Rmpi working with OpenMPI and PBSPro but snow fails
On Thu, 2009-03-05 at 07:45 -0600, luke at stat.uiowa.edu wrote:
On Thu, 5 Mar 2009, Huw Lynes wrote:
You must be doing something differently than I am. I have Rmpi and
pvm installed, but when I ask for a SOCK cluster in a standard R
session that is what I get, even if I load Rmpi first (and it is what
I would expect based on the code). Whe I try to run your example I do
get an error, but that is because you are passing a string to
makeCluster rather than an number. If I use the file
-------------------------------(snow-err.R)-----------------------------------
library(snow)
ncpus <- as.numeric(Sys.getenv("NCPUS"))
cl <- makeCluster(ncpus, type = "SOCK")
clusterCall(cl, function() Sys.info()[c("nodename","machine")])
stopCluster(cl)
------------------------------------------------------------------------------
with
env NCPUS=2 R -f snow-err.R
Right I worked out what I was doing wrong. I was still pointing to the mpi script in my PBS script. I fixed the SOCK script based on your advice and it's now working.
ncpus <- as.numeric(Sys.getenv("NCPUS"))
cl <- makeCluster(2, type = "SOCK")
clusterCall(cl, function() Sys.info()[c("nodename","machine")])
[[1]]
nodename machine
"arccacluster268" "x86_64"
[[2]]
nodename machine
"arccacluster268" "x86_64"
stopCluster(cl)
Just need to do some more de-bugging on the MPI side of it. Thanks, Huw
Huw Lynes | Advanced Research Computing
HEC Sysadmin | Cardiff University
| Redwood Building,
Tel: +44 (0) 29208 70626 | King Edward VII Avenue, CF10 3NB