From b176c47895dfa97cd766f57e8c6eca645d67925d Mon Sep 17 00:00:00 2001 From: Dougal Dobie Date: Wed, 22 Jan 2025 12:43:54 +1100 Subject: [PATCH] Fix measurements arrow creation and replace optimize_ints and optimize_floats with optimise_numeric (#797) * Replace optimize_ints and optimize_floats with optimise_numeric * Updated measurement arrow creation * Added vaex dependency * Switch from tqdmtqdm to multiprocessing * Update dependencies * Update process_map to starmap * Revert to using vaex * Added some notes for V1/2 * Updated changelog --- CHANGELOG.md | 3 + poetry.lock | 1032 +++++++++++++++++++++------- pyproject.toml | 1 + vast_pipeline/pipeline/finalise.py | 10 +- vast_pipeline/pipeline/utils.py | 155 +++-- vast_pipeline/utils/utils.py | 35 +- 6 files changed, 892 insertions(+), 344 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 46f2e91f9..316400866 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Changed +- Upgrade measurements file generation to use dask in order to handle larger runs [#789](https://github.com/askap-vast/vast-pipeline/pull/797) +- Replaced optimise_ints and optimise_floats with single function - optimise_numeric [#789](https://github.com/askap-vast/vast-pipeline/pull/797) - Upgrade forced_phot dependency to v0.2 and force `use_numba=True` [#788](https://github.com/askap-vast/vast-pipeline/pull/788) - Remove bad forced photometry fits immediately after calculation, rather than after they've all been compiled into a single dataframe [#788](https://github.com/askap-vast/vast-pipeline/pull/788) - Optimise associations upload by dropping unnecessary columns prior to a large dataframe merge [#787](https://github.com/askap-vast/vast-pipeline/pull/787) @@ -30,6 +32,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### List of PRs +- [#789](https://github.com/askap-vast/vast-pipeline/pull/797): feat: Convert measurements.arrow generation to use dask, and combine optimise_ints/floats to optimise_numeric - [#795](https://github.com/askap-vast/vast-pipeline/pull/795): fix: Fixed outdated jupyterhub link on pipeline website - [#788](https://github.com/askap-vast/vast-pipeline/pull/788): feat, fix: Speed up forced fitting code by using numba-fied forced_phot code and reordering some calculations - [#787](https://github.com/askap-vast/vast-pipeline/pull/787): fix: Optimise associations merge and minor variable name updates diff --git a/poetry.lock b/poetry.lock index 4bef8b12b..8ac61f952 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,19 @@ # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + 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"331033fb1d016960336aa8ad502bb9e11996a29af936afc8e695ada61e7dc38a" diff --git a/pyproject.toml b/pyproject.toml index 9692b9dcf..0c0335432 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,6 +42,7 @@ holoviews = "^1.14.7" datashader = "^0.14" channels = "^3.0.4" param = "<2.0.0" +vaex-core = "^4.17.1" [tool.poetry.dev-dependencies] mkdocs-material = "^9.4" diff --git a/vast_pipeline/pipeline/finalise.py b/vast_pipeline/pipeline/finalise.py index 3c48b8aea..6971ba96a 100644 --- a/vast_pipeline/pipeline/finalise.py +++ b/vast_pipeline/pipeline/finalise.py @@ -8,7 +8,7 @@ from typing import List, Dict, Tuple from vast_pipeline.models import Run -from vast_pipeline.utils.utils import StopWatch, optimize_floats, optimize_ints +from vast_pipeline.utils.utils import StopWatch, optimise_numeric from vast_pipeline.pipeline.loading import ( make_upload_associations, make_upload_sources, make_upload_related_sources, update_sources @@ -393,11 +393,9 @@ def final_operations( ) # optimize measurement pair DataFrame and save to parquet file - measurement_pairs_df = optimize_ints( - optimize_floats( - measurement_pairs_df.drop(columns=["source"]).rename( - columns={"id_a": "meas_id_a", "id_b": "meas_id_b"} - ) + measurement_pairs_df = optimise_numeric( + measurement_pairs_df.drop(columns=["source"]).rename( + columns={"id_a": "meas_id_a", "id_b": "meas_id_b"} ) ) measurement_pairs_df.to_parquet( diff --git a/vast_pipeline/pipeline/utils.py