2. SitE Report University of Johannesburg Stavros Lambropoulos
South Africa
Stavros Lambropoulos
Network Engineer
SitE Report

3. Overview History of the UJ Research Cluster User Groups Hardware
South African Compute Grid (SA Grid)
Status
Applications
Issues
Future
Links
Contributions

4. History of UJ Research Cluster
UJRC started as an initiative of the High Energy Physics Group
March The UJ-OSG Compute Element passes validation and is registered on VORS
March 2009 – 56 CPU Cores available

5. UseR Groups High Energy Physics (Physics) Astrophysics (Physics)
Molecular Dynamics (Chemistry)
Quantum Chemistry (Chemistry)
Applied Mathematics
Numerical Studies (Engineering)

6. HARDWARE 1 Head Node comprising :
Dell 2950, 2 x 4 Core Xeon Processors
16 GB RAM
900 GB – RAID5
Scientific Linux 4/64 Bit
hosts : NFSv4, Accounts, Torque, Ganglia
We run both OSG and glite at UJ.
We have a single head node that hosts completely separate Virtual Machines for OSG and gLite services.
The two grids use a single batch system (torque-pbs).
All Worker Nodes can run OSG, gLite or local jobs

7. HARDWARE (Contd) Separate Virtual Machines (VMWare Server) for :
OSG CE (1 GB RAM)
OSG UI (submit node) – (2 GB RAM)
gLite CE (1 GB RAM)
gLite UI (submit node) – (1 GB RAM)
40Gb Drive Space for OSG, 80 Gb Drive Space for gLite

8. HARDWARE (Contd) 7 Worker Nodes comprising :
Dell 1425, 2 x 4 Core Opteron Processors
16 GB RAM
Scientific Linux 4/64 Bit
gLite sw locally installed
OSG sw from NFS
Alcatel 6400 Gig Switch

9. HARDWARE (Contd)

10. SA Grid
The South African National Grid is a project to provide a national grid computing infrastructure to support scientific computing and collaboration. This project is coordinated by a consortium of universities, national laboratories and the Meraka Institute, under the cyber infrastructure programme, based on the gLite middleware .

11. Status OSG is operational on SL4 base
Screenshot taken on Friday from the myosg website

12. Status (contd)
Started Discussion on the choice of referent Tier1/Tier2 for ATLAS and ALICE
WN’s, CE’s and UI’s to be updated to SL5 as requested by LHC Computing Grid
Cobbler and Puppet to be used for the new SL5 node installation and management
Updating of Head Node from SL4/VMWare to SL5/Xen is planned

13. Applications 2 Commercial Applications Running Locally :
ANSYS FLUENT – Flow modeling Software
Star-CCM+ - Computational Fluid Dynamics
Other Local Applications :
Geant4 for NA63, MineralPET
NA63 dedicated simulation code
Diamond Lattice Deformation

14. Applications On OSG : On SAGrid : ENGAGE VO runs a few jobs
Full ATLAS VO Support
local ATLAS users submit remote jobs from local UI
Initial discussions have started to allow DOSAR VO
On SAGrid :
Will allow SAGrid VO’s
ALICE VO
ATLAS
DOSAR VO discussion slow as we waiting for formal VO policy to be in place

15. The UJ Research Cluster
and the OSG GRID
UJ – Physics‏ High Energy Physics, ATLAS experiment at CERN
Ketevi Assamagan, Simon Connell, Sergio Ballestrero, Claire Lee, Neil Koch, Phineas Ntsoele
ATHENA installed, using Pythia event generator to study various
Higgs scenarios.

16. Diamond Ore Sorting (Mineral-PET)‏
UJ – Physics‏ ‏
Diamond Ore Sorting (Mineral-PET)‏
Sergio Ballestrero, Simon Connell, Norman Ives, Martin Cook, Winile Sibande
GEANT4 MonteCarlo
Online diamond detection
Monte Carlo simulation
Online diamond detection

17. Issues Limited International Bandwidth Currently Using 11Mb/s
To be Upgraded early next year with the SEACOM cable
1,2 TB cable, UJ has reserved 500Mbits/s

