Bukak Testbed User's guide

About this document

This document is a users' guide for Bukak testbed resources and includes (1) requirements for users, (2) procedures fore getting an account, (3) hardware specifications and available Grid software, (4) resource utilization policy, and (5) support staff available and mailing lists provided to users, Accroding to future administrative decisions, We may modify this document and distribute the revised version through the this web site (http://pplab.cs.kookmin.ac.kr/xwik/) or MGrid web site (http://www.mgrid.or.kr)

Requirements for users.

• Bukak testbed requests all users to fulfil the following conditions.
  • All users must belong to one of member organizations of PRAGMA.
  • All users participating in PRAGMA must comply with the operating principles of PRAGMA.
  • All users must have concrete purposes for using Bukak testbed resources.
  • All users must contribute to PRAGMA through the use of Bukak resources.
  • All users must have a user certificate issued by trusted CA.

How to obtain an account

• In order to get an account for using Bukak testbed, send the following information

1. Full name
2. Affiliation
3. Address
4. Country
5. Phone and facsimile number
6. Email address
7. IP addressess for accessing Bukak testbed
8. Pupose for using Bukak testbed
9. Desired account name(1st, 2nd, 3rd choices)
10. Shell (bash, csh, tcsh, etc.)
11. ssh public key * **
12. User certificate issued by an Bukak CA or Bukak trusted CA. ** ***

Resource information

We are providing a Linux system to PRAGMA testbed, called Bukak.

Bukak is a 2-nodes Linux Cluseter whose interconnection is Giga-bit Ethernet. Each node has Intel(R) Xeon(R) Quad Core CPU  2.00GHz  and 2GB memory. User's home directory are shared among all nodes via NFS.

Primitive Software

The operating system used on Bukak is Fedora Release 12, and general GNU tools are also installed. (Front end node is Fedora Release 11)

• GCC version : 4.4.1 20090725
• GSI-SSH

Service Port : 2222

• GSI-FTP

Service Port : 2811

Grid Software

• Globus Toolkit 4.0.8
  • GLOBUS_LOCATION=/usr/local/gt4.0.8
  • GPT_LOCATION=/usr/local/gt4.0.8
• Local Resource Manager
  • Sun Grid Engine 6.2u4
    • SGE_ROOT=/home/SGE
• Molecular Simulation Softwares
  • NAMD 2.6
    • amd64(x86_64) : /usr/local/share/namd/2.6/amd64
    • i686(32bit) : /usr/local/share/namd/2.6/i686
  • NAMD 2.7b1
    • x86_64(amd64) : /usr/local/share/namd/2.7b1/x86_64
    • x86(32bit) : /usr/local/share/namd/2.7b1/x86
  • NAMD 2.7b2
    • x86_64(amd64) : /usr/local/share/namd/2.7b2/x86_64
    • x86(32bit) : /usr/local/share/namd/2.7b2/x86
• MPICH version 1.2.7p1
• B-shell)

$ GLOBUS_LOCATION=/usr/local/gt4.0.8; export GLOBUS_LOCATION
$ . \${GLOBUS_LOCATION}/etc/globus-user-env.sh

• C-shell)

% setenv GLOBUS_LOCATION /usr/local/gt4.0.8
% soure ${GLOBUS_LOCATION}/etc/globus-user-env.csh

Resource utilization policy

Basically, Bukak resources are not allowed to be occupied by a single user. This policy was decided on since, in principle, Grid resources should not be expected to be available for dedicated use.

• Maximum 4 hours
• Maximum 4 slots for parallel execution.

Installation of additional software

You can install, test and evaluate your software on Bukak clusters. Since Bukak clusters are shared by many users, you are requested to test and debug your software thoroughly before installing it on Bukak clusters so that it will not damage ths systems. If you need supervisor privilege for installing your software, please contact the support staff.

Data Persistency

We don't guarantee data files. If you want preseve important data, you should be backup your datas.

Support staff

• Bukak clusters are maintained by a support staff. Your requests will be processed in a best-effort manner by the staff. The following two mailing lists for users:

• System administrators of Bukak resources are on this mailing list. This mailing list is used for correspondence from all users. Any requests, questions, and comments should be sent to this mailing list.