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= How to run R-MPI on multiple machine with normal user permission =

 * Reference Configuration Guide: 
   * [http://structbio.vanderbilt.edu/comp/soft/amber/start.php Getting started with AMBER]

== Configure mpd for normal user ==

 * Fisrt, login as nornal user. Here we login with user id 'jazz'. Then exchange SSH public key to each computing node.
{{{
login as: jazz
jazz@bio-cluster-12's password:
jazz@bio-cluster-12:~$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/home/jazz/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/jazz/.ssh/id_rsa.
Your public key has been saved in /home/jazz/.ssh/id_rsa.pub.
The key fingerprint is:
XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX jazz@bio-cluster-12
jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06; do scp .ssh/id_rsa.pub bio-cluster-$i:.ssh/authorized_keys; done
}}}
 * setup .mpd.conf for each compute node in $HOME
{{{
jazz@bio-cluster-12:~$ echo "MPD_SECRETWORD=${user}$$" > ~/.mpd.conf
jazz@bio-cluster-12:~$ chmod 600 .mpd.conf
jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06
> do
> scp .mpd.conf bio-cluster-$i:.
> done
.mpd.conf                                     100%   21     0.0KB/s   00:00
.mpd.conf                                     100%   21     0.0KB/s   00:00
.mpd.conf                                     100%   21     0.0KB/s   00:00
.mpd.conf                                     100%   21     0.0KB/s   00:00
.mpd.conf                                     100%   21     0.0KB/s   00:00
.mpd.conf                                     100%   21     0.0KB/s   00:00
}}}
 * setup mpd.hosts on localhost
{{{
jazz@bio-cluster-12:~$ cat > mpd.hosts << EOF
> bio-cluster-11
> bio-cluster-10
> bio-cluster-09
> bio-cluster-08
> bio-cluster-07
> bio-cluster-06
> EOF
}}}
 * run '''mpdboot''' for 7 nodes and use '''mpdtrace''' to check the status of mpd process on each compute node. '''mpdringtest''' can test the speed of message passing. '''mpdallexit''' to terminate all mpd processes.
{{{
jazz@bio-cluster-12:~$ mpdboot -n 7
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_54092 (10.220.202.219)
bio-cluster-08_38361 (10.220.202.223)
bio-cluster-09_52923 (10.220.202.222)
bio-cluster-11_33377 (10.220.202.220)
bio-cluster-10_33103 (10.220.202.221)
bio-cluster-06_59631 (10.220.202.225)
bio-cluster-07_59533 (10.220.202.224)
jazz@bio-cluster-12:~$ mpdringtest 100
time for 100 loops = 0.0729811191559 seconds
jazz@bio-cluster-12:~$ mpdallexit
}}}

== Test 1: single mpd and R-MPI in localhost ==

 * run mpd in localhost
{{{
jazz@bio-cluster-12:~$ mpd &
[1] 1505
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_37007 (10.220.202.219)
}}}
 * run R-MPI with single mpd in localhost
{{{
jazz@bio-cluster-12:~$ R

R version 2.4.0 Patched (2006-11-25 r39997)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

> library(Rmpi)
> mpi.spawn.Rslaves()
        1 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 2 is running on: bio-cluster-12
slave1 (rank 1, comm 1) of size 2 is running on: bio-cluster-12
> mpi.close.Rslaves()
mpi.close.Rslaves()
[1] 1
> mpi.quit(save="no")
mpi.quit(save="no")
jazz@bio-cluster-12:~$
}}}