Neonira
by Neonira

Categories

  • programming
  • EN

Tags

  • R
  • programming

I had to ingest some medium to high volume data from official French government sites, and would like to share my return on experience. Data ingestion here is solved globally, without any other consideration than maximum reduced time for implementation, result reproducibility and raw speed.

Data can be downloaded from following open data French official site www.data.gouv.fr.

For information and demonstration purpose, I will just focus on the two following files.

number of lines number of columns size in bytes filename
21_190_053 33 2_723_590_237 StockUniteLegale_utf8.csv
29_818_083 48 5_224_371_093 StockEtablissement_utf8.csv

I wonder if R will be able to handle those files directly without any data chuncking or other file transformations prior to ingest data.

Typical R CLI sequence will be

library('wyz.time.ops')
fn <- '/data/data.gouv.fr/01-data-source/unites-legales/StockUniteLegale_utf8.csv'
r <- recordTime(read.csv)(fn, header = TRUE, stringsAsFactors = FALSE)
cat('Timing', r$timing$human, '\n')

My expectations

Frankly, I am doubtful of R ability to handle correctly these files under such a direct approach. I expect many causes of fatal error may occur and stop the processing prior its normal ending: memory error, stack overflow, read error, …

All trials are executed with R 3.6.3 on a single Linux machine with following configuration

Let’s proceed to some trials and see what happens.

File StockUniteLegale_utf8.csv

It works!! Very surprised indeed. Was expecting error and much longer time to get a result. Here velocity exceed 49000 lines per seconds.

Replaying same test on identical conditions, fresh start of R studio, same libraries and options loaded, and same machine conditions, I got some variability in time results, ranging from 403 to 498 seconds. Velocity is therefore very variable, and I have no clear and reliable idea of main causes for such behavior garbage collection?.

File StockEtablissement_utf8.csv

This file is nearly twice as large as previous one. Results are mixed. It sometimes leads to a result and sometime to a failure R session aborption. I have not been able to identify root cause of such deviance.

Best performance achieved is 706 seconds, that is a velocity of more than 42000 lines per second, comparable to performance of some trials for previous file.

Results

I was expecting failure in both cases, and got partial failure on second case only, and its root cause is not clearly identified.

Globally, quite impressed by the results, as I was clearly not expecting such processing velocity level with this very direct and straightforward approach.

As a rule of thumb, 40000 lines per second is a useful metric to know to forecast time for CSV data ingestion.

R is impressive!