diff --git a/CHANGELOG.md b/CHANGELOG.md index 3620f419..380f055a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Added +- Added configuration options to specify number of workers and maximum partition size for parallel operations. [#777](https://github.com/askap-vast/vast-pipeline/pull/777) - Added vast_pipeline.utils.delete_run.py to enable deletion of pipeline runs using raw SQL [#775](https://github.com/askap-vast/vast-pipeline/pull/775) #### Changed @@ -27,6 +28,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### List of PRs +- [#777](https://github.com/askap-vast/vast-pipeline/pull/777): feat: Allow user to specify number of cores and memory size of partitions via configuration. - [#776](https://github.com/askap-vast/vast-pipeline/pull/776): fix: Minor memory optimisations - [#775](https://github.com/askap-vast/vast-pipeline/pull/775): fix, feat: Enabled deletion of pipeline runs directly using SQL rather than via django - [#734](https://github.com/askap-vast/vast-pipeline/pull/734): Shortened forced fits measurement names diff --git a/docs/using/runconfig.md b/docs/using/runconfig.md index 864f3bdc..de54bd2f 100644 --- a/docs/using/runconfig.md +++ b/docs/using/runconfig.md @@ -127,6 +127,21 @@ Below is an example of a default `config.yaml` file. Note that no images or othe # aggregate pair metrics that are stored in Source objects. source_aggregate_pair_metrics_min_abs_vs: 4.3 + processing: + # Options to control use of Dask parallelism + # NOTE: These are advanced options and you should only change them if you know what you are doing. + + # The total number of workers available to Dask ('null' means use one less than all cores) + num_workers: null + + # The number of workers to use for disk IO operations (e.g. when reading images for forced extraction) + num_workers_io: 5 + + # The default maximum size (in MB) to allow per partition of Dask DataFrames + # Increasing this will create fewer partitions and will potentially increase the memory footprint + # of parallel tasks. + max_partition_mb: 15 + ``` !!! note diff --git a/poetry.lock b/poetry.lock index 2c9557c2..fceb5448 100644 --- a/poetry.lock +++ b/poetry.lock @@ -211,13 +211,13 @@ xbr = ["base58 (>=2.1.0)", "cbor2 (>=5.2.0)", "click (>=8.1.2)", "ecdsa (>=0.16. 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"zope.testing"] +docs = ["Sphinx", "furo", "repoze.sphinx.autointerface"] +test = ["coverage[toml]", "zope.event", "zope.testing"] +testing = ["coverage[toml]", "zope.event", "zope.testing"] [extras] prod = ["gevent", "gunicorn"] @@ -4371,4 +4449,4 @@ prod = ["gevent", "gunicorn"] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "8153f316f4042aacea8eacc6fb2781de953a53d248905257f9aa10272272c752" +content-hash = "1999025d7ad15dffd95030c93eb80068fd74f567ee2c023020ce7a7d1be00c09" diff --git a/pyproject.toml b/pyproject.toml index 05fc4f58..cb419709 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ whitenoise = "^5.2.0" gevent = { version = "^21.1.2", optional = true } gunicorn = { version = "^20.0.4", optional = true } forced-phot = { git = "https://github.com/askap-vast/forced_phot.git" } -strictyaml = "^1.3.2" +strictyaml = "^1.6.2" colorcet = "^2.0.6" matplotlib = "^3.5.0" holoviews = "^1.14.7" diff --git a/vast_pipeline/config_template.yaml.j2 b/vast_pipeline/config_template.yaml.j2 index 85a93e5f..21b19ff8 100644 --- a/vast_pipeline/config_template.yaml.j2 +++ b/vast_pipeline/config_template.yaml.j2 @@ -163,3 +163,18 @@ variability: # Only measurement pairs where the Vs metric exceeds this value are selected for the # aggregate pair metrics that are stored in Source objects. source_aggregate_pair_metrics_min_abs_vs: {{ source_aggregate_pair_metrics_min_abs_vs }} + +processing: + # Options to control use of Dask parallelism + # NOTE: These are advanced options and you should only change them if