Using Genesis

• Introduction
  • Software Available
• Getting Started
• Finding Information
• Mailing List
• Mail
• Printing
• Changing your Password
• System Accounting
• Disk Space & File Storage
  • Access to computer centre home directories
  • Access to departmental file systems
  • Archiving
• Reporting Problems
• PVM
• CHIMP

Introduction

Genesis is a Silicon Graphics Onyx2 high performance computer residing in the High Performance Computer Centre at the University of Reading. Genesis has a dual rack configuration with 12 processors, an infinite reality graphics engine, 1.5GB of memory and 27 GB of disk space. Further details of the Onyx2 hardware can be found on the SGI WWW site or in the online books in the SGI_ADMIN section. The machine is located in room 185A in the department of Computer Science.

The machine has a 100MB FDDI connection to the campus backbone and to the Silicon Graphics Power Challenge in Meterology. This allows both easy access from all computers on campus and a high speed link between the two supercomputers.

The machine is used by various departments and research groups around the department who purchase processor time on this machine. For further information contact either Peter Parsons, the HPCC Research Fellow, or Prof. Graham Megson the HPCC Director.

This document is a very early draft intended to get the first users started on the system, further documentation will be written at a later date.

Software Available

There is a considerable amount of software installed on the system. A complete list can be found here.

Getting Started

You should first obtain an account on genesis. This can be arranged via either Peter Parsons, the HPCC Research Fellow, or Prof. Graham Megson the HPCC director.

The machine may be used from on the console or remotely across the network. For the purpose of this section it is assumed that the machine is being acessesed accross the campus network from a workstation running X-Windows.

Before rlogin into the Onyx2 you should first give it access to your X display. At the command prompt on your workstation type

"xhost +genesis".

This will allow any X applications running on genesis to display onto your workstations X display. (The use of xhost is considered insecure, a more secure option is to use xauth (which is outside the scope of this document.) You can then access genesis using either rlogin,

"rlogin genesis"

or telnet

"telnet genesis"

(Passwords are set initially to match your Computer Services Centre password.)

Once you have sucessfully logged into ssphcc you should ensure that the DISPLAY environment variable is set to display windows on your workstation. This variable defines where any X programs you start will be displayed. In most cases this is done automatically by the login scripts, it should be set to

your-workstation-name:0.0

You can check the value with the command

"echo $DISPLAY"

and set it with the command

"setenv DISPLAYyour-workstation-name:0.0"

Any programs you run will now be displayed onto your local X display, for example to get a window with a command prompt type

"xterm &"

Once you have successfully logged in and configured the X display you are ready to use genesis. To find out more details on the installed software read the finding information section.

Finding Information

There is a large amount of online documentation installed on the system which can be accessed by the infosearch tool. This documation consists of:

• online books and help cards: This conists of many volumes of detailed manuals covering many aspects of system. These manuals are divided up into a number of main areas, SGI EndUser, SGI Developer, SGI ADMIN and the How Do I help cards.
• man pages: These are the standard UNIX online manuals which detail all the library functions, commands and file formats.
• release notes: The release notes issued with the software, often contain upto the minute details.

The infosearch tool is envoked by typing

"infosearch"

Unfortunately, this tool will not run correctly on all X displays including Black and white sun displays. The command does work correctly from Computer Services Center Sun Labs and on most other workstations.

The man command is a very useful command line tool. Typing

"man item"

will bring up the manual page for that particular item. The keywork search option is particularly useful, for example if you needed a tool to view postscript type

"man -k postscript"

this will bring up the manual page for all the postscript related commands including several viewers.

The notes from the seminar held on the afternoon of the opening may be found in /usr/demos/SEMINAR and viewed using showcase. e.g.

cd /usr/demos/SEMINAR; showcase -v <filename.sc>

Mailing List

A mailing list has been established for users of genesis. Notices about new hardware and software, and planned shutdowns will be posted to this list and users are invited to use this list as a discussion forum.

To subscribe to the mailing list you should send email to hpcc-users-request@reading.ac.uk with subject subscribe. To post to the list send email to hpcc-users@reading.ac.uk.

Mail

Genesis can not be used to read your mail, but mail can be sent from the machine. The mailx command can be used to send mail; pine is not installed.

The HPCC has a number of mailing addresses:

1. hpcc@reading.ac.uk - a general contact address.
2. hpcc-info@reading.ac.uk - an information contact at the centre.
3. hpcc-bugs@reading.ac.uk - to report problems.
4. hpcc-users-request@reading.ac.uk and hpcc-users@reading.ac.uk - the users mailing list for discussion

Printing

At present there is no general printing service available to users of genesis. It is hoped that the Computer Services Centre will agree to the use of their centralised line printers.