18. Issues (contd) Additional complexity to manage both OSG and gLite
Lack of caching by OSG installer, partially solved with local Squid cache
No automated install & config system yet, starting to work on Cobbler and Puppet
NFSv4 problematic on SL4
Monitoring, need to add detailed job monitoring/stats for Torque
NFSv4-on SL4 low load seems acceptable after disabling automount, will see on SL5 under load
Monitoring : MRTG & Ganglia for internal mem/CPU/net in place – Zabbix for SAgrid

19. Issues (contd)
Manpower – Grid services not primary job/role for the 3 people
Low Usage – Marketing of services and availability has been done but researchers are slow to start
No experience gathered on utilization of resource in terms of constraints on memory, disks, CPU and network
VO acceptance policy required

20. Future Hardware Upgrade : DOSAR Workshop in South Africa in 2010
Additional 4 x WN’s being configured
1 x Dell MD1000 Storage shelf (6TB raw)
will be connected to the Head Node. – Ordered
16 x WN’s (Dell M605 blade chassis, with 2 x 6 Cores, 32GB Ram) – Ordered
224 Cores will be available
DOSAR Workshop in South Africa in 2010

21. Links University of Johannesburg http://www.uj.ac.za UJ Physics
South African Grid

22. Contributions Prof. S. Connell – UJ Physics Department
Sergio Ballestrero - Physics & CERN ATLAS TDAQ
Francois Mynhardt – UJ I.C.S Department

23. Questions Clear, floating 3-D text (Intermediate)
To reproduce the text effects on this slide, do the following:
On the Home tab, in the Slides group, click Layout, and then click Blank.
On the Insert tab, in the Text group, click Text Box, and then on the slide, drag to draw the text box.
Enter text in the text box, select the text, and then on the Home tab, in the Font group, select Impact from the Font list, and then enter 130 in the Font Size box.
On the Home tab, in the Paragraph group, click Align Text Left to align the text left in the text box.
On the Home tab, in the Font group, click Character Spacing, and then click More Spacing.
In the Font dialog box, on the Character Spacing tab, in the Spacing list, select Expanded. In the By box, enter 7.
Under Drawing Tools, on the Format tab, in the WordArt Styles group, click the arrow next to Text Fill, point to Gradient, and then click More Gradients.
In the Format Text Effects dialog box, click Text Fill in the left pane, select Gradient Fill in the Text Fill pane, and then do the following :
Click the button next to Preset colors, and then click Silver (fifth row, third option from the left).
In the Type list, select Linear.
Click the button next to Direction, and then click Linear Diagonal (first row, first option from the left).
In the Angle box, enter 220°.
Under Drawing Tools, on the Format tab, in the WordArt Styles group, click Text Effects, point to 3-D Rotation, and then under Perspective click Perspective Heroic Extreme Left (third row, second option from the left).
Under Drawing Tools, on the Format tab, in the WordArt Styles group, click Text Effects, point to Bevel, and then under Bevel click Cool Slant (first row, fourth option from the left).
Under Drawing Tools, on the Format tab, in the bottom right corner of the WordArt Styles group, click the Format Text Effects dialog box launcher. In the Format Text Effects dialog box, click 3-D Format in the left pane and then do the following in the 3-D Format pane:
Under Depth, in the Depth box, enter 15.5 pt.
Under Surface, click the button next to Material, and then under Translucent click Clear (third option from the left). Click the button next to Lighting, and then under Special click Flat (first option from the left).
12. Under Drawing Tools, on the Format tab, in the WordArt Styles group, click Text Effects, point to Shadow, and then under Perspective click Perspective Diagonal Lower Left (second row, first option from the left).
To reproduce the background on this slide, do the following:
Right-click the slide background area, then click Format Background. In the Format Background dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:
In the Angle box, enter 45%.
Under Gradient stops, click Add or Remove until three stops appear in the drop-down list.
Also under Gradient stops, customize the gradient stops that you added as follows:
Select Stop 1 from the list, and then do the following:
In the Stop position box, enter 0%.
Click the button next to Color, and then under Theme Colors click Black, Text 1 (first row, second option from the left).
Select Stop 2 from the list, and then do the following:
In the Stop position box, enter 25%.
Select Stop 3 from the list, and then do the following:
In the Stop position box, enter 100%.
Click the button next to Color, and then under Theme Colors click Aqua, Accent 5, Darker 25% (fifth row, ninth option from the left).