test runner will run using mp
+        # todo: turn off multiprocessing when running tests, as a good test
+        # runner will run using mp
         if 'pydevd' in str(sys.gettrace()):
             logger.info('debugger detected, running without multiprocessing')
             self.multiprocessing = False
@@ -129,7 +146,8 @@ def __enter__(self):
         self._start_time = datetime.now().replace(microsecond=0)
         self._run_prep()
 
-        with TimerLogger(f'running {self.project_label} build steps') as build_timer:
+        with TimerLogger(f'running {self.project_label} '
+                         f'build steps') as build_timer:
             # this will return to the build script
             self._build_timer = build_timer
             return self
@@ -138,10 +156,12 @@ def __exit__(self, exc_type, exc_val, exc_tb):
 
         if not exc_type:  # None if there's no error.
             if CLEANUP_COUNT not in self.artefact_store:
-                logger.info("no housekeeping step was run, using a default hard cleanup")
+                logger.info("no housekeeping step was run, using a "
+                            "default hard cleanup")
                 cleanup_prebuilds(config=self, all_unused=True)
 
-        logger.info(f"Building '{self.project_label}' took {datetime.now() - self._start_time}")
+        logger.info(f"Building '{self.project_label}' took "
+                    f"{datetime.now() - self._start_time}")
 
         # always
         self._finalise_metrics(self._start_time, self._build_timer)
@@ -164,9 +184,20 @@ def build_output(self) -> Path:
         '''
         return self.project_workspace / BUILD_OUTPUT
 
+    @property
+    def mpi(self) -> bool:
+        ''':returns: whether MPI is requested or not in this config.'''
+        return self._mpi
+
+    @property
+    def openmp(self) -> bool:
+        ''':returns: whether OpenMP is requested or not in this config.'''
+        return self._openmp
+
     def add_current_prebuilds(self, artefacts: Iterable[Path]):
         """
-        Mark the given file paths as being current prebuilds, not to be cleaned during housekeeping.
+        Mark the given file paths as being current prebuilds, not to be
+        cleaned during housekeeping.
 
         """
         self.artefact_store[ArtefactSet.CURRENT_PREBUILDS].update(artefacts)
@@ -193,7 +224,8 @@ def _prep_folders(self):
     def _init_logging(self):
         # add a file logger for our run
         self.project_workspace.mkdir(parents=True, exist_ok=True)
-        log_file_handler = RotatingFileHandler(self.project_workspace / 'log.txt', backupCount=5, delay=True)
+        log_file_handler = RotatingFileHandler(
+            self.project_workspace / 'log.txt', backupCount=5, delay=True)
         log_file_handler.doRollover()
         logging.getLogger('fab').addHandler(log_file_handler)
 
@@ -207,9 +239,11 @@ def _init_logging(self):
     def _finalise_logging(self):
         # remove our file logger
         fab_logger = logging.getLogger('fab')
-        log_file_handlers = list(by_type(fab_logger.handlers, RotatingFileHandler))
+        log_file_handlers = list(by_type(fab_logger.handlers,
+                                         RotatingFileHandler))
         if len(log_file_handlers) != 1:
-            warnings.warn(f'expected to find 1 RotatingFileHandler for removal, found {len(log_file_handlers)}')
+            warnings.warn(f'expected to find 1 RotatingFileHandler for '
+                          f'removal, found {len(log_file_handlers)}')
         fab_logger.removeHandler(log_file_handlers[0])
 
     def _finalise_metrics(self, start_time, steps_timer):
@@ -249,14 +283,16 @@ def __init__(self, match: str, flags: List[str]):
             # For source in the um folder, add an absolute include path
             AddFlags(match="$source/um/*", flags=['-I$source/include']),
 
-            # For source in the um folder, add an include path relative to each source file.
+            # For source in the um folder, add an include path relative to
+            # each source file.
             AddFlags(match="$source/um/*", flags=['-I$relative/include']),
 
         """
         self.match: str = match
         self.flags: List[str] = flags
 
-    # todo: we don't need the project_workspace, we could just pass in the output folder
+    # todo: we don't need the project_workspace, we could just pass in the
+    # output folder
     def run(self, fpath: Path, input_flags: List[str], config):
         """
         Check if our filter matches a given file. If it does, add our flags.
@@ -269,12 +305,16 @@ def run(self, fpath: Path, input_flags: List[str], config):
             Contains the folders for templating `$source` and `$output`.
 
         """
-        params = {'relative': fpath.parent, 'source': config.source_root, 'output': config.build_output}
+        params = {'relative': fpath.parent,
+                  'source': config.source_root,
+                  'output': config.build_output}
 
         # does the file path match our filter?
-        if not self.match or fnmatch(str(fpath), Template(self.match).substitute(params)):
+        if not self.match or fnmatch(str(fpath),
+                                     Template(self.match).substitute(params)):
             # use templating to render any relative paths in our flags
-            add_flags = [Template(flag).substitute(params) for flag in self.flags]
+            add_flags = [Template(flag).substitute(params)
+                         for flag in self.flags]
 
             # add our flags
             input_flags += add_flags
@@ -284,15 +324,18 @@ class FlagsConfig():
     """
     Return command-line flags for a given path.
 
-    Simply allows appending flags but may evolve to also replace and remove flags.
+    Simply allows appending flags but may evolve to also replace and
+    remove flags.
 
     """
-    def __init__(self, common_flags: Optional[List[str]] = None, path_flags: Optional[List[AddFlags]] = None):
+    def __init__(self, common_flags: Optional[List[str]] = None,
+                 path_flags: Optional[List[AddFlags]] = None):
         """
         :param common_flags:
             List of flags to apply to all files. E.g `['-O2']`.
         :param path_flags:
-            List of :class:`~fab.build_config.AddFlags` objects which apply flags to selected paths.
+            List of :class:`~fab.build_config.AddFlags` objects which apply
+            flags to selected paths.
 
         """
         self.common_flags = common_flags or []
@@ -311,8 +354,8 @@ def flags_for_path(self, path: Path, config):
 
         """
         # We COULD make the user pass these template params to the constructor
-        # but we have a design requirement to minimise the config burden on the user,
-        # so we take care of it for them here instead.
+        # but we have a design requirement to minimise the config burden on
+        # the user, so we take care of it for them here instead.
         params = {'source': config.source_root, 'output': config.build_output}
         flags = [Template(i).substitute(params) for i in self.common_flags]