These patches to the R source for improving speed were written by Radford M. Neal, Sept. 2010 (first version 3 Sept., revised 7 Sept.) See the README file for how to install them. Below, I describe these patches (in alphabetical order, except for patch-subscript, now split off from patch-vec-subset), indicate what improvement they produce, and also mention any potential issues with using the patch, and bugs that the patches incidently fix. The timing improvements discussed below are what is obtained by applying each patch individually, on an Intel system running Ubuntu Linux with Gcc version 4.2.4. The total improvement from all patches is much bigger, though in a few instances a patch can diminish the effect of another patch, by reducing the magnitude of the inefficiencies that the other patch eliminates. Note though, that the percentage improvement for a given absolute improvement gets bigger as when other patches reduce overall time. For r52822, the total time for all tests in the accompanying speed test suite is 674 seconds. This is reduced to 487 seconds with all patches applied, a reduction of 28%. Particular R programs will, of course, see widely varying reductions depending on what operations they mostly do. patch-dollar Speeds up access to lists, pairlists, and environments using the $ operator. The speedup comes mainly from avoiding the overhead of calling DispatchOrEval if there are no complexities, from passing on the field to extract as a symbol, or a name, or both, as available, and then converting only as necessary, from simplifying and inlining the pstrmatch procedure, and from not translating string multiple times. Relevant timing test script: test-dollar.r This test shows about a 40% decrease in the time needed to extract elements of lists and environments. Changes unrelated to speed improvement: A small error-reporting bug is fixed, illustrated by the following output with r52822: > options(warnPartialMatchDollar=TRUE) > pl <- pairlist(abc=1,def=2) > pl$ab [1] 1 Warning message: In pl$ab : partial match of 'ab' to '' Some code is changed at the end of R_subset3_dflt because it seems to be more correct, as discussed in code comments. patch-evalList Speeds up a large number of operations by avoiding allocation of an extra CONS cell in the procedures for evaluating argument lists. Relevant timing test scripts: all of them, but will look at test-em.r On test-em.r, the speedup from this patch is about 5%. patch-fast-base Speeds up lookup of symbols defined in the base environment, by flagging symbols that have a base environment definition recorded in the global cache. This allows the definition to be retrieved quickly without looking in the hash table. Relevant timing test scripts: all of them, but will look at test-em.r On test-em.r, the speedup from this patch is about 3%. Issue: This patch uses the "spare" bit for the flag. This bit is misnamed, since it is already used elsewhere (for closures). It is possible that one of the "gp" bits should be used instead. The "gp" bits should really be divided up for faster access, and so that their present use is apparent in the code. In case this use of the "spare" bit proves unwise, the patch code is conditional on FAST_BASE_CACHE_LOOKUP being defined at the start of envir.r. patch-fast-spec Speeds up lookup of function symbols that begin with a character other than a letter or ".", by allowing fast bypass of non-global environments that do not contain (and have never contained) symbols of this sort. Since it is expected that only functions will be given names of this sort, the check is done only in findFun, though it could also be done in findVar. Relevant timing test scripts: all of them, but will look at test-em.r On test-em.r, the speedup from this patch is about 8%. Issue: This patch uses the "spare" bit to flag environments known to not have symbols starting with a special character. See remarks on patch-fast-base. In case this use of the "spare" bit proves unwise, the patch code is conditional on FAST_SPEC_BYPASS being defined at the start of envir.r. patch-for Speeds up for loops by not allocating new space for the loop variable every iteration, unless necessary. Relevant timing test script: test-for.r This test shows a speedup of about 5%. Change unrelated to speed improvement: Fixes what I consider to be a bug, in which the loop clobbers a global variable, as demonstrated by the following output with r52822: > i <- 99 > f <- function () for (i in 1:3) { print(i); if (i==2) rm(i); } > f() [1] 1 [1] 2 [1] 3 > print(i) [1] 3 patch-matprod Speeds up matrix products, including vector dot products. The speed issue here is that the R code checks for any NAs, and does the multiply in the matprod procedure (in array.c) if so, since BLAS isn't trusted with NAs. If this check takes about as long as just doing the multiply in matprod, calling a BLAS routine makes no sense. Relevant time test script: test-matprod.r With no external BLAS, this patch speeds up long vector-vector products by a factor of about six, matrix-vector products by a factor of about three, and some matrix-matrix products by a factor of about two. Issue: The matrix multiply code in matprod using an LDOUBLE (long double) variable to accumulate sums, for improved accuracy. On a SPARC system I tested on, operations on long doubles are vastly slower than on doubles, so that the patch produces a large slowdown rather than an improvement. This is also an issue for the "sum" function, which also uses an LDOUBLE to accumulate the sum. Perhaps an ordinarly double should be used in these places, or perhaps the configuration script should define LDOUBLE as double on architectures