Handling a Large Universe of Stock Price Data in R: Profiling with profvis

Posted on May 22, 2020 by Kris Longmore
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Recently, we wrote about calculating mean rolling pairwise correlations between the constituent stocks of an ETF.

The tidyverse tools dplyr and slider solve this somewhat painful data wrangling operation about as elegantly and intuitively as possible.

Why did you want to do that?

We’re building a statistical arbitrage strategy that relies on indexation-driven trading in the constituents. We wrote about an early foray into this trade – we’re now taking the concepts a bit further.

But what about the problem of scaling it up?

When we performed this operation on the constituents of the XLF ETF, our largest intermediate dataframe consisted of around 3-million rows, easily within the capabilities of modern laptops.

XLF currently holds 68 constituent stocks. So for any day, we have  \frac{68*67}{2} = 2,278 correlations to estimate (67 because we don’t want the diagonal of the correlation matrix, take half as we only need its upper or lower triangle).

We calculated five years of rolling correlations, so we had  5*250*2,278 = 2,847,500 correlations in total.

Piece of cake.

The problem gets a lot more interesting if we consider the SPY ETF and its 500 constituents.

For any day, we’d have  \frac{500*499}{2} = 124,750 correlations to estimate. On five years of data, that’s 5*250*124,750 = 155,937,500 correlations in total.

I tried to do all of that at once in memory on my laptop…and failed.

So our original problem of designing the data wrangling pipeline to achieve our goal has now morphed into a problem of overcoming performance barriers.

There are a number of strategies that could be employed to solve this. So over a series of posts, we’ll explore the concept of writing performant R code via various approaches to solving our problem:

  • Getting more RAM by renting a big virtual machine in the cloud
  • Splitting the data into chunks and doing it sequentially in local memory (RAM and hard disk)
  • We could parallelise the above, say using foreach, but speed isn’t really the issue here, it’s RAM
  • Consider different data structures – data.table, Matrix – which will carry less overhead than a regular data.frame or tibble.
  • Horizontal scaling with the future package
  • R packages for dealing with memory issues: ff, bigmemory, MonetDB.R
  • Doing the calculation in Rcpp, since representing data in C++ carries less overhead than in R
  • Use Spark, a cluster computing platform for farming the problem out to multiple machines
  • Use Dataflow, a serverless batch data processing tool available on commercial cloud providers
  • Use Bigquery, a Google Cloud database for storing and querying massive datasets (there are equivalents on AWS)
  • Use Cloud Run, a Google Cloud managed compute platform for scaling containerised applications

These all have their own tradeoffs, from re-writing code for compatibility reasons (and the additional burden of testing for correctness against the original algorithm), to foregoing interactivity, to operating system compatibility, to cost.

We’ll explore these in some detail over the coming days and weeks.

A Workflow for Performant Code

It’s all too easy to focus on optimising code before you really should. That can be an incredible waste of time, and more than invalidate any speedups you get from your optimisation efforts.

In general, the following steps will mostly prevent you from doing this:

  • Get the code working (we did that in the previous post)
  • Profile (we’ll do that shortly)
  • Fix obvious things, for instance, pre-allocating large objects instead of growing them in a loop
  • Weigh options for optimising code, if required:
    • do nothing
    • implement lapply, or better, vectorisation (noting that it can consume a lot of memory)
    • Rcpp
    • parallelisation
    • bytecode compiler for small speedups
    • some combination of the above

Warm-up: Profiling R Code

Profiling is the process of identifying bottlenecks in code.

Before we even think about optimising our code, we need to know what we should be optimising. Profiling is the detective work that helps you understand where your development time is best spent.

And while premature optimisation is to be avoided, performance does matter.

Bottlenecks in your code might surprise you. We all want to be better programmers – profiling code provides useful lessons and is an opportunity to identify and fix bad practices.

So even if you delay optimising your code (you definitely should delay it), there’s little overhead and lots to be gained from profiling your code as you develop it.

And sometimes, you just have to, in order to fix a critical bottleneck.

In our case, we essentially know where the bottleneck is – it’s the enormous data frame of pairwise correlations that we try to compute in memory. But still, we’ll profile the code to demonstrate how it’s done, and to ensure we don’t have any surprises.

