Implement sensible partitioning (#724)

* Added calculate_n_partitions function * Implement calculate_n_partitions_function in parallel_groupby * Implement calculate_n_partitions function in parallel_get_rms_measurements * Implement calculate_n_partitions function in calculate_measurement_pair_metrics * Implement calculate_n_partitions function in parallel_groupby * Set index * Missing commit * Fixed df name * Fixed df name * Fixed df name * Fix partition size var name * Correct calculate_n_partitions import * Fixed circular import * Updated changelog
askap-vast · Jul 12, 2024 · a6a7c91 · a6a7c91
1 parent 6209e0d
commit a6a7c91
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diff --git 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 support calculate_n_partitions for sensible dask dataframe partitioning [#724](https://github.com/askap-vast/vast-pipeline/pull/724)
 - Added support for compressed FITS files [#694](https://github.com/askap-vast/vast-pipeline/pull/694)
 - Added links to Data Central DAS and the Fink Broker to the source page [#697](https://github.com/askap-vast/vast-pipeline/pull/697/)
 - Added `n_new_sources` column to run model to store the number of new sources in a pipeline run [#676](https://github.com/askap-vast/vast-pipeline/pull/676).
@@ -76,6 +77,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 #### Fixed
 
+- Implemented sensible dask dataframe partitioning [#724](https://github.com/askap-vast/vast-pipeline/pull/724)
 - Fixed outdated `runpipeline` section on CLI docs page [#685](https://github.com/askap-vast/vast-pipeline/pull/685).
 - Fixed link to JupyterHub [#676](https://github.com/askap-vast/vast-pipeline/pull/676).
 - Ensure Image models are not created if the catalogue ingest fails [#648](https://github.com/askap-vast/vast-pipeline/pull/648).
@@ -114,6 +116,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 #### List of PRs
 
+- [#724](https://github.com/askap-vast/vast-pipeline/pull/724): fix, feat: Implemented sensible dask dataframe partitioning
 - [#694](https://github.com/askap-vast/vast-pipeline/pull/694): feat: Handle compressed fits files.
 - [#702](https://github.com/askap-vast/vast-pipeline/pull/702): fix: Downgrade ci-docs to python 3.8.
 - [#701](https://github.com/askap-vast/vast-pipeline/pull/701): fix: Update Gr1N poetry to v8, force python 3.8.10.

diff --git a/vast_pipeline/pipeline/association.py b/vast_pipeline/pipeline/association.py
@@ -20,7 +20,7 @@
     reconstruct_associtaion_dfs
 )
 from vast_pipeline.pipeline.config import PipelineConfig
-from vast_pipeline.utils.utils import StopWatch
+from vast_pipeline.utils.utils import StopWatch, calculate_n_partitions
 
 
 logger = logging.getLogger(__name__)
@@ -1588,10 +1588,12 @@ def parallel_association(
     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)
+
     # pass each skyreg_group through the normal association process.
     results = (
-        dd.from_pandas(images_df, n_cpu)
+        dd.from_pandas(images_df.set_index('skyreg_group'), npartitions=n_partitions)
         .groupby('skyreg_group')
         .apply(
             association,

diff --git a/vast_pipeline/pipeline/new_sources.py b/vast_pipeline/pipeline/new_sources.py
@@ -12,7 +12,7 @@
 )
 
 from vast_pipeline.models import Image, Run
-from vast_pipeline.utils.utils import StopWatch
+from vast_pipeline.utils.utils import StopWatch, calculate_n_partitions
 from vast_pipeline.image.utils import open_fits
 
 
@@ -219,9 +219,11 @@ def parallel_get_rms_measurements(
     }
 
     n_cpu = cpu_count() - 1
+    logger.debug(f"Running association with {n_cpu} CPUs")
+    n_partitions = calculate_n_partitions(out, n_cpu)
 
     out = (
-        dd.from_pandas(out, n_cpu)
+        dd.from_pandas(out, npartitions=n_partitions)
         .groupby('img_diff_rms_path')
         .apply(
             get_image_rms_measurements,

diff --git a/vast_pipeline/pipeline/pairs.py b/vast_pipeline/pipeline/pairs.py
@@ -6,6 +6,8 @@
 import pandas as pd
 from psutil import cpu_count
 
+from vast_pipeline.utils.utils import calculate_n_partitions
+
 
 logger = logging.getLogger(__name__)
 
@@ -65,6 +67,8 @@ def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame:
             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)
 
     """Create a DataFrame containing all measurement ID combinations per source.
     Resultant DataFrame will have a MultiIndex(["source", RangeIndex]) where "source" is
@@ -86,7 +90,7 @@ def calculate_measurement_pair_metrics(df: pd.DataFrame) -> pd.DataFrame:
         11128   0   6216  23534
     """
     measurement_combinations = (
-        dd.from_pandas(df, n_cpu)
+        dd.from_pandas(df, npartitions=n_partitions)
         .groupby("source")["id"]
         .apply(
             lambda x: pd.DataFrame(list(combinations(x, 2))), meta={0: "i", 1: "i"},)

diff --git a/vast_pipeline/pipeline/utils.py b/vast_pipeline/pipeline/utils.py
@@ -24,7 +24,8 @@
 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, optimize_ints, optimize_floats,
+    calculate_n_partitions
 )
 from vast_pipeline.models import (
     Band, Image, Run, SkyRegion
@@ -704,7 +705,10 @@ def parallel_groupby(df: pd.DataFrame) -> pd.DataFrame:
         'related_list': 'O'
     }
     n_cpu = cpu_count() - 1
-    out = dd.from_pandas(df, n_cpu)
+    logger.debug(f"Running association with {n_cpu} CPUs")
+    n_partitions = calculate_n_partitions(df, n_cpu)
+
+    out = dd.from_pandas(df.set_index('source'), npartitions=n_partitions)
     out = (
         out.groupby('source')
         .apply(
@@ -763,7 +767,10 @@ def parallel_groupby_coord(df: pd.DataFrame) -> pd.DataFrame:
         'wavg_dec': 'f',
     }
     n_cpu = cpu_count() - 1
-    out = dd.from_pandas(df, n_cpu)
+    logger.debug(f"Running association with {n_cpu} CPUs")
+    n_partitions = calculate_n_partitions(df, n_cpu)
+
+    out = dd.from_pandas(df.set_index('source'), npartitions=n_partitions)
     out = (
         out.groupby('source')
         .apply(calc_ave_coord, meta=col_dtype)

diff --git a/vast_pipeline/utils/utils.py b/vast_pipeline/utils/utils.py
@@ -378,3 +378,26 @@ def dict_merge(
 
 def timeStamped(fname, fmt="%Y-%m-%d-%H-%M-%S_{fname}"):
     return datetime.now().strftime(fmt).format(fname=fname)
+
+def calculate_n_partitions(df, n_cpu, partition_size_mb=100):
+    """
+    This function will calculate how many partitions a dataframe should be
+    split into.
+    
+    Args:
+        df: The pandas dataframe to be partitionined.
+        n_cpu: The number of available CPUs.
+        partition_size: The optimal partition size in MB.
+    Returns:
+        The optimal number of partitions.
+    """
+    mem_usage_mb = df.memory_usage(deep=True).sum() / 1e6
+    n_partitions = int(np.ceil(mem_usage_mb/partition_size_mb))
+
+    # n_partitions should be >= n_cpu for optimal parallel processing
+    if n_partitions < n_cpu:
+        n_partitions=n_cpu
+
+    logger.debug("Using {n_partitions} partions of {partition_size}MB")
+
+    return n_partitions