Big Data with Arrow and DuckDB

Approaches to bigger-than-RAM data in R, using Arrow, DuckDB, and a bit of data.table. Presented at R/Medicine 2022

Transcript

1. Using the {arrow} and {duckdb} packages to wrangle Bigger-Than-RAM Medical Datasets of > 60M rows Peter D.R. Higgins, MD, PhD, MSc (CRDSA) University of Michigan
2. Agenda • The motivating problem • Limits of R in speed and RAM • Arrow • DuckDB • Wrangling very large data
3. Starting Point • I usually analyze small-ish datasets • Carefully collected and validated data • 500-1000 rows • 10,000 rows on a big project • But digital data – from CMS or Clinical Data Warehouses can give us MUCH bigger data • > 100M rows easily, often > 50GB – does not fit in an email… • This does not always work well in R
4. The Motivating Problem • A new paper comes out about payments to gastroenterologists with data from OpenPayments (https://www.cms.gov/openpayments)
5. The paper (https://www.gastrojournal.org/article/S0016-5085(22)00647-3/fulltext) • Indirectly suggests that these docs are being paid off by pharma • But a typical “pharma drug talk” pays ~ $2K • Talk about a new drug or device, while audience eats dinner • On weeknights Mon-Thursday • Most academic places no longer allow this • How do the million-dollar-docs do this? $2K * 500 talks? • Are people really giving 500 pharma drug talks per calendar year? • When do they actually do their main job? • Do they ever go home for dinner? Do they travel constantly? • How is this actually possible? (only 208 weekday [M-Th] dinner talk slots per year)? • Something seems fishy here….
6. The Data • CMS (Center for Medicare and Medicaid Services) publishes granular data on every payment from pharma/device companies to physicians • Added other prescribers (NPs, PAs) in 2021 • Around 6GB, 11-12M rows, 75 variables per year
7. The Motivating Problem • My M1 Mac Mini has 16 GB of RAM • Total data on CMS website from 2013-2021 is 94 GB • Format, # of variables changed in 2016, so will ignore 2013-15 • R works on datasets in memory (RAM)
8. Options • Work on 1 year at a time, extract summary data, then pool across years • Slow, clunky • Find a better way
9. First pilot attempts • Read in one year of data (2016) • 11 million rows, 75 variables • Only 6.4 GB • Should work, might be a little slow… • readr::read_csv() is 2-3x faster than read.csv() – let’s use read_csv() • Using read_csv() – 2873.7 seconds ~ 49 minutes – not good • Now I have 2 problems • Speed • RAM capacity
10. Then I Recalled some Advice
11. Speed-reading • Option 1 – the fread() function from {data.table} • data.table::fread() on 2014 data – 93.3 seconds • MUCH better • 30x speed improvement! • Option 2 – the vroom() function from {vroom} • vroom::vroom() on 2014 data – 14.3 min • Better than read_csv() • 3.5x speed improvement – but slower than {data.table} • Works well with dplyr wrangling
12. Lots to Like about {data.table} • Very fast • Syntax a bit icky to read (though often worth it) • Example of filter, group_by, summarise: • data2019_gi <- data2019[Covered_Recipient_Type == "Covered Recipient Physician" & Physician_Primary_Type == "Medical Doctor" & Physician_Specialty == "Allopathic & Osteopathic Physicians|Internal Medicine|Gastroenterology", .(total_pmt = sum(Total_Amount_of_Payment_USDollars)), keyby = "Physician_Profile_ID"]
13. Data.table package • For sheer speed, definitely worth using. • Syntax takes some time to master • The {dtplyr} package is a good back-end work- around if you are familiar with dplyr verbs • But it does not address the bigger-than-RAM data problem (nor does {vroom})
14. Data on Disk vs. Data in RAM • Data on Disk • Easy to get a big disk – Terabytes now • Used to be slow (physical platters) – now SSD, much faster • Though 16TB SSD is still pretty pricey ~ $1800 • Need “scratch disk” space for writing intermediate data • Standard strategy of SAS • Data in RAM • Was much faster than disc – still faster, but not as dramatic with SSD drives • Limited to gigabytes, not terabytes • Standard vs biggest Mac configuration – 8 GB vs 128 GB • With big data, can often have insufficient RAM • Standard strategy of R
15. Just buy more RAM… • Not unreasonable • RAM is ~ $5-10 per GB • But M1 Mac mini can only address 16GB • Would need a new computer… C’mon, just buy a new computer… I've got a tiny System 76 Linux system with 12 cores and 32GB RAM that would probably work Not today… though it is tempting. And the datasets just keep getting bigger…
