R help - Jun 2009 - help installing Rmpi

Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer, but I cannot get it to install and I am not
very good with linux so it is adding to the headache.  I have looked
through the help archive, but I have not been successful at getting
Rmpi to work.  I am not sure if I am even installing openMPI correctly
in linux.  I would really like to get Rmpi to work so that I can take
advantage of libraries that use Rmpi and more importantly reduce my
computation time from several days to maybe a day.
I am using fedora 11 (64-bit) on a AMD phenom III (AM3) system and I
am not an expert at linux so I run into trouble compiling and
installing software out of inexperience.
I would truly appreciated it if someone could please provide me with
some instructions on how to get openMPI installed correctly on
Fedora11 and Rmpi to work?
I have included the processes I attempted below.
Thank you,
Alan Smith

#####################  what I have attempted so far ################
#I have tried two different ways to install openMPI in fedora in the linux shell
#in the linux shell
cd Download
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.2.tar.gz
tar -xzf openmpi*
cd openmpi*
./configure
make
make install

#AND
#in the linux shell
cd Download
wget
ftp://rpmfind.net/linux/fedora/releases/11/Everything/x86_64/os/Packages/openmpi-1.3.1-1.fc11.x86_64.rpm
sudo yum install openmpi-devel
# I find the program in this path /usr/lib64/openmpi/1.3.1-gcc/openmpi


#I then try to install Rmpi using two methods neither of which work
#Using the linux shell I have tried
wget http://cran.r-project.org/src/contrib/Rmpi_0.5-7.tar.gz
R CMD INSTALL Rmpi_0.5-7.tar.gz
#and
R CMD INSTALL Rmpi_0.5-7.tar.gz
--configure-args=--with-mpi=/usr/lib64/openmpi/1.3.1-gcc
R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi/
#All of these attempt lead to error cannot find mpi head file and tell
me to use  "with-mpi=path/to/mpi" or specify the MPI_ROOT which I
clearly cant find

#I have also tried this in R using
R
install.packages("Rmpi")
#but it gives the same error.



sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base




-- 
Alan Smith

On 11/06/09 22:46, ALAN SMITH wrote:
> Hello R users and developers,
> I would like to install Rmpi so that I may take advantage of all of
> the CPUs in my computer
Package "multicore" *may* be easier for this.
> , but I cannot get it to install [...]
The configuration file for Rmpi is, unfortunately, completely 
brain-damaged with hard-coded assumptions about which subdirectories 
should contain header and library files and no way of overriding it.  
This is what I did:
> [...]
> #I have tried two different ways to install openMPI in fedora in the linux
shell
In any recent version of Fedora don't do any of what you suggest; instead do

# yum install openmpi openmpi-devel openmpi-libs

Then *download* the Rmpi package and unpack it using something like

$ tar xvf Rmpi_0.5-7.tar.gz

(version number may be different).

Then go into the Rmpi directory and change configure.ac.  If you are on 
a x86_64 platform, the following hack should work (for 32 bit try 
s/64/32/g):

+++[cut here]+++
  Process this file with autoconf to produce a configure script.

AC_INIT(DESCRIPTION)

AC_PROG_CC


MPI_LIBS=`pkg-config --libs openmpi-1.3.1-gcc-64`
MPI_INCLUDE=`pkg-config --cflags openmpi-1.3.1-gcc-64`
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"

AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])


PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"

AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)

AC_OUTPUT(src/Makevars)
---[cut here]---

The number 1.3.1 may change in future updates to Fedora, I guess....

Now (still in Rmpi directory) do

$ autoconf
$ cd ..
$ tar zcvf Rmpi-0.5-7-F1.tar.gz Rmpi
$ R CMD INSTALL Rmpi-0.5-7-F1.tar.gz

Which more-or-less works in R:

 > library("Rmpi")
 > mpi.spawn.Rslaves(nslaves=2)
     2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
 > x=c(10,20)
 > mpi.apply(x,runif)
[[1]]
  [1] 0.25142616 0.93505554 0.03162852 0.71783194 0.35916139 0.85082154
  [7] 0.35404191 0.14221315 0.60063773 0.71805190

[[2]]
  [1] 0.84157864 0.63481773 0.38217188 0.67839089 0.27827728 0.35429266
  [7] 0.04898744 0.96601584 0.25687905 0.77381186 0.69011927 0.37391028
[13] 0.19017369 0.51196594 0.51970563 0.15791524 0.21358237 0.69642478
[19] 0.12690207 0.44177656

 >

Hope this helps!

Allan.