在R中后台运行作业

Question

I am working with a 250 by 250 matrix. However, it takes loads and loads of time to compute this. It takes like an hour at least.

Is it possible that I can store this matrix in memory in R, such that everytime I open up R, it is already there.

Ideally, I would like to know if it is possible to run a job on background in R , so that I dont have to wait an hour to get the matrix out and be able to play around with it.

Answer 1

1) You can save the workspace of R when closing R. Usually R asks "Save workspace image?" when you are closing it. If you will answer "Yes" it will save the workspace in a file named ".Rdata" and will load it when staring a new R instance.

2) The better option (more safe) is to save the matrix explicitly. There are several options how it can be done. One of the options is to save it as Rdata file:

save(m, file = "matrix.Rdata")

where m is your matrix.

You can load the matrix at any time with

load("matrix.Rdata")

if you are on the same working directory.

3) There is not such option as background computing for R. But you can open several R instances. Do computation in one instance, and do something else on other instance.

Answer 2

What would help is to output it to a file when you have computed it and then parse that file everytime you open R. Write yourself a computeMatrix() function or script to produce a file with the matrix stored in a sensible format. Also write yourself a loadMatrix() function or script to read in that file and load the matrix into memory for use, then call or run loadMatrix everytime you start R and want to use the matrix.

In terms of running an R job in the background, you can run an R script from the command line with the syntax "R CMD BATCH scriptName" with scriptName replaced by the name of your script.

Answer 3

It might be better to use the ff package and save the matrix as an ff object. This means that the actual matrix will be saved on the disk in an efficient manner, then when you start a new R session you can point to that same file without loading the entire matrix into memory. When you need part of the matrix, only the part you need will be loaded so it will be much quicker. Even if you need the entire matrix loaded into memory it should load faster than reading a text file.