CCC-graphics cluster
For an account on these computers:
- if you wish to use the computational group sub-cluster, contact a staff member of the computational group,
- if you wish to use the bio-nmr group sub-cluster contact Matt Crump.
If your request is approved it will be forwarded to (or you should then email) chem-unix@bristol.ac.uk with your UoB username and name of your supervisor.
For support email chem-unix@bristol.ac.uk.
See this page for information about how to change your password on the cluster.
Each year you will have to renew your account for it to remain open.
You will receive an email about this in January each year, please reply
to this email stating whether or not you wish your account to remain
open.
If/when you leave Bristol, please contact the system administrator and
provide a new email address so that you can continue on the ccc-graphics
email list.
Only secure shell connections are allowed to these computers.
Notice under the Data Protection Act
File storage space is provided on the ccc-graphics cluster solely for your research data and results. Private files should not be kept on the ccc-graphics cluster as they are not held confidentially. Access to your files will be provided to members of staff, and to others if the appropriate member of staff requests it.
The Systems
- laurel.chm.bris.ac.uk 4 x 300 MHz R12000 processors, 2 GB RAM
- hardy.chm.bris.ac.uk 8 x 300 MHz R12000 processors, 4 GB RAM
Computational Group Systems in W233
- luna.chm.bris.ac.uk 250 MHz R10000 processor, 256 MB RAM
- primo.chm.bris.ac.uk 195 MHz R10000 processor, 256 MB RAM
- aries.chm.bris.ac.uk 180 MHz R5000 processor, 64 MB RAM
Bio-NMR Group Systems in N321
- diamond.chm.bris.ac.uk 300 MHz R12000 processor, 512 MB RAM
- amethyst.chm.bris.ac.uk 300 MHz R12000 processor, 512 MB RAM
- topaz.chm.bris.ac.uk 2 x 250 MHz R10000 processors, 1 GB RAM
- emerald.chm.bris.ac.uk 500 MHz sun4u sparc processor, 256 MB RAM
Laurel is the nameserver for the cluster and hardy is the fileserver, that is, your will have the same username, password and home directory on all systems in the cluster. The user disk space on the ccc-graphics cluster is backed up approximately every two weeks.
Laurel and hardy can be used for general calculations, the other systems are workstations, intended for running graphical based modelling programs. In general laurel and hardy should only be used for programs that can only be run on SGI's or that need to be run interactively. The normal systems for running CPU intensive calculations are grendel, dirac and bohr.
Laurel and hardy can normally only communicate with chemistry department computers. If you wish to connect with laurel or hardy from outside the department and have an account on another of the clusters belonging to the department (e.g. grendel), you should first login to the other cluster, and from there login to laurel or hardy. If you do not have an account on another cluster you will need to send the IP address of the computer you will use as your local host to the system administrator to make the connection possible.
Computational group workstations can only communicate with the Chemistry 40 subnet (including chm-fs), grendel, dirac and bohr.
Bio-nmr group workstations can only communicate with the Chemistry 43 subnet, chm-fs, laurel and hardy.
All users can login to laurel and hardy. Other than that, bio-nmr users cannot use the computational group workstations and vice-versa.
The default printer for the computation group systems is the network laser printer in W233.
Users of the bio-nmr group are advised to modify their .cshrc file to differentiate between SGI's and the SUN so they can customise it appropriately. This can be done as e.g.
# For interactive shells, set the prompt to show the host name and event number.
if ( (! $?ENVONLY) && $?prompt ) then
setenv MEKOS `uname`
if ( $MEKOS == "IRIX64" ) then
# do these for an SGI
if ( -o /bin/su ) then
set prompt="`hostname -s` \!# "
else
set prompt="`hostname -s` \!% "
endif
else
# do these for a SUN
if ( -o /bin/su ) then
set prompt="\!# "
else
set prompt="\!% "
endif
endif
endif
Software
Look in /usr/freeware/bin and /usr/local/bin for useful utilities. In particular a2ps, enscript, locate, gnuplot, xmgrace (formerly xmgr), xfig and xv are installed on all the workstations.
- Compilers: Hardy, luna and primo have a full set of SGI
compiler licenses, all systems have the gnu compilers.
- cerius2: Cerius2 is installed on laurel. There is only a
single user licence, so if you wish to use this program you should
contact Professor Allen first. Cerius2 does not work correctly using
X11 tunneling. If you wish to use it you should follow this
procedure.
From a Unix/Linux system: on your local system enter the command:
xhost +laurel.chm.bris.ac.uk
Login to laurel without the -X flag and type the command:
setenv DISPLAY your_local_computer_name:0.0
or setenv DISPLAY your_local_computer_IP:0.0
From a Windows system: switch off the X11 tunnelling and when you have logged in to laurel set the DISPLAY variable as above.
Information Update:
Modern versions of secure shell are increasingly blocking non-X11-tunneling of graphical displays, and it is getting more and more difficult for the above instructions to work. They are a bit better at displaying programs not written to use X11 tunneling. It is always better to try this first. - Tripos software: These programs are available on the
workstations (i.e. not laurel and hardy. To run sybyl, type the
command sybyl7.1. Documentation is available on the
manuals webpage.
- quanta: This program is only available on luna. To run it,
type the command:
source /usr/luna/msi/quanta98/.setquanta
and then start it with the command quanta. - vmd: This visualisation program is available on luna,
primo and aries. To run it, type the command vmd. Documentation
is available on the manuals webpage.
- rasmol v2.6b2: This visualisation program is available on
luna, primo and aries. To run it, type the command rasmol.
Documentation is available on the manuals webpage.
- spdbv: The Swiss-PDB viewer is available on luna, primo
and aries. To run it, type the command spdbv. Online
documentation is available at
http://ca.expasy.org/spdbv/mainpage.htm.
- Maestro/MacroModel: This program can run on all systems in the cluster. To start maestro, type the command maestro. Documentation is available on the manuals webpage.