where long doubles are extraordinarily slow. Due to this issue, not defining MATPROD_CAN_BE_DONE_HERE at the start of array.c will disable this patch. patch-parens Speeds up parentheses by making "(" a special operator whose argument is not evaluated, thereby bypassing the overhead of evalList. Also slightly speeds up curly brackets by inlining a function that is stylistically better inline anyway. Relevant test script: test-parens.r In the parens part of test-parens.r, the speedup is about 9%. patch-protect Speeds up numerous operations by making PROTECT, UNPROTECT, etc. be mostly macros in the files in src/main. This takes effect only for files that include Defn.h after defining the symbol USE_FAST_PROTECT_MACROS. With these macros, code of the form v = PROTECT(...) must be replaced by PROTECT(v = ...). Relevant timing test scripts: all of them, but will look at test-em.r On test-em.r, the speedup from this patch is about 9%. patch-save-alloc Speeds up some binary and unary arithmetic operations by, when possible, using the space holding one of the operands to hold the result, rather than allocating new space. Though primarily a speed improvement, for very long vectors avoiding this allocation could avoid running out of space. Relevant test script: test-complex-expr.r On this test, the speedup is about 5% for scalar operands and about 8% for vector operands. Issues: There are some tricky issues with attributes, but I think I got them right. This patch relies on NAMED being set correctly in the rest of the code. In case it isn't, the patch can be disabled by not defining AVOID_ALLOC_IF_POSSIBLE at the top of arithmetic.c. patch-square Speeds up a^2 when a is a long vector by not checking for the special case of an exponent of 2 over and over again for every vector element. Relevant test script: test-square.r The time for squaring a long vector is reduced in this test by a factor of more than five. patch-sum-prod Speeds up the "sum" and "prod" functions by not checking for NA when na.rm=FALSE, and other detailed code improvements. Relevant test script: test-sum-prod.r For sum, the improvement is about a factor of 2.5 when na.rm=FALSE, and about 10% when na.rm=TRUE. Issue: See the discussion of patch-matprod regarding LDOUBLE. There is no change regarding this issue due to this patch, however. patch-transpose Speeds up the transpose operation (the "t" function) from detailed code improvements. Relevant test script: test-transpose.r The improvement for 200x60 matrices is about a factor of two. There is little or no improvement for long row or column vectors. patch-vec-arith Speeds up arithmetic on vectors of the same length, or when on vector is of length one. This is done with detailed code improvements. Relevant test script: test-vec-arith.r On long vectors, the +, -, and * operators are sped up by about 20% when operands are the same length or one operand is of length one. Rather mysteriously, when the operands are not length one or the same length, there is about a 20% increase in time required, though this may be due to some strange C optimizer peculiarity or some strange cache effect, since the C code for this is the same as before, with negligible additional overhead getting to it. Regardless, this case is much less common than equal lengths or length one. There is little change for the / operator, which is much slower than +, -, or *. patch-vec-subset Speeds up extraction of subsets of vectors or matrices (eg, v[10:20] or M[1:10,101:110]). This is done with detailed code improvements. Relevant test script: test-vec-subset.r There are lots of tests in this script. The most dramatic improvement is for extracting many rows and columns of a large array, where the improvement is by about a factor of four. Extracting many rows from one column of a matrix is sped up by about 30%. Changes unrelated to speed improvement: Fixes two latent bugs where the code incorrectly refers to NA_LOGICAL when NA_INTEGER is appropriate and where LOGICAL and INTEGER types are treated as interchangeable. These cause no problems at the moment, but would if representations were changed. patch-subscript (Formerly part of patch-vec-subset) This patch also speeds up extraction, and also replacement, of subsets of vectors or matrices, but focuses on the creation of the indexes rather than the copy operations. Often avoids a duplication (see below) and eliminates a second scan of the subscript vector for zero subscripts, folding it into a previous scan at no additional cost. Relevant test script: test-vec-subset.r Speeds up some operations with scalar or short vector indexes by about 10%. Speeds up subscripting with a longer vector of positive indexes by about 20%. Issues: The current code duplicates a vector of indexes when it seems unnecessary. Duplication is for two reasons: to handle the situation where the index vector is itself being modified in a replace operation, and so that any attributes can be removed, which is helpful only for string subscripts, given how the routine to handle them returns information via an attribute. Duplication for the second reasons can easily be avoided, so I avoided it. The first reason for duplication is sometimes valid, but can usually be avoided by first only doing it if the subscript is to be used for replacement rather than extraction, and second only doing it if the NAMED field for the subscript isn't zero. I also removed two layers of procedure call overhead (passing seven arguments, so not trivial) that seemed to be doing nothing. Probably it used to do something, but no longer does, but if instead it is preparation for some future use, then removing it might be a mistake.