Working doSNOW foreach openMPI example

Greetings Justin,

Thank you for your post.  The example you show is of high interest
to me, but I can't get it to work with my mpi software, it seems.
below is a bit of feedback.  I am running a redhat linux machine(s)
with openMPI v 1.4.3.

First, identical to your example, except hostfile specification:

  $ mpirun -n --hostfile myhosts --no-save -f rtest.R
  --------------------------------------------------------------------------
  mpirun was unable to launch the specified application as it could not find
  an executable:

  Executable: myhosts
  Node: vixen.egcrc.org

  while attempting to start process rank 0.
  --------------------------------------------------------------------------
  $ 

I put 1 after -n:

  $ mpirun -n 1 --hostfile myhosts --no-save -f rtest.R
  --------------------------------------------------------------------------
  mpirun was unable to launch the specified application as it could not find
  an executable:

  Executable: --no-save
  Node: 10.255.255.254

  while attempting to start process rank 0.
  --------------------------------------------------------------------------
  $ 

Let me try without --no-save:

  $ mpirun -n 1 --hostfile myhosts -f rtest.R
  --------------------------------------------------------------------------
  mpirun was unable to launch the specified application as it could not find
  an executable:

  Executable: -f
  Node: 10.255.255.254

  while attempting to start process rank 0.
  --------------------------------------------------------------------------
  $ 

Get rid of -f:

  $ mpirun -n 1 --hostfile myhosts rtest.R
  [compute-0-0.local:16448] [[42316,0],1]->[[42316,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9) [sd =
9]
  [compute-0-0.local:16448] [[42316,0],1] routed:binomial: Connection to
lifeline [[42316,0],0] lost
  $ 

Here's what happens when I run rtest.R interactively:

  $ R --no-save

  R version 2.10.1 (2009-12-14)
                .
                .
  > library( doSNOW )
  Loading required package: foreach
  Loading required package: iterators
  Loading required package: codetools
  foreach: simple, scalable parallel programming from REvolution Computing
  Use REvolution R for scalability, fault tolerance and more.
  http://www.revolution-computing.com
  Loading required package: snow
  > library( panel )
  > 
  > cl <- makeMPIcluster( 3 )
  Loading required package: Rmpi
        3 slaves are spawned successfully. 0 failed.
  > registerDoSNOW( cl )
  > 
  > clusterEvalQ( cl, library(panel) )
  [[1]]
   [1] "panel"     "snow"      "Rmpi"      "methods"   "stats"
"graphics" 
   [7] "grDevices" "utils"     "datasets"  "base"
  
  [[2]]
   [1] "panel"     "snow"      "Rmpi"      "methods"   "stats"
"graphics" 
   [7] "grDevices" "utils"     "datasets"  "base"
  
  [[3]]
   [1] "panel"     "snow"      "Rmpi"      "methods"   "stats"
"graphics" 
   [7] "grDevices" "utils"     "datasets"  "base"
  
  > 
  > res <- clusterCall( cl, function() {
  +                                 Sys.info()["nodename"]
  +                          }
  +                    )
  > print( do.call(rbind, res) )
       nodename    
  [1,] "vixen.egcrc.org"
  [2,] "vixen.egcrc.org"
  [3,] "vixen.egcrc.org"
  > 
  > sme <-  matrix( rnorm(100), 10, 10)
  > clusterExport ( cl, "sme" )
  > 
  > myfun <- function () {
  +                 for ( i in 1:1000 ) {
  +                         x <- eddcmp ( sme )
  +                 }
  +          }
  > 
  > ged <- 0
  > 
  > system.time( {
  +                 ged <- foreach ( i = 1:10 ) %dopar% {
  +                            myfun ()
  +                        }
  +               } )
     user  system elapsed
    0.964   2.744   3.717
  > 
  > system.time( {
  +                 ged <- foreach ( i = 1:10 ) %do% {
  +                            myfun ()
  +                        }
  +               } )
     user  system elapsed
    8.760   0.004   8.803
  There were 50 or more warnings (use warnings() to see the first 50)
  > 
  > system.time( {
  +                 for ( i in 1:10 ) {
  +                    ged <- myfun (  )
  +                 }
  +               } )
     user  system elapsed
    7.385   0.000   7.407
  There were 50 or more warnings (use warnings() to see the first 50)
  > 
  > stopCluster( cl )
  [1] 1
  > mpi.quit()
  $

Regards,

Tena Sakai
tsakai at gallo.ucsf.edu

Hi, 
Just wanted to share a working example of doSNOW and foreach for an openMPI
cluster.  The function eddcmp() is just an example and returns some inocuous
warnings.  The example first has each node return its nodename, then runs an
example comparing dopar, do and a for loop.  In the directory containing
rtest.R it is run from the command line with:
"mpirun -n --hostfile /home/hostfile --no-save -f rtest.R"

Here is the code for rtest.R:

#################
library(doSNOW)
library(panel)

cl<-makeMPIcluster(3)
registerDoSNOW(cl)

clusterEvalQ(cl,library(panel))

res<-clusterCall(cl, function(){Sys.info()["nodename"]})
print(do.call(rbind,res))

sme<- matrix(rnorm(100),10,10)
clusterExport(cl,"sme")

myfun<-function()
{
for(i in 1:1000)
{
x<-eddcmp(sme)
}
}

ged<-0

system.time({
ged<-foreach(i=1:10) %dopar%
{
myfun()
}
})

system.time({
ged<-foreach(i=1:10) %do%
{
myfun()
}
})

system.time({
for(i in 1:10)
{
ged<-myfun()
}
})

stopCluster(cl)
mpi.quit()

#################
Cheers,
Justin







 
[[alternative HTML version deleted]]

_______________________________________________
R-sig-hpc mailing list
R-sig-hpc at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-hpc