Node Installation Documentation

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This document is my log of how to install a new linux node and add it to the Microsoft HPC 2012 R2 U4 cluster.

Get ready

Install linux and enable SSH

  • I used the normal Ubuntu 14.04 desktop USB, as the others didn't work.
  • It all worked pretty smoothly really.
  • sudo apt-get update
  • sudo apt-get upgrade
  • sudo apt-get install openssh-server
  • sudo usermod -aG sudo user if you need to add any sudo-ers.
  • sudo nano /etc/ssh/sshd_config if you need to set ssh users.
    • Add a line AllowGroups ssh
    • Also, be good and add DenyUsers root and DenyGroups root when you've setup sudo-ers.
    • sudo usermod -aG ssh user to add each user to ssh.
    • sudo service ssh restart to apply changes. Don't lock yourself out muppet-brain.

Sort out infiniband support

  • The cards I used were the old Voltaire ones, so a bit of hacking was needed:-
  • sudo nano /etc/modules - and add ib_mthca rdma_ucm ib_umad ib_uverbs ib_ipoib ib_srp ib_sdp
  • sudo modprobe ib_ipoib
  • sudo nano /etc/network/interfaces and add the below, where x is the node number+1. (eg, fi--didelx15 should be 12.0.0.16). Don't add anything about eth0 or eth1 or it will break.
auto ib0
iface ib0 inet static
    address 12.0.0.x
    netmask 255.255.255.0
    broadcast 12.0.0.255
  • We may need to disable IPv6.
  • sudo nano /etc/sysctl.conf, and add the following somewhere:
net.ipv6.conf.all.disable_ipv6=1
net.ipv6.conf.default.disable_ipv6=1
net.ipv6.conf.lo.disable_ipv6=1

Add the HPC mount for some useful bits

  • sudo mkdir -p /hpclinux
  • sudo apt-get install cifs-utils
  • sudo mount -t cifs //fi--didelxhn/HPCLinux /hpclinux -o user=adminuser,dom=dide.local

Adding to the domain

Install NTP support

  • sudo apt-get install ntp
  • sudo cp /hpclinux/linux_inst/ntp.conf /etc/ntp.conf
  • (That sets the only server to be time.imperial.ac.uk)
  • sudo /etc/init.d/ntp stop
  • sudo ntupdate time.imperial.ac.uk
  • sudo /etc/init.d/ntp start

Domain things

  • sudo apt-get install winbind libpam-winbind libnss-winbind krb5-user krb5-config libpam-krb5
  • The domain, when asked, is DIDE.local - case sensitive.
  • sudo cp /hpclinux/linux_inst/nsswitch.conf /etc/nsswitch.conf - adds winbind to passwd group, and removes [NOTFOUND=return] from hosts.
  • sudo cp /hpclinux/linux_inst/smb.conf /etc/samba/smbconf - lots of config for DIDE.
  • sudo cp /hpclinux/linux_inst/krb5.conf /etc/krb5.conf - lots more config for DIDE.
  • ifconfig -a and make note of the IP address if you haven't already.
  • sudo nano /etc/hosts and replace with:-
127.0.0.1    localhost
129.31.x.y   fi--didelx99.dide.local fi--didelx99.dide.ic.ac.uk fi--didelx99
  • sudo net cache flush
  • sudo service smbd restart
  • sudo service nmbd restart
  • sudo service winbind restart
  • sudo kinit adminuser@DIDE.LOCAL
  • sudo net ads join -U adminuser

Preparing drive mounting

  • sudo apt-get install libpam-mount
  • sudo cp /hpclinux/linux_inst/pam_mount.conf.xml /etc/security/pam_mount.conf.xml - this enables looking for .pam_mount_conf.xml in the home folder, and automatically sets up a mount point (on fi--san02) to that folder beforehand.
  • sudo cp /hpclinux/linux_inst/.pam_mount.conf.xml /etc/skel - for convenience really. Suggest that users copy all the "." files from /etc/skel to their home folder, to get a nice experience when ssh-ing.
  • The home folder is set to /media/home, and automatically mounts \\fi--san02\homes\username. Users should edit .pam_mount.conf.xml in their home folder, and add the volumes they want mounted. For example:-
<?xml version="1.0" encoding="utf-8" ?>
<pam_mount>
  <volume options="nodev,nosuid" user="*" mountpoint="/media/f2gsim" path="GlobalSim" server="fi--didef2.dide.ic.ac.uk" fstype="cifs" />
</pam_mount>

Installing HPC

  • cd /hpclinux
  • sudo python setup.py -install -clusname:fi--didelxhn -certfile:hpc4.pfx