Hi,
 
I'm trying to run R in a SUN Grid Engine environment: the standard MPI
implementation on the Grid is "qlogicmpi_intel-0.1.0", as alternative
there is the possibility to use “qlogicmpi_gnu-0.1.0".
Thanks for help Matteo, Vienna
 
What I did:
 
Creating a job skript:
--------------------
#$ -N "NDVI1"
#$ -pe mpich 5
#$ -V
 
mpirun  -m $TMPDIR/machines -np $NSLOTS /opt/R/bin/R CMD BATCH "./tt.R"
output
-------------------
Run with:
qsub NDVI1
-------------------
qstat: job status is "r" so it seams ok
-------------------
 
The R-script tt.R has an standard example from the Rsge.pdf file just
once Parallel=F and once T:
 
library(Rsge)
 
options(sge.use.cluster=FALSE)
sge.parLapply(c(1:10), function(x) x + 1,debug=TRUE)
 
options(sge.use.cluster=TRUE)
sge.parLapply(c(1:10), function(x) x + 1,debug=TRUE)
 
q("no")
------------------------------------
Output is the following:

R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
 
> 
> library(Rsge)
Loading required package: snow
 
Welcome to Rsge
    Version: 0.6.3 
 
> 
> options(sge.use.cluster=FALSE)
> sge.parLapply(c(1:10), function(x) x + 1,debug=TRUE)
Running locally
[[1]]
[1] 2
 
[[2]]
[1] 3
 
[[3]]
[1] 4
 
[[4]]
[1] 5
 
[[5]]
[1] 6
 
[[6]]
[1] 7
 
[[7]]
[1] 8
 
[[8]]
[1] 9
 
[[9]]
[1] 10
 
[[10]]
[1] 11
 
> 
> options(sge.use.cluster=TRUE)
> sge.parLapply(c(1:10), function(x) x + 1,debug=TRUE)
 [1]  1  2  3  4  5  6  7  8  9 10
[[1]]
 [1]  1  2  3  4  5  6  7  8  9 10
 
[1] "Global Environment variable: "
[1] "Packaged: "
Completed storing environment to disk
Submitting  1 jobs...
[1] "/home/lv70089/MattMA/austria/Rsge_data327b23c6-1.sge.ret"
 Unable to initialize environment because of error: denied: host
"r10n26" is neither submit nor admin host Exiting. 
All jobs completed
ls: *.e*: No such file or directory
rm: cannot remove `*.e*': No such file or directory
rm: cannot remove `*.o*': No such file or directory
[rm: cannot remove `*.o*': No such file or directory
[[1]]
NULL
 
NULL
Warning messages:
1: In
FUN("/home/lv70089/MattMA/austria/Rsge_data327b23c6-1.sge.ret"[[1L]], 
:
  Expected file
/home/lv70089/MattMA/austria/Rsge_data327b23c6-1.sge.ret Does not exist
at: /home/lv70089/MattMA/austria
2: In file.remove(paste(prefix, "-GLOBAL", sep = "")) :
  cannot remove file
'/home/lv70089/MattMA/austria/Rsge_data327b23c6-GLOBAL', reason 'No such
file or directory'
> 
> q("no")
> proc.time()
   user  system elapsed 
  0.220   0.033   1.310 
psed 
  0.221   0.037   1.292 

	[[alternative HTML version deleted]]