Most applications allow you to either print to a file, or to print to a pipe, which allows you to create a file which you can print out from another machine.

Computer Science users may print to the following departmental printers; lw1, lw2, lw4 and lw5. These printers are controlled by the departmental accounting system which prevents unauthorised users from using them.

By request, similar arrangements could be made to give access to other department's postscript printers.

To print a postscript file use the command

"lp -dprinter filename"

and the command

"lpstat -o printer"

to check the queue.

Changing Your Password

Your password is changed by using the

passwd

command. This command will require that you choose a reasonably secure password.

System Accounting

Departments or indvidual users have paid for specific allocation of system resources. Genesis records accounting information for every process which is run. This information is collated for each user of the system. If a single person is working on more than one project which should be accounted for separately they must working under separate accounts for the different projects. Additional user names can be applied for through the computer centre and added to genesis.

Disk Space & File Storage

The disk space allocation policy is still under consideration by the management but the following inital allocations have been made.

1. For temporary storage a four gigabyte partition has been allocated and is mounted on /var/scratch. This is for temporary use only and must not be used as a permanent extension to your home directory. To this end files will automatically be deleted if they have not been accessed for 3 days, or sooner if space is limited.
2. Users home directories have been allocated as follows:
   • 1.2 gigabyte partitions for Chemistry, Physics, Meteorolgy, Engineering and Computer Science.
   • 2 gigabytes for the remaining departments and for proposed indutrial links.

The management are also considering how to fund additional disc space, if required.

Access to computer centre home directories

Many users of the system high performance computer centre have accounts on the computer centre machines which have different home directories to their account on genesis. (/home/sufs1/ru??/<dept>/<user>) Some users will wish to transfer data between these different home directories, for example to use the computer centre archiver to store large data sets. This can be done by using FTP, or by special request your Computer Services Centre home directory can be mounted on genesis

By request the computer centre is willing to export your department's computer centre home directory the high performance computer centre. Once exported your computer centre home will automatically be mounted when accessed, e.g. when you change directory into it. You should be aware that exporting your computer centre home directory will make it accessible to the HPCC support staff.

To request for your department's computer services home directories to be exported to genesis you should write to Hilary Vines at the Computer Centre. You should confirm that you understand that your home directory will be accessible to high performance computer centre support staff. The request should be processed in about a week.

Access to departmental file systems

Some departments have their own UNIX systems which may have a significant amount of storage. For example the Computation Vision group in Computer Science have many gigabytes of images stored on there system, some of which they wish to process on the Onyx2.

By request, departmental UNIX file systems can be mounted onto genesis using the automounter. Users should approach their system manager first and ask them to export the file systems to the host genesis, then they should contact the HPCC support staff.

Such mounted disk space must be used responsibly to ensure that the campus network or the HPCC network does not become overloaded. This service may be withdrawn at short notice, if excess network loading occurs.

Archiving

The computer centre at present offers a free automatic archiving service (commercial projects using computer centre equipment are charged for their use). At present this service allows users to archive files from their Computer Centre Directories, this is detailed on the Computer Services Centre WWW pages.

It is proposed that the High Performance Computer Centre, once up and running, to survey its users and find out if the above archiving system is sufficient. If not the computer centre will be contacted to discuss means of improving this service, and the level of any charges. For example, it might be possible to arrange for the discs on genesis to be mounted on the archiver to allow direct archiving.

The High Performance Computer Centre does not have the resources to run an effective archiving service. It may be possible to use the centres tape drives for a occasional transfer archiving of data initially. As this will consume a significant amount of staff time and DLT tape are relatively expensive it may be necessary to charge for this service. But as the amount of disk space on genesis increases the tape drives will be increasedly needed for system backups.

The need for archiving should be considered carefully, in the longer term the centre should consider the purchase of its own archiver.

Reporting Problems

Please report any problems you find by sending mail to hpcc-bugs@reading.ac.uk

PVM

PVM is a software system that enables a collection of heterogeneous computers to be used as a coherent and flexible concurrent computational resource.

PVM 3 can be found in /usr/local/pvm3. PVM system has been compiled for a shared memory mutliprocessor in both 32bit and 64bit versions.

To use PVM you should source /usr/local/pvm3/pvm3.login ; documentation can be found in the /usr/local/pvm3 directory.

CHIMP

CHIMP (Common High-level Interface to Message Passing) was developed by the Edinburgh Parallel Computing Centre. Since its inception in 1991 CHIMP has evolved from prototype through Version 1 to the current Version 2 interface specification.

CHIMP, and its documentation, can be found in /usr/local/chimp.

To use CHIMP you should source /usr/local/chimp/chimp.login.