oxford university particle physics unix overview

11th October 2012 Graduate Lectures 1

Oxford University Particle Physics Unix Overview

Pete Gronbech

Senior Systems Manager andGridPP Project Manager


Strategy Local Cluster Overview Connecting to it Grid Cluster Computer Rooms How to get help


Particle Physics Strategy The Server / Desktop Divide

Win XP PC Linux Desktop

Des

ktop

sS

erve

rs

General Purpose Unix

Server

Group DAQ

Systems

Linux Worker nodes

Web Server

Linux FileServers

Win XP PC

Win 7 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


Particle Physics Linux Unix Team (Room 661):

Pete Gronbech - Senior Systems Manager and GridPP Project Manager Ewan MacMahon – Grid and Local Systems Administrator Kashif Mohammad – Grid Support Sean Brisbane – Local Server and User Support

Aim to provide general purpose Linux based systems for code development and testing and other Linux based applications.

Interactive login servers and batch queues are provided.

Systems run Scientific Linux which is a free Red Hat Enterprise based distribution.

Systems are currently running SL5, this is the same version as used on the Grid and at CERN. Students should use pplxint5 and 6.

A Grid User Interface is provided on the interactive nodes to allow job submission to the Grid.

Worker nodes form a PBS (aka torque) cluster accessed via batch queues.


Current Clusters

Particle Physics Local Batch cluster

Oxfords Tier 2 Grid cluster

pplxwnnn 8 * Intel 5420 cores

11th October 2012

PP Linux Batch Farm

pplxwn4

Scientific Linux 5

pplxint6pplxint5

8 * Intel 5420 cores

Interactive login nodes

pplxwn5 8 * Intel 5420 cores




6Graduate Lectures

pplxwn25

pplxwn26

pplxwn27pplxwn28

pplxwn29

pplxwn30

pplxwn31pplxwn32 16 * AMD Opteron 6128 cores

16 * AMD Opteron 6128 cores







Users log in to the interactive nodesPplxint5 & 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.


11th October 2012

PP Linux Batch Farm Data Storage

pplxfsn

9TB

pplxfsn

19TB

Data Areas

pplxfsn

19TB

7Graduate 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

30TBData Areas

Particle Physics Computing

44TB

Lustre OSS04

df -h /data/atlasFilesystem Size Used Avail Use% Mounted on/lustre/atlas 183T 147T 27T 85% /data/atlas

df -h /data/lhcbFilesystem Size Used Avail Use% Mounted on/lustre/lhcb 58T 40T 16T 72% /data/lhcb

11th October 2012 8Graduate 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.


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.


Connecting with PuTTYDemo1. Plain ssh terminal connection2. With key and Pageant3. ssh with X windows tunnelled to

passive exceed4. 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

http://www.physics.ox.ac.uk/it/unix/particle/XTunnel%20via%20ssh.htm

http://www.howtoforge.com/ssh_key_based_logins_putty

Puttygen to create an ssh key on Windows


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

Pageant

Run Pageant once after login to load your (windows ssh key)



SouthGrid Member Institutions

Oxford RAL PPD Cambridge Birmingham Bristol Sussex

JET at Culham

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 2TB capacity each. These use hardware RAID and UPS to provide resilience.



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


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.


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.

Cold aisle containment

20


The end for now… Ewan 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

[email protected] Questions…. Network Topology

oxford university particle physics unix overview

Documents

amd opteron

batch queues

batch system worker

linux based applications

coresgraduate lectures11th

helpgraduate lectures11th

grid user interface

different systems nightly