you know what you are doing. + + # The total number of workers available to Dask ('null' means use one less than all cores) + num_workers: {{ num_workers }} + + # The number of workers to use for disk IO operations (e.g. when reading images for forced extraction) + num_workers_io: {{ num_workers_io }} + + # The default maximum size (in MB) to allow per partition of Dask DataFrames + # Increasing this will create fewer partitions and will potentially increase the memory footprint + # of parallel tasks. + max_partition_mb: {{ max_partition_mb }} diff --git a/vast_pipeline/pipeline/association.py b/vast_pipeline/pipeline/association.py index d5e46cb0..06c7d6db 100644 --- a/vast_pipeline/pipeline/association.py +++ b/vast_pipeline/pipeline/association.py @@ -7,7 +7,6 @@ import pandas as pd from typing import Tuple, Dict, List import dask.dataframe as dd -from psutil import cpu_count from astropy import units as u from astropy.coordinates import SkyCoord @@ -20,7 +19,7 @@ reconstruct_associtaion_dfs ) from vast_pipeline.pipeline.config import PipelineConfig -from vast_pipeline.utils.utils import StopWatch, calculate_n_partitions +from vast_pipeline.utils.utils import StopWatch, calculate_workers_and_partitions logger = logging.getLogger(__name__) @@ -1586,11 +1585,12 @@ def parallel_association( # Add an increment to any new source values when using add_mode to avoid # getting duplicates in the result laater id_incr_par_assoc = max(done_source_ids) if add_mode else 0 - - n_cpu = cpu_count() - 1 - logger.debug(f"Running association with {n_cpu} CPUs") - n_partitions = calculate_n_partitions(images_df, n_cpu) - + n_workers, n_partitions = calculate_workers_and_partitions( + images_df, + n_cpu=config['processing']['num_workers'], + max_partition_mb=config['processing']['max_partition_mb'] + ) + logger.debug(f"Running association with {n_workers} CPUs") # pass each skyreg_group through the normal association process. results = ( dd.from_pandas(images_df.set_index('skyreg_group'), npartitions=n_partitions) @@ -1608,7 +1608,7 @@ def parallel_association( id_incr_par_assoc=id_incr_par_assoc, parallel=True, meta=meta - ).compute(n_workers=n_cpu, scheduler='processes') + ).compute(n_workers=n_workers, scheduler='processes') ) # results are the normal dataframe of results with the columns: diff --git a/vast_pipeline/pipeline/config.py b/vast_pipeline/pipeline/config.py index d81a7374..82f63391 100644 --- a/vast_pipeline/pipeline/config.py +++ b/vast_pipeline/pipeline/config.py @@ -16,7 +16,7 @@ def make_config_template(template_path: str, **kwargs) -> str: - """Generate the contents of a run configuration file from on a Jinja2 template. + """Generate the contents of a run configuration file from a Jinja2 template. Args: template_path: Path to a Jinja2 template. @@ -114,6 +114,22 @@ class PipelineConfig: "source_aggregate_pair_metrics_min_abs_vs": yaml.Float(), } ), + yaml.Optional("processing"): yaml.Map( + { + yaml.Optional( + "num_workers", + default=settings.PIPE_RUN_CONFIG_DEFAULTS['num_workers']): + yaml.NullNone() | yaml.Int() | yaml.Str(), + yaml.Optional( + "num_workers_io", + default=settings.PIPE_RUN_CONFIG_DEFAULTS['num_workers_io']): + yaml.NullNone() | yaml.Int() | yaml.Str(), + yaml.Optional( + "max_partition_mb", + default=settings.PIPE_RUN_CONFIG_DEFAULTS['max_partition_mb']): + yaml.Int() + } + ) } ) # path to default run config template @@ -511,6 +527,13 @@ def validate(self, user: User = None): if not os.path.exists(file): raise PipelineConfigError(f"{file} does not exist.") + # ensure num_workers and num_workers_io are + # either None (from null in config yaml) or an integer + for param_name in ('num_workers', 'num_workers_io'): + param_value = self['processing'][param_name] + if (param_value is not None) and (type(param_value) is not int): + raise PipelineConfigError(f"{param_name} can