b/vast_pipeline/pipeline/utils.py index fa704ae14..593d34d72 100644 --- a/vast_pipeline/pipeline/utils.py +++ b/vast_pipeline/pipeline/utils.py @@ -13,18 +13,23 @@ import astropy.units as u import dask import dask.dataframe as dd +import dask.config as dc import psutil +import tempfile +import vaex +import itertools from typing import Any, List, Optional, Dict, Tuple, Union from astropy.coordinates import SkyCoord, Angle from django.conf import settings from django.contrib.auth.models import User from itertools import chain +from multiprocessing import Pool 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, + eq_to_cart, StopWatch, optimise_numeric, calculate_workers_and_partitions ) from vast_pipeline.models import ( @@ -1318,8 +1323,60 @@ def get_parallel_assoc_image_df( return images_df +def _process_measurements_file(m_file: str, + i: int, + out_dir: str, + associations: pd.DataFrame + ) -> None: + """ + Process an individual measurements file and output as a single partition + + Args: + m_file: Path to measurements file. + i: Measurements file index. + out_dir: Path to directory containing parquet partitions + associations: Associations dataframe + + Returns: + None + """ + measurements = pd.read_parquet(m_file, engine='pyarrow') + + # Memory blows up and everything is slow if we try and do a full merge. + # Instead, pull out the indices that are in both dfs and then merge those. + associations_merge = associations[associations.index.isin(measurements['id'])] + measurements = measurements.loc[ + measurements['id'].isin(associations_merge.index) + ] + + # drop timezone from datetime for vaex compatibility. V2 NOTE - remove + measurements['time'] = measurements['time'].dt.tz_localize(None) + + measurements = optimise_numeric(measurements) + measurements = measurements.merge(associations_merge, right_index=True, left_on='id', how="inner").rename(columns={'source_id': 'source'}) + + partition_file = os.path.join(out_dir, f'part.{i}.parquet') + measurements.to_parquet(partition_file, index=False) + +def _repartition_measurements(in_file: str, out_file: str) -> None: + """" + Repartition the combined measurements file to be indexed by source id + + Args: + in_file: path to parquet file to be repartitioned. + out_file: path to parquet file to be written. + Returns: + None + """ + + # Using large datasets, so need to do the shuffling on disk + with dc.set(shuffle='disk'): + dask_df = dd.read_parquet(in_file).repartition(partition_size="100MB") + dask_df = dask_df.set_index('source', drop=True) + dask_df = dask_df.repartition(partition_size="100MB") + dask_df.to_parquet(out_file) -def create_measurements_arrow_file(p_run: Run) -> None: +def create_measurements_arrow_file(p_run: Run, max_workers: Optional[int] =10) -> None: """ Creates a measurements.arrow file using the parquet outputs of a pipeline run. @@ -1327,68 +1384,80 @@ def create_measurements_arrow_file(p_run: Run) -> None: Args: p_run: Pipeline model instance. + max_workers: + Maximum number of workers to use when processing + individual partitions. Defaults to 10. Returns: None """ logger.info('Creating measurements.arrow for run %s.', p_run.name) + + p_run_path = p_run.path + arrow_file = os.path.join(p_run_path, 'measurements.arrow') + logger.info("Will write to final arrow file to %s.", arrow_file) + + # V2 NOTE - the repartitioned data will be the final data product. + # Need to scrap arrow_file and change the repartitioned file to measurements.parquet + processed_temp = tempfile.TemporaryDirectory() + repartitioned_temp = tempfile.TemporaryDirectory() + logger.debug("But in the meantime, writing temporary data to %s and %s", + processed_temp.name, + repartitioned_temp.name + ) - associations = pd.read_parquet( - os.path.join( - p_run.path, - 'associations.parquet' - ) - ) images = pd.read_parquet( os.path.join( - p_run.path, + p_run_path, 'images.parquet' - ) + ), + columns=['measurements_path'] ) - m_files = images['measurements_path'].tolist() + del images m_files += glob.glob(os.path.join( - p_run.path, + p_run_path, 'forced*.parquet' )) - logger.debug('Loading %i