1. 11th October 2012Graduate Lectures1 Oxford University Particle Physics Unix Overview Pete Gronbech Senior Systems Manager and GridPP Project Manager

2. 11th October 2012Graduate Lectures2 l Strategy l Local Cluster Overview l Connecting to it l Grid Cluster l Computer Rooms l How to get help

3. 11th October 2012Graduate Lectures3 Particle Physics Strategy The Server / Desktop Divide Win XP PC Linux Desktop Desktops Servers General Purpose Unix Server Group DAQ Systems Linux Worker nodes Web Server Linux File Servers Win XP PC Win 7 PC Approx 200 Desktop PC’s with Exceed, putty or ssh/X windows used to access PP Linux systems Virtual Machine Host NIS Server torque Server

4. 11th October 2012Graduate Lectures4 Particle Physics Linux l Unix Team (Room 661): n Pete Gronbech - Senior Systems Manager and GridPP Project Manager n Ewan MacMahon – Grid and Local Systems Administrator n Kashif Mohammad – Grid Support n Sean Brisbane – Local Server and User Support l Aim to provide general purpose Linux based systems for code development and testing and other Linux based applications. l Interactive login servers and batch queues are provided. l Systems run Scientific Linux which is a free Red Hat Enterprise based distribution. l Systems are currently running SL5, this is the same version as used on the Grid and at CERN. Students should use pplxint5 and 6. l A Grid User Interface is provided on the interactive nodes to allow job submission to the Grid. l Worker nodes form a PBS (aka torque) cluster accessed via batch queues.

5. 11th October 2012Graduate Lectures5 Current Clusters l Particle Physics Local Batch cluster l Oxfords Tier 2 Grid cluster

6. pplxwnnn 8 * Intel 5420 cores 11th October 2012 PP Linux Batch Farm pplxwn4 Scientific Linux 5 pplxint6 pplxint5 8 * Intel 5420 cores Interactive login nodes pplxwn5 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores 6Graduate Lectures pplxwn25 pplxwn26 pplxwn27 pplxwn28 pplxwn29 pplxwn30 pplxwn31 pplxwn32 16 * AMD Opteron 6128 cores Users log in to the interactive nodes Pplxint5 & 6, the home directories and all the data disks (/home area or /data/group ) are shared across the cluster and visible on the interactive machines and all the batch system worker nodes. Approximately 350 Cores each with 4GB or RAM memory. pplxwnnn 8 * Intel 5420 cores

7. 11th October 2012 PP Linux Batch Farm Data Storage pplxfsn 9TB pplxfsn 19TB Data Areas pplxfsn 19TB 7 Graduate Lectures NFS Servers Home areas Data Areas NFS is used to export data to the smaller experimental groups, where the partition size is less than the total size of a server. The data areas are too big to be backed up. The servers have dual redundant PSUs, RAID 6 and are running on uninterruptable powers supplies. This safeguards against hardware failures, but does not help if you delete files. The home areas are backed up to by two different systems nightly. The OUCS HFS service and a local back up system. If you delete a file tell us a soon as you can when you deleted it and it’s full name. The latest nightly backup of any lost or deleted files from your home directory is available at the read-only location "/data/homebackup/{username} The home areas are quota’d but if you require more space ask us. Store your thesis on /home NOT /data. pplxfsn 30TB Data Areas

8. Particle Physics Computing Lustre MDSLustre OSS02Lustre OSS03 18TB 44TB SL5 Node Lustre OSS01 44TB Lustre OSS04 df -h /data/atlas Filesystem Size Used Avail Use% Mounted on /lustre/atlas 183T 147T 27T 85% /data/atlas df -h /data/lhcb Filesystem Size Used Avail Use% Mounted on /lustre/lhcb 58T 40T 16T 72% /data/lhcb 11th October 20128 Graduate Lectures The Lustre file system is used to group multiple file servers together to provide extremely large continuous file spaces. This is used for the Atlas and LHCb groups.

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10. 11th October 2012Graduate Lectures10 Strong Passwords etc l Use a strong password not open to dictionary attack! n fred123 – No good n Uaspnotda!09 – Much better l Better to use ssh with a passphrased key stored on your desktop.

