[Rd] Default accessor in S4 classes
Hi All, I'm currently trying to write an S4 class that mimics a data.frame, but stores data on disc in HDF5 format. The idea is that the dataset is likely to be too large to fit into a standard desktop machine, and by using subscripts, the user may load bits of the dataset at a time. eg: myLargeData - LargeData(/path/to/file) mySubSet - myLargeData[1:10, seq(1,15,by=3)] I've therefore defined by LargeData class thus LargeData - setClass(LargeData, representation(filename=character)) setMethod(initialize,LargeData, function(.Object,filename) .Object@filename - filename) I've then defined the [ method to call a C++ function (Rcpp), opening the HDF5 file, and returning the required rows/cols as a data.frame. However, what if the user wants to load the entire dataset into memory? Which method do I overload to achieve the following? fullData - myLargeData class(fullData) [1] data.frame or apply transformations: myEigen - eigen(myLargeData) In C++ I would normally overload the double or float operator to achieve this -- can I do the same thing in R? Thanks, Chris __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R with ATLAS avoids Linux cpu affinity
Hi all, I have a problem with cpu affinity in my R-2.11.1 installation compiled against ATLAS running on a Linux (Ubuntu 10.04) cluster under GridEngine. I wish to use Grid Engine's core binding feature to bind user processes into the number of cores they request on the cluster, thus preventing badly behaved multi-threaded libraries from consuming more cores than requested. An example of this is R compiled against multithreaded ATLAS, which needs to be bound into a single core if a user submits a 1 core job. Grid Engine achieves this through the sched_setaffinity system call under Linux 2.6. For most applications (including if I write a test C program that uses ATLAS BLAS), this works well, and prevents threads from 'leaking' outside the cpu set they are assigned. However, R appears to be able to avoid the core binding. This is *very* strange as I was under the impression that any child processes or threads inherit the cpu affinity of the parent. Does anyone have experience of this and could offer a comment or solution? Thanks, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R with ATLAS avoids Linux cpu affinity
On 6 Dec 2010, at 16:03, Dirk Eddelbuettel wrote: AFAICT R should not alter CPU affinity. So if I were you I'd swap the BLAS implementation and try again. As you are on Ubuntu, you can try the MKL that comes with the (now a littler older) Revolution R in Ubuntu 9.10; otherwise I can highly recommend the GotoBLAS2 helper package listed in my paper for a local GotoBLAS2 built. The script may be out of sync with the fairly recent license change of GotoBLAS2 (to the more liberal BSD license permitting redistribution). With some luck we will GotoBLAS2 deb packages in future Debian and Ubuntu releases. Thanks for the comments, Dirk. I take your point about ATLAS having the cores compiled in. I have replaced ATLAS with ACML, and all works fine. Cheers, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