only be an integer or 'null'") + def check_prev_config_diff(self) -> bool: """ Checks if the previous config file differs from the current config file. Used in diff --git a/vast_pipeline/pipeline/finalise.py b/vast_pipeline/pipeline/finalise.py index 2da077f3..b282ccc0 100644 --- a/vast_pipeline/pipeline/finalise.py +++ b/vast_pipeline/pipeline/finalise.py @@ -88,7 +88,9 @@ def final_operations( source_aggregate_pair_metrics_min_abs_vs: float, add_mode: bool, done_source_ids: List[int], - previous_parquets: Dict[str, str] + previous_parquets: Dict[str, str], + n_cpu: int = 0, + max_partition_mb: int = 15 ) -> Tuple[int, int]: """ Performs the final operations of the pipeline: @@ -136,7 +138,9 @@ def final_operations( ) log_total_memory_usage() - srcs_df = parallel_groupby(sources_df) + srcs_df = parallel_groupby(sources_df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb) mem_usage = get_df_memory_usage(srcs_df) logger.info('Groupby-apply time: %.2f seconds', timer.reset()) @@ -179,7 +183,10 @@ def final_operations( # create measurement pairs, aka 2-epoch metrics if calculate_pairs: timer.reset() - measurement_pairs_df = calculate_measurement_pair_metrics(sources_df) + measurement_pairs_df = calculate_measurement_pair_metrics( + sources_df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb) logger.info( 'Measurement pair metrics time: %.2f seconds', timer.reset()) diff --git a/vast_pipeline/pipeline/forced_extraction.py b/vast_pipeline/pipeline/forced_extraction.py index 56e7aec4..143d72e7 100644 --- a/vast_pipeline/pipeline/forced_extraction.py +++ b/vast_pipeline/pipeline/forced_extraction.py @@ -5,7 +5,6 @@ import pandas as pd import dask.dataframe as dd import dask.bag as db -from psutil import cpu_count from glob import glob from astropy import units as u @@ -19,7 +18,7 @@ from vast_pipeline.pipeline.loading import make_upload_measurements from forced_phot import ForcedPhot -from ..utils.utils import StopWatch +from ..utils.utils import StopWatch, calculate_workers_and_partitions from vast_pipeline.image.utils import open_fits @@ -259,7 +258,7 @@ def finalise_forced_dfs( def parallel_extraction( df: pd.DataFrame, df_images: pd.DataFrame, df_sources: pd.DataFrame, min_sigma: float, edge_buffer: float, cluster_threshold: float, - allow_nan: bool, add_mode: bool, p_run_path: str + allow_nan: bool, add_mode: bool, p_run_path: str, n_workers: int = 5 ) -> pd.DataFrame: """ Parallelize forced extraction with Dask @@ -289,6 +288,8 @@ def parallel_extraction( True when the pipeline is running in add image mode. p_run_path: The system path of the pipeline run output. + n_workers: + The desired number of workers for Dask Returns: Dataframe with forced extracted measurements data, columns are @@ -374,7 +375,7 @@ def image_data_func(image_name: str) -> Dict[str, Any]: npartitions=len(list_meas_parquets) ) .map(get_data_from_parquet, p_run_path, add_mode) - .compute() + .compute(num_workers=n_workers, scheduler="processes") ) mapping = pd.DataFrame(mapping) # remove not used columns from images_df and merge into mapping @@ -393,7 +394,6 @@ def image_data_func(image_name: str) -> Dict[str, Any]: ) del col_to_drop - n_cpu = cpu_count() - 1 bags = db.from_sequence(list_to_map, npartitions=len(list_to_map)) forced_dfs = ( bags.map(lambda x: extract_from_image( @@ -402,7 +402,7 @@ def image_data_func(image_name: str) -> Dict[str, Any]: allow_nan=allow_nan, **x )) - .compute() + .compute(num_workers=n_workers, scheduler='processes') ) del bags # create intermediates dfs combining the mapping data and the forced @@ -497,7 +497,8 @@ def forced_extraction( sources_df: pd.DataFrame, cfg_err_ra: float, cfg_err_dec: float, p_run: Run, extr_df: pd.DataFrame, min_sigma: float, edge_buffer: float, cluster_threshold: float, allow_nan: bool, add_mode: bool, - done_images_df: