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: ​Getting started with AMBER