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Why you should care about data layout in the file system with Cheng Lian and Vida Ha


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Efficient data access is one of the key factors for having a high performance data processing pipeline. Determining the layout of data values in the filesystem often has fundamental impacts on the performance of data access. In this talk, we will show insights on how data layout affects the performance of data access. We will first explain how modern columnar file formats like Parquet and ORC work and explain how to use them efficiently to store data values. Then, we will present our best practice on how to store datasets, including guidelines on choosing partitioning columns and deciding how to bucket a table.

Published in: Data & Analytics
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Why you should care about data layout in the file system with Cheng Lian and Vida Ha

  1. 1. Why you should care about data layout in the file system Cheng Lian, @liancheng Vida Ha, @femineer Spark Summit 2017 1
  2. 2. TEAM About Databricks Started Spark project (now Apache Spark) at UC Berkeley in 2009 22 PRODUCT Unified Analytics Platform MISSION Making Big Data Simple
  3. 3. Apache Spark is a powerful framework with some temper 3
  4. 4. 4 Just like super mario
  5. 5. 5 Serve him the right ingredients
  6. 6. 6 Powers up and gets more efficient
  7. 7. 7 Keep serving
  8. 8. 8 He even knows how to Spark!
  9. 9. 9 However, once served a wrong dish...
  10. 10. 10 Meh...
  11. 11. 11 And sometimes...
  12. 12. 12 It can be messy...
  13. 13. 13 Secret sauces we feed Spark 13
  14. 14. File Formats 14
  15. 15. Choosing a compression scheme 15 The obvious • Compression ratio: the higher the better • De/compression speed: the faster the better
  16. 16. Choosing a compression scheme 16 Splittable v.s. non-splittable • Affects parallelism, crucial for big data • Common splittable compression schemes • LZ4, Snappy, BZip2, LZO, and etc. • GZip is non-splittable • Still common if file sizes are << 1GB • Still applicable for Parquet
  17. 17. Columnar formats Smart, analytics friendly, optimized for big data • Support for nested data types • Efficient data skipping • Column pruning • Min/max statistics based predicate push-down • Nice interoperability • Examples: • Spark SQL built-in support: Apache Parquet and Apache ORC • Newly emerging: Apache CarbonData and Spinach 17
  18. 18. Columnar formats Parquet • Apache Spark default output format • Usually the best practice for Spark SQL • Relatively heavy write path • Worth the time to encode for repeated analytics scenario • Does not support fine grained appending • Not ideal for, e.g., collecting logs • Check out Parquet presentations for more details 18
  19. 19. Semi-structured text formats Sort of structured but not self-describing • Excellent write path performance but slow on the read path • Good candidates for collecting raw data (e.g., logs) • Subject to inconsistent and/or malformed records • Schema inference provided by Spark (for JSON and CSV) • Sampling-based • Handy for exploratory scenario but can be inaccurate • Always specify an accurate schema in production 19
  20. 20. Semi-structured text formats JSON • Supported by Apache Spark out of the box • One JSON object per line for fast file splitting • JSON object: map or struct? • Spark schema inference always treats JSON objects as structs • Watch out for arbitrary number of keys (may OOM executors) • Specify an accurate schema if you decide to stick with maps 20
  21. 21. Semi-structured text formats JSON • Malformed records • Bad records are collected into column _corrupted_record • All other columns are set to null 21
  22. 22. Semi-structured text formats CSV • Supported by Spark 2.x out of the box • Check out the spark-csv package for Spark 1.x • Often used for handling legacy data providers & consumers • Lacks of a standard file specification – Separator, escaping, quoting, and etc. • Lacks of support for nested data types 22
  23. 23. Raw text files 23 Arbitrary line-based text files • Splitting files into lines using • Keep your lines a reasonable size • Keep file size < 1GB if compressed with a non-splittable compression scheme (e.g., GZip) • Handing inevitable malformed data • Use a filter() transformation to drop bad lines, or • Use a map() transformation to fix bad line
  24. 24. Directory layout 24
  25. 25. Partitioning year=2017 genre=classic albums albumsgenre=folk 25 Overview • Coarse-grained data skipping • Available for both persisted tables and raw directories • Automatically discovers Hive style partitioned directories
