Posts filed under ‘Statistics – Computing’

Subset replacement in pqR: Now faster and better

The latest version of pqR that I just released uses a new way of implementing subset replacement operations — such as a[i]<-1 or L$M[1:100,i]<-v. The new approach is much faster, and eliminates some strange behaviour of the previous approach.

This change affects only interpreted code. The bytecode compiler (available since R-2.13.0) introduced a different mechanism, which is also faster than the previous approach used by the interpreter (though it still has some of the strange behaviour). This faster mechanism was one of the main reasons for byte-compiled code to be faster than interpreted code (although it would have been possible to use the new mechanism in the interpreter as well). With pqR’s new implementation of subset replacement, this advantage of byte-compiled over interpreted code is much reduced.

In addition to being faster, pqR’s new approach is also more coherent than the previous approach (still current in the interpreter for R Core releases to at least R-3.1.1), which despite its gross inefficiency and confused semantics has remained essentially unchanged for 18 years. Unfortunately, the new approach in pqR is not as coherent as it might be, because past confusion has resulted in some packages doing “wrong” things, which have to be accommodated, as least in the short term.

(more…)

2014-10-13 at 11:01 pm 7 comments

New version of pqR with faster variable lookup, faster subset replacement, and more

I’ve released a new version, pqR-2014-09-30, of my speedier, “pretty quick”, implementation of R, with some major performance improvements, and some features from recent R Core versions. It also has fixes for bugs (some also in R-3.1.1) and installation glitches.

Details are in pqR NEWS. Here I’ll highlight some of the more interesting improvements.
(more…)

2014-10-06 at 4:38 pm 1 comment

New release of pqR, with a curated repository

I have released a new version, pqR-2014-06-19, of my speedier, “pretty quick”, implementation of R.  This and the previous release (pqR-2014-02-23) are maintenance releases, with bug fixes, improved documentation, and better test procedures.

The result is that pqR now works with a large collection of 3438 packages.

(more…)

2014-06-21 at 10:59 pm 2 comments

Inaccurate results from microbenchmark

The microbenchmark package is a popular way of comparing the time it takes to evaluate different R expressions — perhaps more popular than the alternative of just using system.time to see how long it takes to execute a loop that evaluates an expression many times. Unfortunately, when used in the usual way, microbenchmark can give inaccurate results.

The inaccuracy of microbenchmark has two main sources — first, it does not correctly allocate the time for garbage collection to the expression that is responsible for it, and second, its summarizes the results by the median time for many repetitions, when the mean is what is needed. The median and mean can differ drastically, because just a few of the repetitions will include time for a garbage collection. These flaws can result in comparisons being reversed, with the expression that is actually faster looking slower in the output of microbenchmark. (more…)

2014-02-02 at 2:31 pm 8 comments

New version of pqR, now with task merging

 
I’ve now released pqR-2013-12-29, a new version of my speedier implementation of R.  There’s a new website, pqR-project.org, as well, and a new logo, seen here.

The big improvement in this version is that vector operations are sped up using task merging.

With task merging, several arithmetic operations on a vector may be merged into a single operation, reducing the time spent on memory stores and fetches of intermediate results. I was inspired to add task merging to pqR by Renjin and Riposte (see my post here and the subsequent discussion). (more…)

2014-01-01 at 10:11 pm 4 comments

Deferred evaluation in Renjin, Riposte, and pqR

The previously sleepy world of R implementation is waking up.  Shortly after I announced pqR, my “pretty quick” implementation of R, the Renjin implementation was announced at UserR! 2013.  Work also proceeds on Riposte, with release planned for a year from now. These three implementations differ greatly in some respects, but interestingly they all try to use multiple processor cores, and they all use some form of deferred evaluation.

Deferred evaluation isn’t the same as “lazy evaluation” (which is how R handles function arguments). Deferred evaluation is purely an implementation technique, invisible to the user, apart from its effect on performance. The idea is to sometimes not do an operation immediately, but instead wait, hoping that later events will allow the operation to be done faster, perhaps because a processor core becomes available for doing it in another thread, or perhaps because it turns out that it can be combined with a later operation, and both done at once.

Below, I’ll sketch how deferred evaluation is implemented and used in these three new R implementations, and also comment a bit on their other characteristics. I’ll then consider whether these implementations might be able to borrow ideas from each other to further expand the usefulness of deferred evaluaton. (more…)

2013-07-24 at 11:03 pm 17 comments

Fixing R’s NAMED problems in pqR

In R, objects of most types are supposed to be treated as “values”, that do not change when other objects change. For instance, after doing the following:

  a <- c(1,2,3)
  b <- a
  a[2] <- 0

b[2] is supposed to have the value 2, not 0. Similarly, a vector passed as an argument to a function is not normally changed by the function. For example, with b as above, calling f(b), will not change b even if the definition of f is f <- function (x) x[2] <- 0.

This semantics would be easy to implement by simply copying an object whenever it is assigned, or evaluated as the argument to a function. Unfortunately, this would be unacceptably slow. Think, for example, of passing a 10000 by 10000 matrix as an argument to a little function that just accesses a few elements of the matrix and returns a value computed from them.  The copying would take far longer than the computation within the function, and the extra 800 Megabytes of memory required might also be a problem.

So R doesn’t copy all the time.  Instead, it maintains a count, called NAMED, of how many “names” refer to an object, and copies only when an object that needs to be modified is also referred to by another name.  Unfortunately, however, this scheme works rather poorly.  Many unnecessary copies are still made, while many bugs have arisen in which copies aren’t made when necessary. I’ll talk about this more below, and discuss how pqR has made a start at solving these problems. (more…)

2013-07-02 at 9:44 pm 3 comments

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