16. How to Wrangle Bigger-Than-RAM data in R? • Search Twitter!
17. Twitter Suggests… • The {arrow} package • Uses a data structure that works across languages (R, Py, Julia, etc.) • Very efficient • But can it read big data fast?
18. Speed-reading • Option 3 – the read_csv_arrow() function from {arrow} for single files • Arrow::read_csv_arrow() on 2014 data – 68.8 sec – very nice! • Encouraging on the speed front, slightly faster than {data.table}.
19. What is Arrow? • The {arrow} R package is part of the Apache Arrow project • Relies on the Arrow C++ library • Uses a standardized columnar memory format , organized for efficient analytic operations on modern hardware • Enables zero-copy data sharing between R and Python • A cross-language development platform for in-memory data • Available in C, C++, C#, Go, Java, JavaScript, Julia, MATLAB, Python, R, Ruby, and Rust.
20. Columnar is Fast • The Apache Arrow format “allows computational routines to maximize their efficiency when scanning and iterating over large chunks of data”. • The contiguous columnar layout enables vectorization using the latest SIMD (Single Instruction, Multiple Data) operations included in modern processors. • Like parallel processing with multiple cores, but at a micro (vector) level The SIMD instruction set is a feature available in Pentium+ Intel, AMD, and Apple Silicon chips
21. Speed-Wrangling • Comparison of basic filter-group_by-summarize workflow • 11.7 M rows, 6.4 GB, 2016 data Approach Seconds Pure data.table 0.3 seconds data.table with {dtplyr} translation 1.5 seconds Arrow with dplyr verbs 4.7 seconds Vroom with dplyr verbs Way too long to measure Currently supported {dplyr} verbs in Arrow filter select mutate, transmute rename, relocate arrange Use collect() before group_by() or summarize() or other dplyr verbs • {data.table} is freaky fast • {dtplyr} translated {data.table} is almost as fast • {arrow} is in the same ballpark, though slower • Everyday {dplyr} is MUCH slower for big data
22. Side Benefit of Multi-Lingual Arrow • Arrow-formatted data can be used (unmodified) by many languages • Collaboration the old way – collaborator has a useful Python routine • Copy data from R to Python format • Run Python routine • Copy results back to R format • With {arrow} – multilingual with less friction • Insert a Python chunk into Rmd (or Qmd) • Run routine – Python can read R results in arrow format • R can read Python results in arrow format, no copying of data
23. But what about the Bigger-Than-RAM problem? • Can {arrow} handle this? • Arrow 6.0+ can analyze and process multi-file, larger-than-memory datasets • {disk.frame} soft-deprecated in favor of {arrow} • You can manipulate and analyze Arrow data with dplyr verbs • Not clear if you can {arrow} x {data.table} ?? • [TODO: test with dtplyr, is speed affected?]
