R-MPI

1.What is R-MPI

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2.Software Requirement

• MPI implements
  • mpich2, mpich, ​LAM/MPI (7.0.2 or higher)
    • For mpich2 installation, please reference here
  • OpenMPI may causes some problem, not for sure.
• R (2.0.0 or higher)
  • Assuming that your system is ubuntu or you got apt-get commands, you can just install R by :

    root@client-01:~# apt-get install r-base-core
    

• gcc-4.2
  • As previous step, you should install gcc-4.2 by :

    root@client-01:~# apt-get install gcc-4.2
    

  • If you want use lower version of gcc, please link the gcc-4.2 to your location of your gcc compiler. Such as:

    root@client01:~# ln -s /usr/bin/gcc /usr/bin/gcc-4.2
    

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3.Install Rmpi

• Download for Rmpi from ​here. The latest version is 0.5-5.

  root@client-01:/opt# wget http://www.stats.uwo.ca/faculty/yu/Rmpi/download/linux/Rmpi_0.5-5.tar.gz
  

• Assuming that your system have installed R, gcc-4.2 and any one of MPI implements already. Then we can start to install Rmpi as follows

  root@client-01:/opt# R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/opt/mpich2
  

• Rmpi have been installed successfully so far.

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4.Test for Rmpi

• At first, you need to start mpi at Master node (such as client-01).
  For example, mpich2,

  root@client-01:/opt# mpdboot -n 3 -f /root/mpich2-1.0.7rc1/mpd.hosts
  root@client-01:/opt# mpdtrace
  client-01
  client-03
  client-02
  

• Test for ​example program
  Notice that this example has a plot in it so trying it in X-windows.

  root@client-01:/opt# wget http://ace.acadiau.ca/math/ACMMaC/Rmpi/task_pull.R
  root@client-01:/opt# mpirun -np 1 R --slave CMD BATCH task_pull.R
  

• If success, there will be two files generated out, they are Rplots.ps, task_pull.Rout.
  

• Simple check of R-MPI environment
  • Reference code from ​Rmpi Sample Program, Acadia Centre for Mathematical Modelling and Computation

    # R
    > if (!is.loaded("mpi_initialize")) {
    + library("Rmpi")
    + }
    

• If you did not install LAM/MPI, you should see this message

  > if (!is.loaded("mpi_initialize")) {
  + library("Rmpi")
  + }
  
          LAM/MPI runtime environment is not operating.
          Starting LAM/MPI runtime environment.
  

• For more test program, please reference ​R_note.

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5.Reference

• ​The R Project Offical Website
• ​Rmpi Project Offical Website
• ​The R User Conference 2008
• ​Rmpi: Interface (Wrapper) to MPI (Message-Passing Interface)
• ​Debian Rmpi Package

• ​Chinese Documentation for GNU R - 中文手冊