Hi Jens, Thanks for your prompt and informative answers. ff is a fabulous package and your suggestions helped me solve my problems at hands.
As I need to incrementally increase each of several large matrices (about 1000 rows *10000 columns, 1000 matrices) by a row every day. I wonder how efficiently it is to do the following command on a frequent basis. nrow(matFF) <- nrow(matFF)+1 as far as I know for mmap, a fixed size of file is preallocated. I don't know the ff implementation and how it handle file size changes. Does the command in the line above preallocate, say 10% more space of the current size so that no large file copying is needed each time the nrow is changed? Another problem I am facing is that I have over 2000 large matrices that need the help of ff. Suppose I have a list of 2000 ff objects. My computing environment is 64bit linux, 64Gb mem. I remember there is some limitations on the maximum of files that can be opened in linux. If I need to access each matrix, would you think I can open each matrix and leave them open or I need to close it after it is opened and used? Thanks a lot Jeff -----Original Message----- From: "Jens Oehlschlägel" [mailto:oehl_l...@gmx.de] Sent: Wednesday, November 25, 2009 8:04 AM To: h...@andrew.cmu.edu Cc: r-h...@lists.r-project.org Subject: [R] questions on the ff package Jeff, > I need to save a matrix as a memory-mapped file and load it back later. > To save the matrix, I use > mat = matrix(1:20, 4, 5) > matFF = ff(mat, dim=dim(mat), filename="~/a.mat" > , overwrite=TRUE, dimnames = dimnames(mat)) # This stores the data in an ff file, # but not the metadata in R's ff object. # To do the latter you need to do save(matFF, file="~/matFF.RData") # Assuming that your ff file remains in the same location, # in a new R session you simply load(file="~/matFF.RData") # and the ff file is available automagically > However, I don't always know the dimension when loading the matrix back. > If I miss the dim attributes, ff will return it as vector. > Is there a way to load the matrix without specifying the dimension? # You can create an ff object using your existing ff file by matFF <- ff(filename="~/a.mat", vmode="double", dim=c(4,5)) # You can do the same at unknown file size with matFF <- ff(filename="~/a.mat", vmode="double") # which gives you the length of the ff object length(matFF) # if you know the number of columns you can calculate the number of rows and give your ff object the interpretation of a matrix dim(matFF) <- c(length(matFF)/5, 5) > the matrix may grow in terms of the number of rows. > Is there an efficient way to do this? # there are two ways to grow a matrix by rows # 1) you create the matrix in major row order matFF <- ff(1:20, dim=c(4,5), dimorder=c(2:1)) # then you require a higher number of rows nrow(matFF) <- 6 # as you can see there are new empty rows in the file matFF # 2) Instead of a matrix you create a ffdf data.frame # which you can also give more rows using nrow<- # An example of this is in read.table.ffdf # which reads a csv file in chunks and extends the # number of rows in the ffdf Jens Oehlschlägel -- Preisknaller: GMX DSL Flatrate für nur 16,99 Euro/mtl.! http://portal.gmx.net/de/go/dsl02 ______________________________________________ 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.