pd.DataFrame, done_source_ids: List[int] + done_images_df: pd.DataFrame, done_source_ids: List[int], + n_cpu: int = 5 ) -> Tuple[pd.DataFrame, int]: """ Check and extract expected measurements, and associated them with the @@ -533,6 +534,8 @@ def forced_extraction( done_source_ids: List of the source ids that were already present in the previous run (used in add image mode). + n_cpu: + The desired number of workers for Dask. Returns: The `sources_df` with the extracted sources added. @@ -604,11 +607,14 @@ def forced_extraction( f" (from {total_to_extract} total)" ) + # Don't care about n_partitions in this step + n_workers, _ = calculate_workers_and_partitions(None, n_cpu) + timer.reset() extr_df = parallel_extraction( extr_df, images_df, sources_df[['source', 'image', 'flux_peak']], min_sigma, edge_buffer, cluster_threshold, allow_nan, add_mode, - p_run.path + p_run.path, n_workers=n_workers ) logger.info( 'Force extraction step time: %.2f seconds', timer.reset() @@ -712,7 +718,7 @@ def forced_extraction( n_forced = ( dd.read_parquet(forced_parquets, columns=['id']) .count() - .compute() + .compute(num_workers=n_workers, scheduler='processes') .values[0] ) else: diff --git a/vast_pipeline/pipeline/main.py b/vast_pipeline/pipeline/main.py index a0425ccc..3d935099 100644 --- a/vast_pipeline/pipeline/main.py +++ b/vast_pipeline/pipeline/main.py @@ -266,6 +266,8 @@ def process_pipeline(self, p_run: Run) -> None: sources_df.loc[sources_df['forced'] == False, missing_source_cols], images_df, skyregs_df, + n_cpu=self.config['processing']['num_workers'], + max_partition_mb=self.config['processing']['max_partition_mb'] ) # STEP #4 New source analysis @@ -274,7 +276,9 @@ def process_pipeline(self, p_run: Run) -> None: missing_sources_df, self.config["new_sources"]["min_sigma"], self.config["source_monitoring"]["edge_buffer_scale"], - p_run + p_run, + n_cpu=self.config['processing']['num_workers_io'], + max_partition_mb=self.config['processing']['max_partition_mb'] ) # Drop column no longer required in missing_sources_df. @@ -299,7 +303,8 @@ def process_pipeline(self, p_run: Run) -> None: self.config["source_monitoring"]["allow_nan"], self.add_mode, done_images_df, - done_source_ids + done_source_ids, + n_cpu=self.config['processing']['num_workers_io'] ) mem_usage = get_df_memory_usage(sources_df) logger.debug(f"Step 5: sources_df memory usage: {mem_usage}MB") @@ -319,7 +324,9 @@ def process_pipeline(self, p_run: Run) -> None: self.config["variability"]["source_aggregate_pair_metrics_min_abs_vs"], self.add_mode, done_source_ids, - self.previous_parquets + self.previous_parquets, + n_cpu=self.config['processing']['num_workers'], + max_partition_mb=self.config['processing']['max_partition_mb'] ) log_total_memory_usage() diff --git a/vast_pipeline/pipeline/new_sources.py b/vast_pipeline/pipeline/new_sources.py index 14d2b3df..4ef9dd08 100644 --- a/vast_pipeline/pipeline/new_sources.py +++ b/vast_pipeline/pipeline/new_sources.py @@ -3,7 +3,6 @@ import numpy as np import dask.dataframe as dd -from psutil import cpu_count from astropy import units as u from astropy.coordinates import SkyCoord from astropy.wcs import WCS @@ -13,7 +12,7 @@ from vast_pipeline.models import Image, Run -from vast_pipeline.utils.utils import StopWatch, calculate_n_partitions +from vast_pipeline.utils.utils import StopWatch, calculate_workers_and_partitions from vast_pipeline.pipeline.utils import get_df_memory_usage from vast_pipeline.image.utils import open_fits @@ -197,7 +196,8 @@ def get_image_rms_measurements( def parallel_get_rms_measurements( - df: pd.DataFrame, edge_buffer: float = 1.0 + df: pd.DataFrame, edge_buffer: float = 1.0, + n_cpu: int = 0, max_partition_mb: int = 15 ) -> pd.DataFrame: """ Wrapper function to use 'get_image_rms_measurements' @@ -211,6 +211,11 @@ def parallel_get_rms_measurements( edge_buffer: Multiplicative