From hyu at stats.uwo.ca  Thu Oct  4 07:11:23 2007
From: hyu at stats.uwo.ca (Hao Yu)
Date: Thu, 4 Oct 2007 01:11:23 -0400 (EDT)
Subject: [Rd] Rmpi_0.5-4 and OpenMPI questions
In-Reply-To: <18180.18474.131705.985610@ron.nulle.part>
References: <18180.18474.131705.985610@ron.nulle.part>
Message-ID: <1325.129.100.76.161.1191474683.squirrel@www.stats.uwo.ca>

Hi Dirk,

Thank for pointing out additional flags needed in order to compile Rmpi
correctly. Those flags can be added in configure.ac once openmpi dir is
detected. BTW -DMPI2 flag was missed in your Rmpi since the detection of
openmpi was not good. It should be
####
        if test -d  ${MPI_ROOT}/lib/openmpi; then
                echo "Found openmpi dir in ${MPI_ROOT}/lib"
                MPI_DEPS="-DMPI2"
        fi
####

I tried to run Rmpi under snow and got the same error messenger. But after
checking makeMPIcluster, I found that n=3 was a wrong argument. After
makeMPIcluster finds that count is missing,
count=mpi.comm.size(0)-1 is used. If you start R alone, this will return
count=0 since there is only one member (master). I do not know why snow
did not use count=mpi.universe.size()-1 to find total nodes available.
Anyway after using
cl=makeMPIcluster(count=3),
I was able to run parApply function.

I tried
R -> library(Rmpi) -> library(snow) -> c1=makeMPIcluster(3)

Also
mpirun -host hostfile -np 1 R --no-save
library(Rmpi) -> library(snow) -> c1=makeMPIcluster(3)

Hao

PS: hostfile contains all nodes info so in R mpi.universe.size() returns
right number and will spawn to remote nodes.

Rmp under Debian 3.1 and openmpi 1.2.4 seems OK. I did find some missing
lib under Debian 4.0.


Dirk Eddelbuettel wrote:
>
> Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to
> make
> the changes to support Open MPI.
>
> I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi)
> under
> R 2.6.0 but I cannot convince myself yet whether it works or not.  Simple
> tests work.  E.g. on my Debian testing box, with Rmpi installed directly
> using Open Mpi 1.2.3-2 (from Debian) and using 'r' from littler:
>
> edd at ron:~> orterun -np 3 r -e 'library(Rmpi); print(mpi.comm.rank(0))'
> [1] 0
> [1] 1
> [1] 2
> edd at ron:~>
>
> but I basically cannot get anything more complicated to work yet.  R /
> Rmpi
> just seem to hang, in particular snow and and getMPIcluster() just sit
> there:
>
>> cl <- makeSOCKcluster(c("localhost", "localhost"))
>> stopCluster(cl)
>> library(Rmpi)
>> cl <- makeMPIcluster(n=3)
> Error in makeMPIcluster(n = 3) : no nodes available.
>>
>
> I may be overlooking something simple here, in particular the launching of
> apps appears to be different for Open MPI than it was with LAM/MPI (or
> maybe
> I am just confused because I also look at LLNL's slurm for use with Open
> MPI ?)
>
> Has anybody gotten Open MPI and Rmpi to work on simple demos?  Similarly,
> is
> anybody using snow with Rmpi and Open MPI yet?
>
> Also, the Open MPI FAQ is pretty clear on their preference for using mpicc
> for compiling/linking to keep control of the compiler and linker options
> and
> switches.  Note that e.g. on my Debian system
>
> edd at ron:~> mpicc --showme:link
> -pthread -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
> -lutil -lm -ldl
>
> whereas Rmpi built with just the default from R CMD:
>
> gcc-4.2 -std=gnu99 -shared  -o Rmpi.so RegQuery.o Rmpi.o conversion.o
> internal.o -L/usr/lib -lmpi -lpthread -fPIC   -L/usr/lib/R/lib -lR
>
> Don't we need libopen-rte and libopen-pal as the MPI FAQ suggests?
>
> Many thanks, Dirk
>
> --
> Three out of two people have difficulties with fractions.
>


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[Rd] Rmpi_0.5-4 and OpenMPI questions
Hao Yu