From PRAGMAgridWIKI

Contents 1 University of Zurich, Switzerland 1.1 Cluster Maintenance 1.2 Contacts 1.3 Web Pages 1.4 Cluster Hardware 1.5 OS and System Software 1.6 Resource Status 1.7 Application Status 1.8 Applications Notes 1.9 User Mapping 1.10 Prioritized Tasks

University of Zurich, Switzerland

Cluster Maintenance

As of 4 Aug 2008 a part of the ocikbpra cluster needs to be scheduled for another project. Until further notice the nodes 0-7 are available for PRAGMA use, while nodes 8-15 are reserved. The scheduling is done automatically so users do not need to be concerned about nodes numbers specifics and can submit their jobs as before.

Contacts

• Technical staff:
  • System administrator - Mike Packard
  • Software architect - Nadya Williams
• Application drivers:
  • GAMESS/APBS - Celine Amoreira, Prof. Dr. Kim Baldridge
  • SIESTA - Prof. Dr. Alberto Garcia, Dr. Laura Zoppi
• Management personnel:
  • Grid computing project leader - Dr. Wibke Sudholt
  • Research group head - Prof. Dr. Kim Baldridge
• Account requests and technical problems:
  • Mike Packard
  • Nadya Williams

Web Pages

• Grid Computing Team
• Baldridge Group
• University of Zurich

Cluster Hardware

• Number of nodes:
  • Frontends - 1(public network)
  • Compute nodes - 16 (private network)
• CPU/Memory:
  • Frontends - Intel(R) Xeon(TM) 2 CPU 2.80 GHz / 2 GB RAM
  • Compute nodes 0 - 7 - Intel(R) Xeon(TM) 2 CPU 2.80 GHz / 2 GB RAM
  • Compute nodes 8 - 15 - Intel(R) Xeon(R) 2 CPU 1.60 GHz / 2 GB RAM
• HDD:
  • Frontend - 135 GB (/export/$HOME)
  • Compute nodes 0 - 7 21 GB (not shared)
  • Compute nodes 8 - 15 61 GB (not shared)

OS and System Software

• Rocks v4.3 (Mars Hill)
• Rolls:
  • apbs
  • bio
  • condor
  • grid
  • hpc
  • java
  • sce
  • sge
  • web-server
• Middleware:
  • Globus Toolkit v4.0.4
    • gsiftp port is 7811
    • MDS port is 7135
    • gatekeeper port is 2119
    • NOTE: all users please use specify ports in your scripts as needed.
  • Gfarm v1.4.1
  • Nimrod Portal v1.2.0

Resource Status

• ocikbpra.uzh.ch realtime status
• SCMSWeb status
• Probe status

Application Status

List of applications installed on the cluster. In case of multiple versions, the default one is in this font.

• GAMESS versions
  • 27 JUN 2005 (R2) (in /opt/gamess)
  • 7 SEP 2006 (R4) (in /share/apps/gamess_2006)
  • 24 MAR 2007 (R3) (in /share/apps/gamess_2007)
• APBS v.0.5.1 (in /opt/apbs)
• SIESTA v2.1.58
• Autodock v3.0.5 (in /share/apps/nordugrid/software/apps/autodock-3.0.5)

Applications Notes

• Please use the name ocikbpra.unizh.ch and not ocikbpra.uzh.ch whenever needed in your setup configuration and shell scripts when running your applications.
• Globus users please use the following on-default ports:
  • gsiftp port is 7811
  • MDS port is 7135

User Mapping

This table provides mapping from a real user name to an account.

Name	Account		Name	Account
AvianFlu Grid	afguser		Alberto Garcia	agarcia
Steve Androulakis	androulakis		Arielle Yablonovitch	ayablono
Blair Bethwaite	blair		Colin Enticott	cme
Jongbae Moon	eairs		Fang-Pang Lin	fplin
Grid Accounting	gridacct		Habibah Wahab	habibah
Haley Selma Hunter-Zinck	hhunterz		Hsing Pao	hsing
Tsutomu Ikegami	ikegami		John Sanabria	jas
James Frey	jfrey		Jysoo Lee	jysoo
Lisa Yung	liyung		Lynn Shiao Tai	lstai
Laura Zoppi	lzoppi		Mark Aaron Bate	mark
Marshall James Levesque	mlevesqu		Maria Amalia Prada Fernandez	mpradafe
Phillip Dao Pham	pdpham		Randy Lee	ralee
Rachel Leeann Chu	rchu		Yusuke Tanimura	tanisuke
Osamu Tatebe	tatebe		Tim Ho	tim
Thanh Truong	truong		Varahenage Ranmali Perera	vperera
Wilfred Li	wilfred		Simon Xianhe Han	xhan
Yoshio Tanaka	yoshio		Zhao-Hui Ding	zding
Cindy Zheng	zhengc		Sameer Tilak	sameer

Prioritized Tasks

• Gfarm installation - agent and client installed on July 3, 2007