Benchmarking data.table

2024-02-26

This document is meant to guide on measuring performance of data.table. Single place to document best practices and traps to avoid.

1. fread: clear caches

Ideally each fread call should be run in fresh session with the following commands preceding R execution. This clears OS cache file in RAM and HD cache.

free -g
sudo sh -c 'echo 3 >/proc/sys/vm/drop_caches'
sudo lshw -class disk
sudo hdparm -t /dev/sda

When comparing fread to non-R solutions be aware that R requires values of character columns to be added to R’s global string cache. This takes time when reading data but later operations benefit since the character strings have already been cached. Consequently, in addition to timing isolated tasks (such as fread alone), it’s a good idea to benchmark the total time of an end-to-end pipeline of tasks such as reading data, manipulating it, and producing final output.

2. subset: threshold for index optimization on compound queries

Index optimization for compound filter queries will be not be used when cross product of elements provided to filter on exceeds 1e4 elements.

DT = data.table(V1=1:10, V2=1:10, V3=1:10, V4=1:10)
setindex(DT)
v = c(1L, rep(11L, 9))
length(v)^4               # cross product of elements in filter
#[1] 10000                # <= 10000
DT[V1 %in% v & V2 %in% v & V3 %in% v & V4 %in% v, verbose=TRUE]
#Optimized subsetting with index 'V1__V2__V3__V4'
#on= matches existing index, using index
#Starting bmerge ...done in 0.000sec
#...
v = c(1L, rep(11L, 10))
length(v)^4               # cross product of elements in filter
#[1] 14641                # > 10000
DT[V1 %in% v & V2 %in% v & V3 %in% v & V4 %in% v, verbose=TRUE]
#Subsetting optimization disabled because the cross-product of RHS values exceeds 1e4, causing memory problems.
#...

3. subset: index aware benchmarking

For convenience data.table automatically builds an index on fields you use to subset data. It will add some overhead to first subset on particular fields but greatly reduces time to query those columns in subsequent runs. When measuring speed, the best way is to measure index creation and query using an index separately. Having such timings it is easy to decide what is the optimal strategy for your use case. To control usage of index use following options:

options(datatable.auto.index=TRUE)
options(datatable.use.index=TRUE)

Two other options control optimization globally, including use of indices:

options(datatable.optimize=2L)
options(datatable.optimize=3L)

options(datatable.optimize=2L) will turn off optimization of subsets completely, while options(datatable.optimize=3L) will switch it back on. Those options affect many more optimizations and thus should not be used when only control of indices is needed. Read more in ?datatable.optimize.

4. by reference operations

When benchmarking set* functions it only makes sense to measure the first run. These functions update their input by reference, so subsequent runs will use the already-processed data.table, biasing the results.

Protecting your data.table from being updated by reference operations can be achieved using copy or data.table:::shallow functions. Be aware copy might be very expensive as it needs to duplicate whole object. It is unlikely we want to include duplication time in time of the actual task we are benchmarking.

5. try to benchmark atomic processes

If your benchmark is meant to be published it will be much more insightful if you will split it to measure time of atomic processes. This way your readers can see how much time was spent on reading data from source, cleaning, actual transformation, exporting results. Of course if your benchmark is meant to present to present an end-to-end workflow, then it makes perfect sense to present the overall timing. Nevertheless, separating out timing of individual steps is useful for understanding which steps are the main bottlenecks of a workflow. There are other cases when atomic benchmarking might not be desirable, for example when reading a csv, followed by grouping. R requires populating R’s global string cache which adds extra overhead when importing character data to an R session. On the other hand, the global string cache might speed up processes like grouping. In such cases when comparing R to other languages it might be useful to include total timing.

6. avoid class coercion

Unless this is what you truly want to measure you should prepare input objects of the expected class for every tool you are benchmarking.

7. avoid microbenchmark(..., times=100)

Repeating a benchmark many times usually does not give the clearest picture for data processing tools. Of course, it makes perfect sense for more atomic calculations, but this is not a good representation of the most common way these tools will actually be used, namely for data processing tasks, which consist of batches of sequentially provided transformations, each run once. Matt once said:

I’m very wary of benchmarks measured in anything under 1 second. Much prefer 10 seconds or more for a single run, achieved by increasing data size. A repetition count of 500 is setting off alarm bells. 3-5 runs should be enough to convince on larger data. Call overhead and time to GC affect inferences at this very small scale.

This is very valid. The smaller time measurement is the relatively bigger noise is. Noise generated by method dispatch, package/class initialization, etc. Main focus of benchmark should be on real use case scenarios.

8. multithreaded processing

One of the main factors that is likely to impact timings is the number of threads available to your R session. In recent versions of data.table, some functions are parallelized. You can control the number of threads you want to use with setDTthreads.

setDTthreads(0)    # use all available cores (default)
getDTthreads()     # check how many cores are currently used

9. inside a loop prefer set instead of :=

Unless you are utilizing index when doing sub-assign by reference you should prefer set function which does not impose overhead of [.data.table method call.

DT = data.table(a=3:1, b=letters[1:3])
setindex(DT, a)

# for (...) {                 # imagine loop here

  DT[a==2L, b := "z"]         # sub-assign by reference, uses index
  DT[, d := "z"]              # not sub-assign by reference, not uses index and adds overhead of `[.data.table`
  set(DT, j="d", value="z")   # no `[.data.table` overhead, but no index yet, till #1196

# }

10. inside a loop prefer setDT instead of data.table()

As of now data.table() has an overhead, thus inside loops it is preferred to use as.data.table() or setDT() on a valid list.