files...', len(m_files)) - measurements = dd.read_parquet(m_files, engine='pyarrow').compute() + logger.debug("Will create measurements from %i files...", len(m_files)) - measurements = measurements.loc[ - measurements['id'].isin(associations['meas_id'].values) - ] - - measurements = ( - associations.loc[:, ['meas_id', 'source_id']] - .set_index('meas_id') - .merge( - measurements, - left_index=True, - right_on='id' + associations = dd.read_parquet( + os.path.join( + p_run_path, + 'associations.parquet' + ), + columns=['source_id'], + index='meas_id' + ).compute() + + logger.debug("Processing %d partitions with %d workers", len(m_files), max_workers) + + + with Pool(max_workers) as pool: + iterable_arg = zip( + m_files, + range(len(m_files)), + itertools.repeat(processed_temp.name), + itertools.repeat(associations), ) - .rename(columns={'source_id': 'source'}) - ) + pool.starmap(_process_measurements_file, iterable_arg) + + logger.debug("Repartitioning dataframe") + _repartition_measurements(processed_temp.name, repartitioned_temp.name) - # drop timezone from datetime for vaex compatibility - # TODO: Look to keep the timezone if/when vaex is compatible. - measurements['time'] = measurements['time'].dt.tz_localize(None) + logger.debug("Opening and exporting in vaex") - logger.debug('Optimising dataframes.') - measurements = optimize_ints(optimize_floats(measurements)) + # V2 NOTE - remove in V2 + vaex_df = vaex.open(repartitioned_temp.name) + vaex_df.export(arrow_file) - logger.debug("Loading to pyarrow table.") - measurements = pa.Table.from_pandas(measurements) + logger.debug("Cleaning up temporary data") + repartitioned_temp.cleanup() + processed_temp.cleanup() - logger.debug("Exporting to arrow file.") - outname = os.path.join(p_run.path, 'measurements.arrow') - - local = pa.fs.LocalFileSystem() - - with local.open_output_stream(outname) as file: - with pa.RecordBatchFileWriter(file, measurements.schema) as writer: - writer.write_table(measurements) + logger.debug("Done.") def create_measurement_pairs_arrow_file(p_run: Run) -> None: @@ -1413,7 +1482,7 @@ def create_measurement_pairs_arrow_file(p_run: Run) -> None: ) logger.debug('Optimising dataframe.') - measurement_pairs_df = optimize_ints(optimize_floats(measurement_pairs_df)) + measurement_pairs_df = optimise_numeric(measurement_pairs_df) logger.debug("Loading to pyarrow table.") measurement_pairs_df = pa.Table.from_pandas(measurement_pairs_df) diff --git a/vast_pipeline/utils/utils.py b/vast_pipeline/utils/utils.py index e06e95029..03781ae5e 100644 --- a/vast_pipeline/utils/utils.py +++ b/vast_pipeline/utils/utils.py @@ -308,43 +308,22 @@ def parse_coord(coord_string: str, coord_frame: str = "icrs") -> SkyCoord: return coord -def optimize_floats(df: pd.DataFrame) -> pd.DataFrame: +def optimise_numeric(df): """ - Downcast float columns in a pd.DataFrame to the smallest + Downcast integer and float columns in a pd.DataFrame to the smallest data type without losing any information. - Credit to Robbert van der Gugten. - - Args: - df: - input dataframe, no specific columns. - - Returns: - The input dataframe with the `float64` type columns downcasted. - """ - floats = df.select_dtypes(include=["float64"]).columns.tolist() - df[floats] = df[floats].apply(pd.to_numeric, downcast="float") - - return df - - -def optimize_ints(df: pd.DataFrame) -> pd.DataFrame: - """ - Downcast integer columns in a pd.DataFrame to the smallest - data type without losing any information. - - Credit to Robbert van der Gugten. - Args: df: Input dataframe, no specific columns. Returns: - The input dataframe with the `int64` type columns downcasted. + The input dataframe with the `int64` and `float64` columns downcasted. """ - ints = df.select_dtypes(include=["int64"]).columns.tolist() - df[ints] = df[ints].apply(pd.to_numeric, downcast="integer") - + for col in df.select_dtypes(include=["float64"]).columns: + df[col] = df[col].apply(pd.to_numeric, downcast="float") + for col in df.select_dtypes(include=["int64"]).columns: + df[col] = df[col].apply(pd.to_numeric, downcast="integer") return df