First Step: Timing

Getting simple timings as a basic measure of performance is straightforward.

  • system.time() is useful for timing blocks of code by running them once – but timing one evaluation can be misleading.
  • Rprof() can be used for timing execution of functions and statements.
  • microbenchmark is a de-facto standard among many R users. It provides statistical timing measurements and has some nice plot outputs. There’s also rbenchmark.

We’ll start by timing our code for calculating mean rolling pairwise correlations using microbenchmark.

First, we load our packages and data (you can get the data from our GitHub repository – which if you clone will enable you to run the relevant Rmd document directly). It consists of prices for SPX constituents since 2015; we filter on a flag we added to indicate whether a particular stock was in the index on a particular date:


load(here::here("data", "spxprices_2015.RData"))

spx_prices <- spx_prices %>%
  filter(inSPX ==TRUE)

Next we “functionise” the steps in our pipeline of operations. This will make profiling more straightforward, and the output of microbenchmark easier to interpret:

# calculate returns to each stock
get_returns <- function(df) {
  df %>%
    group_by(ticker) %>%
    arrange(date, .by_group = TRUE) %>%
    mutate(return = close / dplyr::lag(close) - 1) %>%
    select(date, ticker, return)

# full join on date
fjoin_on_date <- function(df) {
  df %>%
    full_join(df, by = "date")

# ditch corr matrix diagonal, one half
wrangle_combos <- function(combinations_df) {
  combinations_df %>%
    ungroup() %>% 
  # drop diagonal 
    filter(ticker.x != ticker.y) %>% 
  # remove duplicate pairs (eg A-AAL, AAL-A)
    mutate(tickers = ifelse(ticker.x < ticker.y, glue("{ticker.x}, {ticker.y}"), glue("{ticker.y}, {ticker.x}"))) %>%
    distinct(date, tickers, .keep_all = TRUE) 

pairwise_corrs <- function(combination_df, period) {
  combination_df %>%
    group_by(tickers) %>%
    arrange(date, .by_group = TRUE) %>%
    mutate(rollingcor = slider::slide2_dbl(
      .x = return.x, 
      .y = return.y, 
      .f = ~cor(.x, .y), 
      .before = period, 
      .complete = TRUE)
      ) %>%
    select(date, tickers, rollingcor)


mean_pw_cors <- function(correlations_df) {
  correlations_df %>%
    group_by(date) %>%
    summarise(mean_pw_corr = mean(rollingcor, na.rm = TRUE))

Now, let’s see what happens if we try to run the pipeline on the full dataset:

returns_df <- get_returns(spx_prices)
combos_df <- fjoin_on_date(returns_df)
wrangled_combos_df <- wrangle_combos(combos_df)
corr_df <- pairwise_corrs(wrangled_combos_df, period = 60)
meancorr_df <- mean_pw_cors(corr_df)

# Error: cannot allocate vector of size 3.7 Gb

I can’t allocate enough RAM to hold one of the dataframes in memory.

I could change R’s memory allocation (by default on Windows I think it’s 4GB) by doing memory.limit(size = new_size), but from experience, I know that simply going large won’t solve this particular problem, at least on my machine.

Now if we ask microbenchmark to time our code for us, we’ll get some insights into where this breaks down.

Admittedly this is something of an awkward use-case – the typical use-case is comparing the speed of different implementations of the same thing, but here we’re using microbenchmark to get insight into the timings of each key step in our pipeline, to infer potential bottlenecks (which may or may not be related to our memory issue, but it’s a decent starting point).