factor to be passed to the 'get_image_rms_measurements' function. + n_cpu: + The desired number of workers for Dask + max_partition_mb: + The desired maximum size (in MB) of the partitions for Dask. + Returns: The original input dataframe with the 'img_diff_true_rms' column @@ -230,10 +235,13 @@ def parallel_get_rms_measurements( 'img_diff_true_rms': 'f', } - n_cpu = cpu_count() - 1 - logger.debug(f"Running association with {n_cpu} CPUs") - n_partitions = calculate_n_partitions(out, n_cpu) - + n_workers, n_partitions = calculate_workers_and_partitions( + df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb + ) + logger.debug(f"Running get_image_rms_measurements with {n_workers} CPUs") + out = ( dd.from_pandas(out, npartitions=n_partitions) .groupby('img_diff_rms_path') @@ -241,7 +249,7 @@ def parallel_get_rms_measurements( get_image_rms_measurements, edge_buffer=edge_buffer, meta=col_dtype - ).compute(num_workers=n_cpu, scheduler='processes') + ).compute(num_workers=n_workers, scheduler='processes') ) # We don't need all of the RMS measurements, just the lowest. Keeping all @@ -272,7 +280,8 @@ def parallel_get_rms_measurements( def new_sources( sources_df: pd.DataFrame, missing_sources_df: pd.DataFrame, - min_sigma: float, edge_buffer: float, p_run: Run + min_sigma: float, edge_buffer: float, p_run: Run, n_cpu: int = 5, + max_partition_mb: int = 15 ) -> pd.DataFrame: """ Processes the new sources detected to check that they are valid new @@ -294,6 +303,10 @@ def new_sources( 'get_image_rms_measurements' function. p_run: The pipeline run. + n_cpu: + The desired number of workers for Dask + max_partition_mb: + The desired maximum size (in MB) of the partitions for Dask. Returns: The original input dataframe with the 'img_diff_true_rms' column @@ -466,7 +479,8 @@ def new_sources( logger.debug("Getting rms measurements...") new_sources_df = parallel_get_rms_measurements( - new_sources_df, edge_buffer=edge_buffer + new_sources_df, edge_buffer=edge_buffer, + n_cpu=n_cpu, max_partition_mb=max_partition_mb ) logger.debug(f"Time to get rms measurements: {debug_timer.reset()}s") diff --git a/vast_pipeline/pipeline/pairs.py b/vast_pipeline/pipeline/pairs.py index a7c5eb10..8d678cc1 100644 --- a/vast_pipeline/pipeline/pairs.py +++ b/vast_pipeline/pipeline/pairs.py @@ -4,9 +4,8 @@ import dask.dataframe as dd import numpy as np import pandas as pd -from psutil import cpu_count -from vast_pipeline.utils.utils import calculate_n_partitions +from vast_pipeline.utils.utils import calculate_workers_and_partitions logger = logging.getLogger(__name__) @@ -46,7 +45,8 @@ def calculate_m_metric(flux_a: float, flux_b: float) -> float: return 2 * ((flux_a - flux_b) / (flux_a + flux_b)) -def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame: +def calculate_measurement_pair_metrics( + df: pd.DataFrame, n_cpu: int = 0, max_partition_mb: int = 15) -> pd.DataFrame: """Generate a DataFrame of measurement pairs and their 2-epoch variability metrics from a DataFrame of measurements. For more information on the variability metrics, see Section 5 of Mooley et al. (2016), DOI: 10.3847/0004-637X/818/2/105. @@ -54,6 +54,10 @@ def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame: Args: df (pd.DataFrame): Input measurements. Must contain columns: id, source, flux_int, flux_int_err, flux_peak, flux_peak_err, has_siblings. + n_cpu: + The desired number of workers for Dask + max_partition_mb: + The desired maximum size (in MB) of the partitions for Dask. Returns: Measurement pairs and 2-epoch metrics. Will contain columns: @@ -66,10 +70,14 @@ def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame: vs_peak, vs_int - variability t-statistic m_peak, m_int - variability modulation index """ - n_cpu = cpu_count() - 1 - logger.debug(f"Running association with {n_cpu} CPUs") - n_partitions = calculate_n_partitions(df.set_index('source'), n_cpu) - + + n_workers, n_partitions = calculate_workers_and_partitions( + df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb + ) + logger.debug(f"Running association with {n_workers} CPUs") + """Create a DataFrame containing all measurement ID combinations per source. Resultant DataFrame will have a MultiIndex(["source", RangeIndex]) where "source" is the source ID and RangeIndex is an unnamed temporary ID for each measurement pair, @@ -94,7 +102,7 @@ def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame: .groupby("source")["id"] .apply( lambda x: pd.DataFrame(list(combinations(x, 2))), meta={0: "i", 1: "i"},) - .compute(num_workers=n_cpu, scheduler="processes") + .compute(num_workers=n_workers, scheduler="processes") ) """Drop the RangeIndex from the MultiIndex as it isn't required and rename the columns. diff --git a/vast_pipeline/pipeline/utils.py b/vast_pipeline/pipeline/utils.py index 2b0409c5..fa704ae1 100644 --- a/vast_pipeline/pipeline/utils.py +++ b/vast_pipeline/pipeline/utils.py @@ -19,14 +19,13 @@ from astropy.coordinates import SkyCoord, Angle from django.conf import settings from django.contrib.auth.models import User -from psutil import cpu_count from itertools import chain from vast_pipeline.image.main import FitsImage, SelavyImage from vast_pipeline.image.utils import open_fits from vast_pipeline.utils.utils import ( eq_to_cart, StopWatch, optimize_ints, optimize_floats, - calculate_n_partitions + calculate_workers_and_partitions ) from vast_pipeline.models import ( Band, Image, Run, SkyRegion @@ -669,13 +668,15 @@ def groupby_funcs(df: pd.DataFrame) -> pd.Series: return pd.Series(d).fillna(value={"v_int": 0.0, "v_peak": 0.0}) -def parallel_groupby(df: pd.DataFrame) -> pd.DataFrame: +def parallel_groupby(df: pd.DataFrame, n_cpu: int = 0, max_partition_mb: int = 15) -> pd.DataFrame: """ Performs the parallel source dataframe operations to calculate the source metrics using Dask and returns the resulting dataframe. Args: df: The sources dataframe produced by the previous pipeline stages. + n_cpu: The desired number of workers for Dask + max_partition_mb: The desired maximum size (in MB) of the partitions for Dask. Returns: The source dataframe with the calculated metric columns. @@ -707,10 +708,11 @@ def parallel_groupby(df: pd.DataFrame) -> pd.DataFrame: 'eta_peak': 'f', 'related_list': 'O' } - n_cpu = cpu_count() - 1 - logger.debug(f"Running association with {n_cpu} CPUs") - n_partitions = calculate_n_partitions(df, n_cpu) - + n_workers, n_partitions = calculate_workers_and_partitions( + df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb) + logger.debug(f"Running association with {n_workers} CPUs") out = dd.from_pandas(df.set_index('source'), npartitions=n_partitions) out = ( out.groupby('source') @@ -718,7 +720,7 @@ def parallel_groupby(df: pd.DataFrame) -> pd.DataFrame: groupby_funcs, meta=col_dtype ) - .compute(num_workers=n_cpu, scheduler='processes') + .compute(num_workers=n_workers, scheduler='processes') ) out['n_rel'] = out['related_list'].apply( @@ -751,7 +753,7 @@ def calc_ave_coord(grp: pd.DataFrame) -> pd.Series: return pd.Series(d) -def parallel_groupby_coord(df: pd.DataFrame) -> pd.DataFrame: +def parallel_groupby_coord(df: pd.DataFrame, n_cpu: int = 0, max_partition_mb: int = 15) -> pd.DataFrame: """ This function uses Dask to perform the average coordinate and unique image and epoch lists calculation. The result from the Dask compute is returned @@ -759,6 +761,8 @@ def parallel_groupby_coord(df: pd.DataFrame) -> pd.DataFrame: Args: df: The sources dataframe produced by the pipeline. + n_cpu: The desired number of workers for Dask + max_partition_mb: The desired maximum size (in MB) of the partitions for Dask. Returns: The resulting average coordinate values and unique image and epoch @@ -770,15 +774,17 @@ def parallel_groupby_coord(df: pd.DataFrame) -> pd.DataFrame: 'wavg_ra': 'f', 'wavg_dec': 'f', } - n_cpu = cpu_count() - 1 - logger.debug(f"Running association with {n_cpu} CPUs") - n_partitions = calculate_n_partitions(df, n_cpu) + n_workers, n_partitions = calculate_workers_and_partitions( + df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb) + logger.debug(f"Running association with {n_workers} CPUs") out = dd.from_pandas(df.set_index('source'), npartitions=n_partitions) out = ( out.groupby('source') .apply(calc_ave_coord, meta=col_dtype) - .compute(num_workers=n_cpu, scheduler='processes') + .compute(num_workers=n_workers, scheduler='processes') ) return out @@ -899,7 +905,8 @@ def check_primary_image(row: pd.Series) -> bool: def get_src_skyregion_merged_df( - sources_df: pd.DataFrame, images_df: pd.DataFrame, skyreg_df: pd.DataFrame + sources_df: pd.DataFrame, images_df: pd.DataFrame, skyreg_df: pd.DataFrame, + n_cpu: int = 0, max_partition_mb: int = 15 ) -> pd.DataFrame: """ Analyses the current sources_df to determine what the 'ideal coverage' @@ -916,6 +923,10 @@ def get_src_skyregion_merged_df( skyreg_df: Contains the sky regions of the pipeline run. I.e. all sky region objects for the run loaded into a dataframe. + n_cpu: + The desired number of workers for Dask + max_partition_mb: + The desired maximum size (in MB) of the partitions for Dask. Returns: DataFrame containing missing image information (see source code for @@ -986,7 +997,9 @@ def get_src_skyregion_merged_df( # calculate some metrics on sources # compute only some necessary metrics in the groupby timer = StopWatch() - srcs_df = parallel_groupby_coord(sources_df) + srcs_df = parallel_groupby_coord(sources_df, + n_cpu=n_cpu, + max_partition_mb=max_partition_mb) logger.debug('Groupby-apply time: %.2f seconds', timer.reset()) del sources_df diff --git a/vast_pipeline/utils/utils.py b/vast_pipeline/utils/utils.py index 4719191b..a57dd0c7 100644 --- a/vast_pipeline/utils/utils.py +++ b/vast_pipeline/utils/utils.py @@ -13,6 +13,7 @@ from astropy.coordinates import SkyCoord, Longitude, Latitude import numpy as np import pandas as pd +from psutil import cpu_count logger = logging.getLogger(__name__) @@ -421,6 +422,33 @@ def calculate_n_partitions(df, n_cpu, partition_size_mb=15): partition_size_mb = int(np.ceil(mem_usage_mb / n_partitions)) - logger.debug(f"Using {n_partitions} partions of {partition_size_mb}MB") + logger.debug("Using %d partions of %dMB", n_partitions, partition_size_mb) return n_partitions + +def calculate_workers_and_partitions(df, n_cpu=None, max_partition_mb=15): + """ + Return number of workers and the number of partitions for Dask + + Args: + df: The pandas dataframe to be partitionined. + Don't calculate partitions if df is None + num_cpu_max: The maximum number of workers to allocate. + The default of None means use one less than all available cores + max_partition_mb: The maximum partition size in MB. + + Returns: + (num_workers, n_partitions): Calculated workers and partitions. + """ + num_cpu = cpu_count() - 1 + num_workers = num_cpu if n_cpu is None else n_cpu + if num_workers > num_cpu: + logger.debug("%d desired workers is greater than available cores. Limiting to %s.", + num_workers, num_cpu) + num_workers = num_cpu + n_partitions = 0 + if df is not None: + n_partitions = calculate_n_partitions(df, num_workers, + partition_size_mb=max_partition_mb) + + return num_workers, n_partitions diff --git a/webinterface/settings.py b/webinterface/settings.py index 5e57e49a..6336dd43 100644 --- a/webinterface/settings.py +++ b/webinterface/settings.py @@ -336,6 +336,9 @@ 'suppress_astropy_warnings': True, 'pair_metrics': True, 'source_aggregate_pair_metrics_min_abs_vs': 4.3, + 'num_workers': 'null', + 'num_workers_io': 5, + 'max_partition_mb': 15 } # default max concurrent pipeline runs