  26. 26. CREATE TABLE ratings USING PARQUET PARTITIONED BY (year, genre) AS SELECT artist, rating, year, genre FROM music Partitioning SQL DataFrame API spark .table(“music”) .select(’artist, ’rating, ’year, ’genre) .write .format(“parquet”) .partitionBy(’year, ’genre) .saveAsTable(“ratings”) 26
  27. 27. Partitioning year=2017 albums albums genre=classic genre=folk 27 Filter predicates Use simple filter predicates containing partition columns to leverage partition pruning
  28. 28. Partitioning Filter predicates • year = 2000 AND genre = ‘folk’ • year > 2000 AND rating > 3 • year > 2000 OR genre <> ‘rock’ 28
  29. 29. Partitioning 29 Filter predicates • year > 2000 OR rating = 5 • year > rating
  30. 30. Partitioning Avoid excessive partitions • Stress metastore for persisted tables • Stress file system when reading directly from the file system • Suggestions • Avoid using too many partition columns • Avoid using partition columns with too many distinct values – Try hashing the values – E.g., partition by first letter of first name rather than first name 30
  31. 31. Partitioning Using persisted partitioned tables with Spark 2.1+ • Per-partition metadata gets persisted into the metastore • Avoids unnecessary partition discovery (esp. valuable for S3) Check our blog post for more details 31 Scalable partition handling
  32. 32. • Pre-shuffles and optionally pre-sorts the data while writing • Layout information gets persisted in the metastore • Avoids shuffling and sorting when joining large datasets • Only available for persisted tables Bucketing Overview 32
  33. 33. CREATE TABLE ratings USING PARQUET PARTITIONED BY (year, genre) CLUSTERED BY (rating) INTO 5 BUCKETS SORTED BY (rating) AS SELECT artist, rating, year, genre FROM music Bucketing SQL 33 DataFrame ratings .select(’artist, ’rating, ’year, ’genre) .write .format(“parquet”) .partitionBy(“year”, “genre”) .bucketBy(5, “rating”) .sortBy(“rating”) .saveAsTable(“ratings”)
  34. 34. Bucketing In combo with columnar formats • Bucketing • Per-bucket sorting • Columnar formats • Efficient data skipping based on min/max statistics • Works best when the searched columns are sorted 34
  35. 35. Bucketing 35
  36. 36. Bucketing 36 min=0, max=99 min=100, max=199 min=200, max=249
  37. 37. Bucketing In combo with columnar formats Perfect combination, makes your Spark jobs FLY! 37
  38. 38. More tips 38
  39. 39. File size and compaction Avoid small files • Cause excessive parallelism • Spark 2.x improves this by packing small files • Cause extra file metadata operations • Particularly bad when hosted on S3 39
  40. 40. File size and compaction 40 How to control output file sizes • In general, one task in the output stage writes one file • Tune parallelism of the output stage • coalesce(N), for • Reduces parallelism for small jobs • repartition(N), for • Increasing parallelism for all jobs, or • Reducing parallelism of final output stage for large jobs • Still preserves high parallelism for previous stages
  41. 41. True story Customer • Spark ORC Read Performance is much slower than Parquet • The same query took • 3 seconds on a Parquet dataset • 4 minutes on an equivalent ORC dataset 41
  42. 42. True story Me • Ran a simple count(*), which took • Seconds on the Parquet dataset with a handful IO requests • 35 minutes on the ORC dataset with 10,000s of IO requests • Most task execution threads are reading ORC stripe footers 42
  43. 43. True story 43
  44. 44. True story 44 import import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.Path val conf = new Configuration def countStripes(file: String): Int = { val path = new Path(file) val reader = OrcFile.createReader(path, OrcFile.readerOptions(conf)) val metadata = reader.getMetadata metadata.getStripeStatistics.size }
  45. 45. True story 45 Maximum file size: ~15 MB Maximum ORC stripe counts: ~1,400
  46. 46. True story 46 Root cause Malformed (but not corrupted) ORC dataset • ORC readers read the footer first before consuming a strip • ~1,400 stripes within a single file as small as 15 MB • ~1,400 x 2 read requests issued to S3 for merely 15 MB of data
  47. 47. True story 47 Root cause Malformed (but not corrupted) ORC dataset • ORC readers read the footer first before consuming a strip • ~1,400 stripes within a single file as small as 15 MB • ~1,400 x 2 read requests issued to S3 for merely 15 MB of data Much worse than even CSV, not mention Parquet
  48. 48. True story 48 Why? • Tiny ORC files (~10 KB) generated by Streaming jobs • Resulting one tiny ORC stripe inside each ORC file • The footers might take even more space than the actual data!
