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

• Reference Configuration Guide:
  • ​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)
  

• BTW, you can also use mpdboot to run mpd in localhost

  jazz@bio-cluster-12:~$ mpdboot
  [1]+  Done                    mpd
  jazz@bio-cluster-12:~$ mpdtrace -l
  bio-cluster-12_44810 (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:~$