24. Let’s try it • The files • The code to create a dataset on disk • All 6 data files in one folder (data_years) dataset <- arrow::open_dataset("data_years", format = 'csv’) |> arrow::to_duckdb() • Data stored as columnar (arrow) • Then stored as database on disk Year GB 2016 6.4 2017 6.3 2018 6.0 2019 5.7 2020 3.1 2021 6.3 Total 33.8 GB >> 16 GB of RAM
25. What is duckDB? • Designed to be used as an embeddable on-the-fly database (like SQLite) • No databasse setup required – just load the {duckdb} library and go • DuckDB is an OLAP database – Online Analytical Processing • Columnar structure, organized by field/variable • Designed to make complex queries fast >> making data lookup tables fast (OLTP) • Takes advantage of SIMD (single instruction, multiple data) instruction set to achieve speed-up with modern CPUs
26. OLAP vs OLTP Databases Online Analytical Processing • Optimized for interactive queries • Columnar structure • Keeps data for each variable together • Takes advantage of SIMD (Single Instruction Multiple Data) processing Online Transactional Processing • Optimized for fast lookup • Row structure
27. Database on disk? What is that? • Stored as a List, not a data frame • Structure is mostly pointers R> object.size(ds_all) 153432 bytes • Not 33.8 GB in RAM – only 153KB
28. Now you can wrangle with {dplyr} • {arrow} has a {dplyr} back-end • Can write code with many (not all) dplyr verbs • Translated into arrow with duckDB • Partitions data into RAM-sized chunks • Runs calculations on each partition • Can wrangle – here for a descriptive data summary • This produces no result (yet) ds_all %>% filter(Physician_Specialty == "Gastroenterology") |> group_by(Physician_First_Name, Physician_Last_Name) |> summarize(total_usd = sum(Total_Amount_of_Payment_US Dollars))
29. Collecting your partitioned results with collect() ds_all %>% filter(Physician_Specialty == "Gastroenterology") |> collect() |> group_by(Physician_First_Name, Physician_Last_Name) |> summarize(total_usd = sum(Total_Amount_of_Payment_USDo llars)) • Add the collect() function to the end of your dplyr verbs to collect the results • This is the only visible indication of what is going on • Disk database partitioning and analysis is largely abstracted away, and auto-magically happens under the hood with {arrow} and {duckdb}
30. Nice Tabular Results • Processes 66 M rows (34GB) outside of RAM in 71 sec • A task that was not possible in 16 GB of RAM with other tools
31. • Did 50 people actually give 250 drug talks per year? • No, nearly all of the top 50 in payments were from royalties from patents • #1 Greater than $1M per year in royalties for John Fordtran • #2 – royalties for Bennett Roth $500K - $1M per year Back to the Question
32. Mr. Golytely – Dr. John Satterfield Fordtran
33. The Roth Net – Dr. Bennett Roth
34. There’s Always That One Guy • (Arthur) Asher Kornbluth • $495K income in 2018 • A total of 504 payments from 8 companies • No royalties; a mix of drug talks ($342K), consulting ($50K), food/beverage ($8K), travel/lodging ($50K), and advisory boards $44K) • Note that there were 78 others with > $500K over 6y without royalties
35. Alternatives to Bigger-Than-RAM Wrangling • Buy more RAM • Though you seem to always end up trying to keep up with bigger and bigger data • Rent some RAM (short-term) in the Cloud • If you have access to a local (often University) cluster • Or an Amazon Web Services S3, Google, or Azure instance • Walk through of RStudio in AWS in this video playlist • https://www.youtube.com/playlist?list=PL0hSJrxggIQoer5TwgW6qWHnVJfqzcX3l • Key videos for RStudio – 12 and 13 in the playlist
36. Examples of AWS Rental Options Name Cores GB of RAM Type of Virtual Machine R & RStudio Amazon Machine Images (AMI) Available
37. Take Home Points - Speed • {dplyr} read_csv() is 2-3x faster than the base read.csv() • But it gets slooow with 10M+ rows of data • Faster options for reading in big data • {vroom} vroom() • {data.table} fread() • {arrow} read_csv_arrow() • Faster options for wrangling big data • {data.table} • {dtplyr} (front-end for data.table} • {arrow} with dplyr back-end (only for arrow data structures)
38. Take Home Points – Bigger-Than-RAM data • SAS folks have owned bragging rights for years with data on disk • “Only SAS can process bigger-than-RAM datasets!” • Now with {arrow} and {duckdb}, R can do this also in 4 easy steps: 1. Read in as arrow-structured data, with read_csv_arrow() or with arrow::open_dataset() for multiple files in a folder 2. Convert your data to a duckDB dataset on disk with to_duckdb() 3. Wrangle as usual with {dplyr} syntax (most verbs) 4. Remember to collect() your results!
39. Thank You • Questions?