[R] Rmpi performance

[Luke Tierney]

On Fri, 13 Oct 2006, Michela Cameletti wrote:

> Dear R users,
> we are trying to do some parallel computing using library(snow).
> In particular we have a cluster with 3 nodes
>
>> cl <- makeCluster(3, type = "MPI")
>        3 slaves are spawned successfully. 0 failed.
>
>
> and we want to compute the function op_mat (see below) first with the
> master and then with the cluster using system.time for checking the
> computational performance.
>
> op_mat = function(mat) {
>
> +           inv = solve(mat)
> +           det_inv = det(inversa)
> +           tr_inv  = sum(diag(inversa))
> +           return(list(c(det=det_inv,tr=tr_inv)))
> + }

What is inversa?

>
>> nn = 3000
>> XX = matrix(rnorm(nn*nn),nn,nn)
> # with the master
>> system.time(op_matrici(XX))
> [1] 42.283  1.883 44.168  0.000  0.000
> # with the cluster
>> system.time(clusterCall(cl,op_matrici,XX))
> [1] 11.523 12.612 71.562  0.000  0.000
>
> You can see that using the master it takes 44.168 seconds for computing
> the function on matrix XX while it takes 71.562 seconds (more time!!!)

Of coure it takes more time to do the same computation plus
communication!

The amount of additional time seems high if your nodes are comparable
in speed to your master and you really are getting gigabit
performance.  I would look for a visualization tool an idea of what is
happening--perhaps xmpi if your MPI is LAM.

Best,

luke


> with the cluster. Can you give us some advice in order to understand why
> the cluster is slower than the master?
> Thank you very much in advance,
> bye
> Michela  and Marco
> Ps: we have a gigabit ethernet between the master and the nodes
>
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-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu