Jonathan, On some filesystems (e.g. NTFS, see below) it is possible to create 'sparse' memory-mapped files, i.e. reserving the space without the cost of actually writing initial values. Package 'ff' does this automatically and also allows to access the file in parallel. Check the example below and see how big file creation is immediate. Jens Oehlschlägel > library(ff) > library(snowfall) > ncpus <- 2 > n <- 1e8 > system.time( + x <- ff(vmode="double", length=n, filename="c:/Temp/x.ff") + ) User System verstrichen 0.01 0.00 0.02 > # check finalizer, with an explicit filename we should have a 'close' finalizer > finalizer(x) [1] "close" > # if not, set it to 'close' inorder to not let slaves delete x on slave shutdown > finalizer(x) <- "close" > sfInit(parallel=TRUE, cpus=ncpus, type="SOCK") R Version: R version 2.15.0 (2012-03-30) snowfall 1.84 initialized (using snow 0.3-9): parallel execution on 2 CPUs. > sfLibrary(ff) Library ff loaded. Library ff loaded in cluster. Warnmeldung: In library(package = "ff", character.only = TRUE, pos = 2, warn.conflicts = TRUE, : 'keep.source' is deprecated and will be ignored > sfExport("x") # note: do not export the same ff multiple times > # explicitely opening avoids a gc problem > sfClusterEval(open(x, caching="mmeachflush")) # opening with 'mmeachflush' inststead of 'mmnoflush' is a bit slower but prevents OS write storms when the file is larger than RAM [[1]] [1] TRUE [[2]] [1] TRUE > system.time( + sfLapply( chunk(x, length=ncpus), function(i){ + x[i] <- runif(sum(i)) + invisible() + }) + ) User System verstrichen 0.00 0.00 30.78 > system.time( + s <- sfLapply( chunk(x, length=ncpus), function(i) quantile(x[i], c(0.05, 0.95)) ) + ) User System verstrichen 0.00 0.00 4.38 > # for completeness > sfClusterEval(close(x)) [[1]] [1] TRUE [[2]] [1] TRUE > csummary(s) 5% 95% Min. 0.04998 0.95 1st Qu. 0.04999 0.95 Median 0.05001 0.95 Mean 0.05001 0.95 3rd Qu. 0.05002 0.95 Max. 0.05003 0.95 > # stop slaves > sfStop() Stopping cluster > # with the close finalizer we are responsible for deleting the file explicitely (unless we want to keep it) > delete(x) [1] TRUE > # remove r-side metadata > rm(x) > # truly free memory > gc() Gesendet: Donnerstag, 03. Mai 2012 um 00:23 Uhr Von: "Jonathan Greenberg" <j...@illinois.edu> An: r-help <r-help@r-project.org>, r-sig-...@r-project.org Betreff: [R-sig-hpc] Quickest way to make a large "empty" file on disk? R-helpers: What would be the absolute fastest way to make a large "empty" file (e.g. filled with all zeroes) on disk, given a byte size and a given number number of empty values. I know I can use writeBin, but the "object" in this case may be far too large to store in main memory. I'm asking because I'm going to use this file in conjunction with mmap to do parallel writes to this file. Say, I want to create a blank file of 10,000 floating point numbers. Thanks! --j -- Jonathan A. Greenberg, PhD Assistant Professor Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 607 South Mathews Avenue, MC 150 Urbana, IL 61801 Phone: 415-763-5476 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [1]http://www.geog.illinois.edu/people/JonathanGreenberg.html [[alternative HTML version deleted]] _______________________________________________ R-sig-hpc mailing list r-sig-...@r-project.org [2]https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
References 1. http://www.geog.illinois.edu/people/JonathanGreenberg.html 2. https://stat.ethz.ch/mailman/listinfo/r-sig-hpc ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.