11. 11th October 2012Graduate Lectures11 Connecting with PuTTY Demo 1. Plain ssh terminal connection 2. With key and Pageant 3. ssh with X windows tunnelled to passive exceed 4. ssh, X windows tunnel, passive exceed, KDE Session http://www.physics.ox.ac.uk/it/unix/particle/XTunnel%20via%20ssh.htm http://www.howtoforge.com/ssh_key_based_logins_putty

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13. Puttygen to create an ssh key on Windows 11th October 2012Graduate Lectures13 Paste this into ~/.ssh/authorized_keys on pplxint If you are likely to then hop to other nodes add : ForwardAgent yes to a file called config in the.ssh dir on pplxint Save the public and private parts of the key to a subdirectory of your h: drive

14. Pageant l Run Pageant once after login to load your (windows ssh key) 11th October 2012Graduate Lectures14

15. 11th October 2012Graduate Lectures15 SouthGrid Member Institutions l Oxford l RAL PPD l Cambridge l Birmingham l Bristol l Sussex l JET at Culham

16. Current capacity l Compute Servers n Twin and twin squared nodes –1300 CPU cores l Storage n Total of ~700TB n The servers have between 12 and 36 disks, the more recent ones are 2TB capacity each. These use hardware RAID and UPS to provide resilience. 11th October 2012Graduate Lectures16

17. 11th October 2012Graduate Lectures17 Get a Grid Certificate Must remember to use the same web browser to request and retrieve the Grid Certificate. Once you have it in your browser you can export it to the Linux Cluster to run grid jobs. Details of these steps and how to request membership of the SouthGrid VO (if you do not belong to an existing group such as ATLAS, LHCb) are here: http://www.gridpp.ac.uk/southgrid/VO/instructions.html

18. 11th October 2012Graduate Lectures18 Two New Computer Rooms provide excellent infrastructure for the future The New Computer room built at Begbroke Science Park jointly for the Oxford Super Computer and the Physics department, provides space for 55 (11KW) computer racks. 22 of which will be for Physics. Up to a third of these can be used for the Tier 2 centre. This £1.5M project was funded by SRIF and a contribution of ~£200K from Oxford Physics. The room was ready in December 2007. Oxford Tier 2 Grid cluster was moved there during spring 2008. All new Physics High Performance Clusters will be installed here.

19. 11th October 2012Graduate Lectures19 Local Oxford DWB Physics Infrastructure Computer Room Completely separate from the Begbroke Science park a computer room with 100KW cooling and >200KW power has been built. ~£150K Oxford Physics money. Local Physics department Infrastructure computer room. Completed September 2007. This allowed local computer rooms to be refurbished as offices again and racks that were in unsuitable locations to be re housed.

20. Cold aisle containment 20

21. 11th October 2012Graduate Lectures21 The end for now… l Ewan will give more details of use of the clusters next week l Help Pages n http://www.physics.ox.ac.uk/it/unix/default.htm http://www.physics.ox.ac.uk/it/unix/default.htm n http://www2.physics.ox.ac.uk/research/particle- physics/particle-physics-computer-support http://www2.physics.ox.ac.uk/research/particle- physics/particle-physics-computer-support l Email n pp_unix_admin@physics.ox.ac.uk l Questions…. l Network Topology

22. 11th October 2012Graduate Lectures22 Network l Gigabit JANET connection to campus July 2005. l Second JANET gigabit connection Sept 2007. l JANET campus connection upgraded to dual 10 gigabit links August 2009 l Gigabit Juniper firewall manages internal and external Physics networks. l 10Gb/s network links installed between Tier-2 and Tier-3 clusters in 2012. l Physics-wide wireless network. Installed in DWB public rooms, Martin Wood, AOPP and Theory. New firewall provides routing and security for this network.

23. 11th October 2012Graduate Lectures23 Network Access Campus Backbone Router Super Janet 4 2* 10Gb/s with Super Janet 5 OUCS Firewall depts Physics Firewall Physics Backbone Router 1Gb/s 10Gb/s 1Gb/s 10Gb/s Backbone Edge Router depts 100Mb/s 1Gb/s depts 100Mb/s Backbone Edge Router 10Gb/s

24. 11th October 2012Graduate Lectures24 Physics Backbone desktop Server switch Physics Firewall Physics Backbone Router 1Gb/s 100Mb/s 1Gb/s Particle Physics desktop 100Mb/s 1Gb/s 100Mb/s Clarendon Lab 1Gb/s Linux Server Win 2k Server Astro 1Gb/s Theory 1Gb/s Atmos 1Gb/s Server switch 10Gb/s Linux Server 10Gb/s Linux Server 1Gb/s

25. 12 th June 201225 Future Physics Backbone desktop Server switch Physics Firewall Physics Backbone Switch Dell 8024F 10Gb/s 1Gb/s Particle Physics Dell 8024F desktop 1Gb/s Clarendon Lab Dell 8024F 10Gb/s Win 2k Server Astro Dell 8024F 10Gb/s 1Gb/s Theory Dell 8024F 10Gb/s Atmos Dell 8024F 10Gb/s Server Switch S4810 10Gb/s Linux Server 10Gb/s Linux Server 10Gb/s Super FRODO Frodo 10Gb/s 1Gb/s