As the process is quite long-running, we only run it twice (the default is 100), measure the output in seconds, and only operate on a subset of our data:

prices_subset <- spx_prices %>% 
  filter(date >= "2019-07-01", date < "2020-01-01")

mb <- microbenchmark(
  returns_df <- get_returns(prices_subset),
  combos_df <- fjoin_on_date(returns_df),
  wrangled_combos_df <- wrangle_combos(combos_df),
  corr_df <- pairwise_corrs(wrangled_combos_df, period = 60),
  meancorr_df <- mean_pw_cors(corr_df),
  times = 2,
  unit = "s",
  control = list(order = "block", warmup = 1)

## Unit: seconds
##                                                        expr         min          lq         mean
##                    returns_df <- get_returns(prices_subset)   0.0493790   0.0493790   0.05453255
##                      combos_df <- fjoin_on_date(returns_df)   2.3088978   2.3088978   2.34896230
##             wrangled_combos_df <- wrangle_combos(combos_df)  54.3862645  54.3862645  55.17421270
##  corr_df <- pairwise_corrs(wrangled_combos_df, period = 60) 262.8221508 262.8221508 267.15088150
##                        meancorr_df <- mean_pw_cors(corr_df)   0.8372799   0.8372799   0.84102875
##        median          uq         max neval cld
##    0.05453255   0.0596861   0.0596861     2 a  
##    2.34896230   2.3890268   2.3890268     2 a  
##   55.17421270  55.9621609  55.9621609     2  b 
##  267.15088150 271.4796122 271.4796122     2   c
##    0.84102875   0.8447776   0.8447776     2 a

The bottleneck is quite obvious: it’s the operation that calculates the rolling pairwise correlations. No surprise there.

If you call boxplot on the output of microbenchmark, you get a nice graphical view of the results:

boxplot(mb, unit = "s", log = FALSE)

plot of chunk unnamed-chunk-6

So now we’ve got some basic insight into which operations represent bottlenecks in our pipeline.
However, we often want to get more detailed information. For instance, microbenchmark only tells us about time, it doesn’t tell us about memory usage – and in this case, running out of RAM is the important thing.

Looking into this requires a different profiling tool. Rprof ships with base R, but recently I’ve been using profvis, which has a highly interpretable graphical output.

Using profvis

profvis is simple to use: just wrap an expression or function call in profvis({...}) and observe the HTML output, which opens in a new tab in R Studio, and which you can save via the prof_output argument.

profvis can handle a block of code:

  returns_df <- get_returns(prices_subset)
  combos_df <- fjoin_on_date(returns_df)
  wrangled_combos_df <- wrangle_combos(combos_df)
  corr_df <- pairwise_corrs(wrangled_combos_df, period = 60)
  meancorr_df <- mean_pw_cors(corr_df)
}, prof_output = 'profile_out.Rprof')

The graphical output shows the time spent on each line of code in milliseconds. The graph is interactive within R Studio – you can zoom and move around to get better views.

You can also see each line of code and the memory allocated and deallocated (negative values), and the time spent on each line:

We can see that the vast majority of time was spent in the pairwise_corrs function, and that it allocated about 18.5GB of memory.

It’s no surprise that this function is our bottleneck, but seeing the RAM usage quantified like that is certainly useful. Remember also that we’re only using a small subset of our data here. Our actual problem is much bigger.

So it’s quite clear that in order to solve this particular problem, we need to find a way around R’s memory limitations with respect to the pairwise_corrs operation.

Finally, we should take a look at the rolling pairwise correlations that we calculated for the subset of our larger problem, since we really like visualisation (and to check that things at least look superficially sensible):

meancorr_df %>%
  na.omit() %>%
  ggplot(aes(x = date, y = mean_pw_corr)) +
    geom_line() +
      x = "Date",
      y = "Mean Pairwise Correlation",
      title = "Rolling Mean Pairwise Correlation",
      subtitle = "SPX Constituents"

plot of chunk unnamed-chunk-8


In this post, we introduced the idea of scaling up our mean rolling pairwise correlation operation to accommodate the constituents of the S&P 500. We listed some options for doing so, noting that they all involve various trade-offs.

Basic profiling indicated that, as expected, the operation that performs the pairwise rolling correlations is the bottleneck, allocating over 18 GB of RAM even on a small subset of the total problem.

Since R computations are by default carried out in-memory, we have a problem. The following posts will explore various solutions.

If you liked this you’ll probably like these too…

How to Calculate Rolling Pairwise Correlations in the Tidyverse

Financial Data Manipulation in dplyr for Quant Traders

How to Run Trading Algorithms on Google Cloud Platform in 6 Easy Steps

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