Oxford University Particle Physics Unix Overview

1. Oxford University Particle Physics Unix Overview Pete Gronbech Senior Systems Manager and GridPP Project Manager Graduate Lectures

2. Strategy • Local Cluster Overview • Connecting to it • Grid Cluster • Computer Rooms • How to get help Graduate Lectures

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

4. Particle Physics Linux • Unix Team (Room 661): • Pete Gronbech - Senior Systems Manager and GridPP Project Manager • Ewan MacMahon – Grid Systems Administrator • Kashif Mohammad – Grid and Local Support • Sean Brisbane – Local Server and User Support • General purpose interactive Linux based systems for code development, short tests and access to Linux based office applications. These are accessed remotely. • Batch queues are provided for longer and intensive jobs. Provisioned to meet peak demand and give a fast turnaround for final analysis. • Systems run Scientific Linux which is a free Red Hat Enterprise based distribution. • The Grid & CERN are just migrating to SL6. The local cluster is following and currently has one interactive node with a growing set of worker nodes available from "pplxint8". • Most cluster systems are still currently running SL5. These can be accessed from pplxint5 and 6. • We will be able to offer you the most help running your code on the newer SL6. Some experimental software frameworks still require SL5. Graduate Lectures

5. Current Clusters • Particle Physics Local Batch cluster • Oxfords Tier 2 Grid cluster Graduate Lectures

6. PP Linux Batch Farm Scientific Linux 5 pplxwn42 16 * E5-2650 cores pplxwn41 16 * E5-2650 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 300 Cores each with 4GB of RAM memory. pplxwn32 16 * Intel 5650 cores pplxwn31 16 * Intel 5650 cores pplxwn28 16 * AMD Opteron 6128 cores pplxwn27 16 * AMD Opteron 6128 cores pplxwn26 16 * AMD Opteron 6128 cores pplxwn25 16 * AMD Opteron 6128 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwnnn 8 * Intel 5420 cores pplxwn10 8 * Intel 5420 cores pplxwn9 8 * Intel 5420 cores pplxint5 Interactive login nodes pplxint6 Graduate Lectures

7. PP Linux Batch Farm Scientific Linux 6 Migration to SL6 ongoing. New SL6 interactive node pplxint8. Use this by preference. Worker nodes will be migrated from the SL5 cluster to SL6 over the next month. Currently four servers with 16 cores each with 4GB of RAM memory per core but more will arrive as required. ie 64 job slots. pplxwnnn 16 * Intel 2650 cores pplxwnnn 16 * Intel 2650 cores pplxwn50 16 * Intel 2650 cores pplxwn49 16 * Intel 2650 cores Interactive login nodes pplxint8 Graduate Lectures

8. PP Linux Batch Farm Data Storage NFS is used to export data to the smaller experimental groups, where the partition size is less than the total size of a server. NFS Servers 9TB The data areas are too big to be backed up. The servers have dual redundant PSUs, RAID 6 and are running on uninterruptible powers supplies. This safeguards against hardware failures, but does not help if you delete files. Data Areas pplxfsn 40TB 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. Data Areas pplxfsn 30TB Data Areas pplxfsn 19TB Home areas pplxfsn Graduate Lectures

9. Lustre MDS Lustre OSS01 Lustre OSS02 Lustre OSS04 Lustre OSS03 18TB 44TB 44TB 18TB SL5 Node SL5 Node SL5 Node SL6 Node Particle Physics Computing 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. df -h /data/atlas Filesystem Size Used Avail Use% Mounted on /lustre/atlas 244T 215T 18T 93% /data/atlas df -h /data/lhcb Filesystem Size Used Avail Use% Mounted on /lustre/lhcb 95T 82T 8.5T 91% /data/lhcb Graduate Lectures

10. Graduate Lectures

11. Strong Passwords etc • Use a strong password not open to dictionary attack! • fred123 – No good • Uaspnotda!09 – Much better • Better to use ssh with a passphrased key stored on your desktop. Graduate Lectures

12. Connecting with PuTTY Question: How many of you are using Windows? & Linux? On the desktop Demo • Plain ssh terminal connection • With key and Pageant • ssh with X windows tunnelled to passive exceed • ssh, X windows tunnel, passive exceed, KDE Session http://www2.physics.ox.ac.uk/it-services/ppunix/ppunix-cluster http://www.howtoforge.com/ssh_key_based_logins_putty Graduate Lectures

13. Graduate Lectures

14. Puttygen to create an ssh key on Windows Paste this into ~/.ssh/authorized_keys on pplxint Enter a secure passphrase then save the public and private parts of the key to a subdirectory of your h: drive Graduate Lectures

15. Pageant • Run Pageant once after login to load your (windows ssh key) Graduate Lectures

16. SouthGrid Member Institutions • Oxford • RAL PPD • Cambridge • Birmingham • Bristol • Sussex • JET at Culham Graduate Lectures

17. Current capacity • Compute Servers • Twin and twin squared nodes • 1300 CPU cores • Storage • Total of ~700TB • The servers have between 12 and 36 disks, the more recent ones are 3TB capacity each. These use hardware RAID and UPS to provide resilience. Graduate Lectures

18. Get a Grid Certificate Must remember to use the same PC to request and retrieve the Grid Certificate. The new UKCA page uses a JAVA based CERT WIZARD Graduate Lectures

19. Two 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. Graduate Lectures

20. 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. Graduate Lectures

21. Cold aisle containment Graduate Lectures

22. The end for now… • Sean will give more details of use of the clusters next week • Help Pages • http://www.physics.ox.ac.uk/it/unix/default.htm • http://www2.physics.ox.ac.uk/research/particle-physics/particle-physics-computer-support • Email • pp_unix_admin@physics.ox.ac.uk • Questions…. • Network Topology Graduate Lectures