Using RcppArmadillo with bigmemory

Scott Ritchie — written Jul 25, 2014 — source

The bigmemory package allows users to create matrices that are external to R, stored either in RAM or on disk, allowing them to be bigger than the system RAM, and allowing them to be shared across R sessions.

While these objects are defined by the big.matrix class in R, they are really just wrappers that point to external memory. The actual objects are implemented in C++, thus can be easily manipulated from Rcpp.

Armadillo is a C++ library that provides fast linear algebra functionality. It can be used in conjunction with Rcpp through the RcppArmadillo package.

This example demonstrates how to use the functionality provided by Armadillo on big.matrix objects using Rcpp. To learn how to work with big.matrix objects in Rcpp without using RcppArmadillo see this previous gallery post.

Utilising the functions provided by armadillo simply requires the Rcpp objects and big.matrix objects to be case to the appropriate types that armadillo knows how to work with. To demonstrate this, we again implement the equivalent of the colSums function, but allow the user to specify which columns they want to apply the function to in advance.

// To enable the functionality provided by Armadillo's various macros,
// simply include them before you include the RcppArmadillo headers.
#define ARMA_NO_DEBUG

#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo, BH, bigmemory)]]

using namespace Rcpp;
using namespace arma;

// The following header file provides the definitions for the BigMatrix
// object
#include <bigmemory/BigMatrix.h>

// Bigmemory now accesses Boost headers from the BH package,
// we need to make sure we do so as well in this Rcpp::depends comment.
// Boost headers can generate some warning with the default compilation
// options for R.  To suppress these, we can enable C++11 mode which gets
// us 'long long' types.
//
// If your compiler is to old, just disable / remove the following line
// [[Rcpp::plugins(cpp11)]]


// Implementation of colSums
//
// Because BigMatrix objects can come with four different underlying
// types, we need to split our functionality into a "dispatch" function,
// which makes the appropriate typecasts based on the matrix type, and an
// "implementation" function which does the actual calculations.
//
template <typename T>
Col<T> BigArmaColSums(const Mat<T>& aBigMat, IntegerVector subsetCols) {
  // The functions for subsetting an arma::Mat expect the indices to
  // be in of type 'uvec' (shorthand for 'Col<unsigned int>'), so we
  // need to conver the IntegerVector to that type.
  //
  // We subtract 1 to convert the R indices into C++ indices, since
  // indices in R start at 1, but in C++ they start at 0.
  uvec colidx = as<uvec>(subsetCols) - 1;

  // To subset by columns, we use the .cols method for the arma::Mat
  // class. This allows us to access non-contiguous columns.
  return sum(aBigMat.cols(colidx));
}

// Dispatch function for colSums
//
// We need to write this wrapper to handle the different types used
// when constructing a big.matrix
//
// [[Rcpp::export]]
NumericVector BigArmaColSums(SEXP pBigMat, IntegerVector subsetCols) {
  // First we tell Rcpp that the object we've been given is an external
  // pointer.
  XPtr<BigMatrix> xpMat(pBigMat);

  // First we should make sure that none of the requested columns are
  // outside of the provided matrix. If we let the code access an area
  // of memory it shouldn't, bad things will happen!
  if (is_true(any(subsetCols < 1)) ||
      is_true(any(subsetCols > xpMat->ncol()))) {
    throw std::out_of_range("Some of requested columns are outside of the matrix!");
  }

  // The actual data for the matrix is stored in the matrix() field.
  // This is just a pointer to an array, which is laid out in memory in
  // the column major format. Armadillo matrices are also stored in column
  // major format. We can therefore use the advanced `arma::mat` constructor
  // with `copy_aux_mem` set to `false` to effectively "cast" this memory
  // to an object RcppArmadillo understands.
  //
  // Note that this is an 'unsafe' cast, since we're telling armadillo
  // to use existing memory, rather than to create a new matrix. So we need
  // to be careful that the memory we're telling it to use has the correct
  // dimensions!
  //
  unsigned int type = xpMat->matrix_type();
  // The data stored in the big.matrix can either be represent by 1, 2,
  // 4, or 8 bytes. See the "type" argument in `?big.matrix`.
  if (type == 1) {
    Col<char> colSums = BigArmaColSums(
      arma::Mat<char>((char *)xpMat->matrix(), xpMat->nrow(), xpMat->ncol(), false),
      subsetCols
    );
    return NumericVector(colSums.begin(), colSums.end());
  } else if (type == 2) {
    Col<short> colSums = BigArmaColSums(
      arma::Mat<short>((short *)xpMat->matrix(), xpMat->nrow(), xpMat->ncol(), false),
      subsetCols
    );
    return NumericVector(colSums.begin(), colSums.end());
  } else if (type == 4) {
    Col<int> colSums = BigArmaColSums(
      arma::Mat<int>((int *)xpMat->matrix(), xpMat->nrow(), xpMat->ncol(), false),
      subsetCols
    );
    return NumericVector(colSums.begin(), colSums.end());
  } else if (type == 8) {
    Col<double> colSums = BigArmaColSums(
      arma::Mat<double>((double *)xpMat->matrix(), xpMat->nrow(), xpMat->ncol(), false),
      subsetCols
    );
    return NumericVector(colSums.begin(), colSums.end());
  } else {
    // We should never get here, but it resolves compiler warnings.
    throw Rcpp::exception("Undefined type for provided big.matrix");
  }
}

So lets see how this function performs in comparison to colSums, BigColSums.

library(microbenchmark)
library(bigmemory)
Loading required package: methods
Loading required package: bigmemory.sri
Loading required package: BH

bigmemory >= 4.0 is a major revision since 3.1.2; please see packages
biganalytics and and bigtabulate and http://www.bigmemory.org for more information.
# Lets test the performance on 100 random columns from a 60*1000 matrix.
set.seed(4)
ridx <- sample(1:1000, 100)
m <- matrix(rnorm(60*1000), nrow=60)
bigm <- as.big.matrix(m)

options(width=100) # Make sure output looks ok
microbenchmark(res1 <- colSums(m[,ridx]), res2 <- BigArmaColSums(bigm@address, ridx))
Unit: microseconds
                                       expr   min    lq median    uq     max neval
                 res1 <- colSums(m[, ridx]) 56.24 57.98  59.13 75.12 1068.41   100
 res2 <- BigArmaColSums(bigm@address, ridx) 12.48 13.84  19.53 36.55   61.63   100
# and make sure the results are the same:
all.equal(res1, res2)
[1] TRUE

tags: armadillo  bigmemory  matrix 

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