[Rd] likely bug in 'serialize' or please explain the memory usage

From: Sklyar, Oleg (London) <osklyar_at_maninvestments.com>
Date: Tue, 03 Nov 2009 11:27:58 +0000


Hi all,

assume the following problem: a function call takes a function object and a data variable and calls this function with this data on a remote host. It uses serialization to pass both the function and the data via a socket connection to a remote host. The problem is that depending on the way we call the same construct, the function may be serialized to include the data, which was not requested as the example below demonstrates (runnable). This is a problem for parallel computing. The problem described below is actually a problem for Rmpi and any other parallel implementation we tested leading to endless executions in some cases, where the total data passed is huge.

Assume the below 'mycall' is the function that takes data and a function object, serializes them and calls the remote host. To make it runable I just print the size of the serialized objects. In a parallel apply implemention it would serialize individual list elements and a function and pass those over. Assuming 1 element is 1Mb and having 100 elements and a function as simple as function(z) z we would expect to pass around 100Mb of data, 1 Mb to each individual process. However what happens is that in some situations all 100Mb of data are passed to all the slaves as the function is serialized to include all of the data! This always happens when we make such a call from an S4 method when the function we is defined inline, see last example.

Anybody can explain this, and possibly suggest a solution? Well, one is -- do not define functions to call in the same environment as the caller :(

I do not have immediate access to the newest version of R, so would be grateful if sombody could test it in that and let me know if the problem is still there. The example is runnable.

Thanks,
Oleg

Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
osklyar_at_maninvestments.com



mycall = function(x, fun) {

    FUN = serialize(fun, NULL)
    DAT = serialize(x, NULL)     

    cat(sprintf("length FUN=%d; length DAT=%d\n", length(FUN), length(DAT)))

    invisible(NULL) ## return results of a call on a remote host with FUN and DAN
}

## the function variant I will be passing into mycall
innerfun = function(z) z
x = runif(1e6)

## test run from the command line

mycall(x, innerfun)
# output: length FUN=106; length DAT=8000022

## test run from within a function

outerfun1 = function(x) mycall(x, innerfun) outerfun1(x)
# output: length FUN=106; length DAT=8000022

## test run from within a function, where function is defined within
outerfun2 = function(x) {

    nestedfun = function(z) z
    mycall(x, nestedfun)
}
outerfun2(x)
# output: length FUN=253; length DAT=8000022

setGeneric("outerfun3", function(x) standardGeneric("outerfun3"))
## define a method

## test run from within a method

setMethod("outerfun3", "numeric",

    function(x) mycall(x, innerfun))
outerfun3(x)
# output@ length FUN=106; length DAT=8000022

## test run from within a method, where function is defined within
setMethod("outerfun3", "numeric",

    function(x) {

        nestedfun = function(z) z
        mycall(x, nestedfun)

    })
## THIS WILL BE WRONG!

outerfun3(x)
# output: length FUN=8001680; length DAT=8000022

R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] stats graphics grDevices utils datasets methods base



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