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

== Issue description ==

 * We found that if we run mpd with superuser privilege (i.e. root permission), normal user in each node can not connect to mpd to run R-MPI.
   * First, we had finished the ip and hostname mapping by modifying /etc/hosts, and then use scp to exchange ssh public key to each compute node.
{{{
bio-cluster-12:~# cat /etc/hosts
X.X.X.12 bio-cluster-12
X.X.X.11 bio-cluster-11
X.X.X.10 bio-cluster-10
X.X.X.9  bio-cluster-09
X.X.X.8  bio-cluster-08
X.X.X.7  bio-cluster-07
X.X.X.6  bio-cluster-06

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
}}}
   * We had created the same mpd.conf in each node
{{{
bio-cluster-12:~# cat > /etc/mpd.conf << "EOF"
> secretword=this_is_password
> EOF

bio-cluster-12:~# for i in 11 10 09 08 07 06; do scp /etc/mpd.conf bio-cluster-$i:/etc/.; done
}}}
   * The mpd.hosts file is as following:
{{{
bio-cluster-12:~# cat mpd.hosts
bio-cluster-11
bio-cluster-10
bio-cluster-09
bio-cluster-08
bio-cluster-07
bio-cluster-06
}}}
   * run mpdboot with superuser privilege
{{{

}}}
 * Reference Solution: [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:~$ 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.
{{{
jazz@bio-cluster-12:~$ mpdboot -n 7
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_54092 (140.129.162.12)
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
}}}
 *