  49. 49. True story 49 Why? Tiny files got compacted into larger ones using ALTER TABLE ... PARTITION (...) CONCATENATE; The CONCATENATE command just, well, concatenated those tiny stripes and produced larger (~15 MB) files with a huge number of tiny stripes.
  50. 50. True story 50 Lessons learned Again, avoid writing small files in columnar formats • Output files using CSV or JSON for Streaming jobs • For better write path performance • Compact small files into large chunks of columnar files later • For better read path performance
  51. 51. True story 51 The cure Simply read the ORC dataset and write it back using So that stripes are adjusted into more reasonable sizes.
  52. 52. Schema evolution Columns come and go • Never ever change the data type of a published column • Columns with the same name should have the same data type • If you really dislike the data type of some column • Add a new column with a new name and the right data type • Deprecate the old one • Optionally, drop it after updating all downstream consumers 52
  53. 53. Schema evolution Columns come and go Spark built-in data sources that support schema evolution • JSON • Parquet • ORC 53
  54. 54. Schema evolution Common columnar formats are less tolerant of data type mismatch. E.g.: • INT cannot be promoted to LONG • FLOAT cannot be promoted to DOUBLE JSON is more tolerating, though • LONG → DOUBLE → STRING 54
  55. 55. True story Customer Parquet dataset corrupted!!! HALP!!! 55
  56. 56. True story What happened? Original schema • {col1: DECIMAL(19, 4), col2: INT} Accidentally appended data with schema • {col1: DOUBLE, col2: DOUBLE} All files written into the same directory 56
  57. 57. True story What happened? Common columnar formats are less tolerant of data type mismatch. E.g.: • INT cannot be promoted to LONG • FLOAT cannot be promoted to DOUBLE Parquet considered these schemas as incompatible ones and refused to merge them. 57
  58. 58. True story BTW JSON schema inference is more tolerating • LONG → DOUBLE → STRING However • JSON is NOT suitable for analytics scenario • Schema inference is unreliable, not suitable for production 58
  59. 59. True story The cure Correct the schema • Filter out all the files with the wrong schema • Rewrite those files using the correct schema Exhausting because all files are appended into a single directory 59
  60. 60. True story Lessons learned • Be very careful on the write path • Consider partitioning when possible • Better read path performance • Easier to fix the data when something went wrong 60
  61. 61. Recap File formats Directory layout • Partitioning • Bucketing • Compression schemes • Columnar (Parquet, ORC) • Semi-structured (JSON, CSV) • Raw text format 61 Other tips • File sizes and compaction • Schema evolution
  62. 62. UNIFIED ANALYTICS PLATFORM Try Apache Spark in Databricks! • Collaborative cloud environment • Free version (community edition) 6262 DATABRICKS RUNTIME 3.0 • Apache Spark - optimized for the cloud • Caching and optimization layer - DBIO • Enterprise security - DBES Try for free today.
  63. 63. Early draft available for free today! 6363
  64. 64. Thank you Q & A 64