R help - Jul 2008 - problem with mpiexec and Rmpi

Dear R People:

I'm having some trouble with mpiexec and Rmpi.

I would like to be able to pass in the number of "children" via the
mpiexec command (from the command line).

this is in SUSE10.1, with R-2.7.1

Here are my files:
 cat eb.R
library(Rmpi)
mpi.remote.exec(paste("i
am",mpi.comm.rank(),"of",mpi.comm.size()))
mpi.quit()
hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> cat e.in
source("eb.R")

hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> mpiexec -n 3 ./R --no-save -q
-f e.in >e.out
Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
mpi.comm.size())) :
  It seems no slaves running.
Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
mpi.comm.size())) :
  It seems no slaves running.
Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
mpi.comm.size())) :
  It seems no slaves running.
Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
hodgesse at erinstoy:~/Desktop/R-2.7.1/bin>

Does anyone have any suggestions, please?  The scary part:  I can get
this to work on Windows but not on SUSE10.1

thanks in advance,
Sincerely,
Erin


Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com

Hi Erin --

"Erin Hodgess" <erinm.hodgess at gmail.com> writes:
> Dear R People:
>
> I'm having some trouble with mpiexec and Rmpi.
>
> I would like to be able to pass in the number of "children" via
the
> mpiexec command (from the command line).
>
> this is in SUSE10.1, with R-2.7.1
>
> Here are my files:
>  cat eb.R
> library(Rmpi)
> mpi.remote.exec(paste("i
am",mpi.comm.rank(),"of",mpi.comm.size()))
> mpi.quit()
> hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> cat e.in
> source("eb.R")
>
> hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> mpiexec -n 3 ./R --no-save
-q
> -f e.in >e.out
With a hostfile
<<hostfile>>
localhost slots=4

You can start 1 process and have access to a defined universe
<<batch0.R>>
library(Rmpi)
mpi.universe.size()
mpi.spawn.Rslaves()
unlist(mpi.remote.exec(paste(mpi.comm.rank())))
mpi.quit()

mtmorgan at lamprey:~/tmp> mpirun -np 1 --hostfile hostfile R --slave -f
batch0.R
[1] 4
        4 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 5 is running on: lamprey 
slave1 (rank 1, comm 1) of size 5 is running on: lamprey 
slave2 (rank 2, comm 1) of size 5 is running on: lamprey 
slave3 (rank 3, comm 1) of size 5 is running on: lamprey 
slave4 (rank 4, comm 1) of size 5 is running on: lamprey 
slave1 slave2 slave3 slave4
   "1"    "2"    "3"    "4"

A different style of programming (single program multiple data) is

<<batch1.R>>
## everybody does this...
library("Rmpi")
id <- mpi.comm.rank(0) ## different data!
allIds <- mpi.gather.Robj(id, 0, 0)

## rank 0 does this...
if (mpi.comm.rank(0) == 0)
    print(allIds)

## everybody does this...
mpi.quit()

mtmorgan at lamprey:~/tmp> mpirun -np 10 R --slave -f batch1.R
 [1] 0 1 2 3 4 5 6 7 8 9

Note the '0' argument for comm, overriding 1 (the default; a more
robust program would manage the communicators better).

mtmorgan at lamprey:~/tmp> mpirun --version
mpirun (Open MPI) 1.2

Martin
> Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
> mpi.comm.size())) :
>   It seems no slaves running.
> Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
> Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
> mpi.comm.size())) :
>   It seems no slaves running.
> Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
> Error in mpi.remote.exec(paste("i am", mpi.comm.rank(),
"of",
> mpi.comm.size())) :
>   It seems no slaves running.
> Calls: source -> eval.with.vis -> eval.with.vis -> mpi.remote.exec
> hodgesse at erinstoy:~/Desktop/R-2.7.1/bin>
>
> Does anyone have any suggestions, please?  The scary part:  I can get
> this to work on Windows but not on SUSE10.1
>
> thanks in advance,
> Sincerely,
> Erin
>
>
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: erinm.hodgess at gmail.com
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

On 1 July 2008 at 14:03, Erin Hodgess wrote: | I'm having some trouble with
mpiexec and Rmpi.
| 
| I would like to be able to pass in the number of "children" via the
mpiexec
| command (from the command line).
| 
| this is in SUSE10.1, with R-2.7.1
| 
| Here are my files: cat eb.R library(Rmpi) mpi.remote.exec(paste("i
|  am",mpi.comm.rank(),"of",mpi.comm.size())) mpi.quit()
|  hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> cat e.in
source("eb.R")
| 
| hodgesse at erinstoy:~/Desktop/R-2.7.1/bin> mpiexec -n 3 ./R --no-save -q
-f
| e.in >e.out Error in mpi.remote.exec(paste("i am",
mpi.comm.rank(), "of",
| mpi.comm.size())) : It seems no slaves running.  Calls: source ->
| eval.with.vis -> eval.with.vis -> mpi.remote.exec Error in
| mpi.remote.exec(paste("i am", mpi.comm.rank(), "of",
mpi.comm.size())) : It
| seems no slaves running.  Calls: source -> eval.with.vis ->
eval.with.vis
| -> mpi.remote.exec Error in mpi.remote.exec(paste("i am",
mpi.comm.rank(),
| "of", mpi.comm.size())) : It seems no slaves running.  Calls: source
->
| eval.with.vis -> eval.with.vis -> mpi.remote.exec
| hodgesse at erinstoy:~/Desktop/R-2.7.1/bin>
| 
| Does anyone have any suggestions, please?  The scary part: I can get this
| to work on Windows but not on SUSE10.1

Things do differ slightly between MPI imnplementations -- but I have no
difficulties with Open MPI on Debian and Ubuntu.  Open MPI is the successor
to LAM, it also renamed mpirun etc to orterun [ where orte stands for Open
Run Time Environment, as I recall ].  Anyway, using a one-line littler
invocation works for me;

edd at ron:~$ orterun -n 2 -H ron,joe r -lRmpi -e'cat("Hello",
mpi.comm.rank(0),
"of", mpi.comm.size(), "on", mpi.get.processor.name(),
"\n")' Hello 0 of 0 on
ron Hello 1 of 0 on joe edd at ron:~$

Here 'r' is littler; it uses the -l flag to load the specified library
and
the -e flag to pass the string for evaluation.

'ron' is a Debian testing box, 'joe' is an Ubuntu hardy box, and
both are
running the standard packages for Debian and Ubuntu:

	r-cran-rmpi for Rmpi libopenmpi1 for Open MPI littler for 'r'

I happen to maintain all of those in Debian and noticed that Open MPI was
broken in Ubuntu 'hardy' as they foobared the build; but that is now
fixed. Ubuntu users should get an updated package via hardy-updates.

As for your problem, you haven't told us which MPI toolkit you are running.
It may be LAM in which case you probably want to read up on lamboot and the
hosts file or argument -- but that is just a guess.

Hope this helps, Dirk

-- 
Three out of two people have difficulties with fractions.