Node Installation Documentation

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/smb.conf - 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