Bohr - bohr.chm.bris.ac.uk

NB bohr is obsolescent and has been replaced by curie. Accounts are no longer being created on bohr. Much of the information below is also relvant to curie.

For an account on this computer email chem-unix@bristol.ac.uk with your UoB username, name of supervisor and preferred login shell (if you have a preference).

For support email chem-unix@bristol.ac.uk.

Passwords- See this page for information about usernames and passwords on bohr.

Queuing system- bohr uses a queuing system for running jobs. See this page for important information about how it works.

Each year you will have to renew your account on bohr 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 bohr email list.

Notice under the Data Protection Act

File storage space is provided on bohr solely for your research data and results. Private files should not be kept on bohr 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 System

Bohr is a beowulf cluster, that is, a cluster of computers connected together. The master computer is called the front end, the others are called nodes. There are 42 nodes. You login to the front end, which is used for compiling, editing files etc, not for running jobs. Run jobs by submitting them to the queuing system, which will distribute them among the nodes. The operating system is linux.
The users' filestore is backed up nightly with a combination of full and incremental backups. The full backup happens every 2-3 weeks at the weekend and takes two days, so backup frequency is lower on those weekends.

There are 3 groups of nodes, but they are all connected to the same switch and can work together-

The Front End

Only secure shell connections will be accepted to this computer.

To map directories on bohr to a drive on a Windows system (within the department) use \\bohr\[your_username] or \\bohr\users or \\bohr\users1 as required. (This mechanism will always use your standard UOB username and password, no matter what your unix password is).

The front end is for editing files and compiling programs etc. Run jobs by submitting them to the queuing system. Short tests may be carried out on the front end (10-20 mins), anything longer must be submitted to the queuing system. Tests and large compile jobs on the front end MUST be run at low priority using nice -n 19 <command>
i.e. to run a program called a.out, use the command
nice -n 19 a.out
Processes running which fail to meet these requirements will be killed.

There are two main shells available, bash (an extension to the Bourne shell) and tcsh (an extension to the C shell). If you wish your login shell changed, contact the system administrator.

There are two user partitions, /users and /users1.

Note that bohr is a 64-bit system. It will run 32-bit binaries, but in that case you will not gain the advantage in speed of the 64-bit system. You should recompile your programs on bohr.

To ease transfer of files between grendel, dirac and bohr:
dirac's /home, /home2 and /home3 partitions are cross-mounted on bohr as /dirac/dirac, /dirac/dirac2 and /dirac/dirac3.
grendel's /home, /home2, /home3, etc partitions are cross-mounted on bohr as /grendel/grendel, /grendel/grendel2, /grendel/grendel3, etc.
These are automounts, that is, they will automatically mount when you try to access them, and unmount when you have finished.