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High-Performance Advanced Analytics with Spark-Alchemy
Spark has made writing big data pipelines much easier than before. But a lot of effort is required to maintain performant and stable data pipelines in production over time. Did I choose the right type of infrastructure for my application? Did I set the Spark configurations correctly? Can my application keep running smoothly as the volume of ingested data grows over time? How to make sure that my pipeline always finishes on time and meets its SLA?
These questions are not easy to answer even for a handful of jobs, and this maintenance work can become a real burden as you scale to dozens, hundreds, or thousands of jobs. This talk will review what we found to be the most useful piece of information and parameters to look at for manual tuning, and the different options available to engineers who want to automate this work, from open-source tools to managed services provided by the data platform or third parties like the Data Mechanics platform.
1 .High-Performance Analytics with spark-alchemy Sim Simeonov, Founder & CTO, Swoop @simeons / sim at swoop dot com
2 .Improving patient outcomes LEADING HEALTH DATA LEADING CONSUMER DATA • 280M unique US patients • 300M US Consumers • 7 years longitudinal data • 3,500+ consumer attributes • De-identified, HIPAA-safe • De-identified, privacy-safe Claims NPI Data 1 st Party Data Demographics Psychographics Lifestyle ICD 9 or 10, CPT, Attributed to the Proprietary tech to Propertyrecords Animal lover Magazine subscriptions Rx and J codes patient integrate data Internet transactions Fisherman Catalog purchases Petabyte scale privacy-preserving ML/AI
5 .The key to high-performance analytics process fewer rows of data
6 . the most important attribute of a high-performance analytics system is the reaggregatability of its data
7 . count(distinct …) is the bane of high-performance analytics because it is not reaggregatable
9 .Demo system: prescriptions in 2018 • Narrow sample root |-- date: date • 10.7 billion rows / 150Gb |-- generic: string • Small-ish Spark 2.4 cluster |-- brand: string |-- product: string • 80 cores, 600Gb RAM |-- patient_id: long • Delta Lake, fully cached |-- doctor_id: long
10 .select * from prescriptions Generic name Brand name National Drug Code (NDC)
11 .Count scripts, generics & brands by month select to_date(date_trunc("month", date)) as date, count(distinct generic) as generics, count(distinct brand) as brands, count(*) as scripts from prescriptions group by 1 Time: 145 secs 0Gb order by 1 put: 10.7B rows / 1 In b M rows / 1G Shuffle: 39
12 .Divide & conquer decompose aggregate(…) into reaggregate(preaggregate(…)) Do this many times Do this once
13 .Preaggregate by generic & brand by month create table prescription_counts_by_month select to_date(date_trunc("month", date)) as date, generic, brand, count(*) as scripts from prescriptions group by 1, 2, 3
14 .Count scripts, generics & brands by month v2 select to_date(date_trunc("month", date)) as date, count(distinct generic) as generics, count(distinct brand) as brands, count(*) as scripts from prescription_counts_by_month group by 1 r) e: 3 secs (50x faste Tim 0Mb order by 1 pu t: 2.6 M rows / 10 In 0Mb M rows / 10 Shuffle: 2.6
15 .Only 50x faster because of job startup cost select *, raw_count / agg_count as row_reduction from (select count(*) as raw_count from prescriptions) cross join (select count(*) as agg_count from prescription_counts_by_month)
16 .The curse of high cardinality (1 of 2) high row reduction is only possible when preaggregating low cardinality dimensions, such as generic (7K) and brand (20K), but not product (350K) or patient_id (300+M)
17 .The curse of high cardinality (2 of 2) small shuffles are only possible with low cardinality count(distinct …)
18 .Adding a high-cardinality distinct count select to_date(date_trunc("month", date)) as date, count(distinct generic) as generics, count(distinct brand) as brands, count(distinct patient_id) as patients, count(*) as scripts from prescriptions Time: 370 secs :( 1Gb group by 1 put: 10.7B rows / 2 b In 2G order by 1 B rows / 10 Shuffle: 7.5
19 .Maybe approximate counting can help?
20 .Approximate counting, default 5% error select to_date(date_trunc("month", date)) as date, approx_count_distinct(generic) as generics, approx_count_distinct(brand) as brands, approx_count_distinct(patient_id) as patients, count(*) as scripts from prescriptions 1 20 secs (3x faster) group by 1 Time: ows / 21Gb 10 .7B r Input: 7Mb order by 1 : 6K rows / Shuffle
21 .3x faster is not good enough approx_count_distinct() still has to look at every row of data
22 . How do we preaggregate high cardinality data to compute distinct counts?
23 .Divide & conquer using HyperLogLog 1. Preaggregate Create an HLL sketch from data for distinct counts 2. Reaggregate Merge HLL sketches (into HLL sketches) 3. Present Compute cardinality of HLL sketches
24 .HLL in spark-alchemy https://github.com/swoop-inc/spark-alchemy
26 .Preaggregate with HLL sketches create table prescription_counts_by_month_hll select to_date(date_trunc("month", date)) as date, generic, brand, count(*) as scripts, hll_init_agg(patient_id) as patient_ids, from prescriptions group by 1, 2, 3
27 .Reaggregate and present with HLL sketches select to_date(date_trunc("month", date)) as date, count(distinct generic) as generics, count(distinct brand) as brands, hll_cardinality(hll_merge(patient_ids)) as patients, count(*) as scripts from prescription_counts_by_month_hll ter) e: 7 secs (50x fas Tim 0Mb M rows / 20 b group by 1 Inpu t: 2.6 ows / 100M order by 1 ffle: 2.6M r Shu
28 .the intuition behind HyperLogLog
29 .Distribute n items randomly in k buckets * * * E(min) ≅ + ⇒ 𝑛 ≅ /(12+) E(distance) ≅ + more buckets == greater precision