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Turning control back over to the terminal

2 messages · Ross Boylan, Martin Morgan

Ross Boylan
# 
I'm invoking R from withing a shell script like this
R --no-save --no-restore --gui=none > `hostname`  2>&1 <<BYE
# various commands here
BYE

I would like to regain control from the invoking terminal at some point.
I tried source(stdin()) but got a syntax error, presumably stdin is the
little shell here snippet (the part between <<BYE
and BYE).

Is there some way to accomplish this?  I am trying to regain control
inside an R session that has been launched inside an MPI environment
(and I'm usually running inside emacs).  This is on a Mac OS X cluster.

I suppose there might be a way to do this with expect, but I'm hoping
for something simpler.  Potentially, I could make the script itself act
differently on the head node (the only one I want to debug right now),
including changing the redirection there.
Martin Morgan
# 
Hi Ross --

Not a direct answer to your question, but here's an idea.

I guess you've got some script in a file batch.sh

#! /bin/bash
R --no-save --no-restore --gui=none > `hostname`  2>&1 <<BYE
# some mpi commands
# other mpi commands
BYE

and you do something like

mpiexec -np 10 batch.sh

Instead, you might create a file script.R

script.R
--------

library("Rmpi")
mpi.spawn.Rslaves(nslaves=10)

variousCmds <- function() {
  ## some mpi commands
  if( mpi.comm.rank() == 0 && interactive()) {
    while( (res <- readline( prompt=" > ")) != "DONE" ) {
      try(cat(eval(parse(text=res)), "\n"))
      ## or other, e.g., browser()
    }
  }
  ## other mpi commands
}

mpi.bcast.Robj2slave( variousCmds )
mpi.bcast.cmd( variousCmds())
variousCmds()

mpi.close.Rslaves()

Then just run R and

source("script.R")

to debug, and

R --vanilla < script.R

to run. This assumes that the 'some' and 'other' mpi commands include
communication of results between nodes, so that you don't have to rely
on the the return value of variousCmds to harvest the results. This
could be great fun, because you can edit the script file (in emacs,
for e.g.) and rerun without exiting R.

http://ace.acadiau.ca/math/ACMMaC/Rmpi/index.html provided some
inspiration for this, thanks!

Martin

Ross Boylan <ross at biostat.ucsf.edu> writes: