Astrophysics Group Computing Guidelines

This page is intended as an easily absorbed list of do and don't items for using the Astrophysics Group computing facilities.

Connecting to Other Machines

If you want a terminal on a remote machine, eg aquila, use ssh to connect to that machine and run your program. If you are connecting from windows, you can use the putty program from here or the MobaXterm program if you want to display graphics. From a Mac or another Linux machines you can use the ssh command to connect, ssh -XY username@aquila.star.bris.ac.uk (linux) or ssh -CXY username@aquila.star.bris.ac.uk from a Mac. You can omit the -XY and -CXY if your program does not require displaying graphics. If you want a full remote desktop, consider the x2go program.

Running your Program

If your program is going to be quick, just ssh to your desktop or a group server, see our servers page here, and run it. If your program is going to take a long time, you have several options.

Use the screen program to run your code, disconnect and log off the server. Come back later when the code is finished and reconnect to your session.
To run your program at a specific time, use the at command and ensure your program writes output to a logfile.
Run your program in the background capturing all output, log out of the server and check the output file from another machine. An example would be my_program > logfile &
We can also submit self-contained jobs on the Particle Physics DICE cluster. Ask Rhys for instructions how to do this.

Desktop Machines

Don't run CPU intensive screensavers, consider not using a screen saver, the screen blanker uses no CPU.

Enable power saving features so that your monitor switches off if it is not used for a while (see your system manager for help with this).

Log out of, or quit, programs that you are not using such as browsers or email clients.

Check what your machine is running using the top command, eg if you hear the fans churning away, there may be a rogue program running, use the kill command to stop it.

File Storage and Backups

Your home directory should be used for things that need nightly backups, this could be work in progress, a thesis, papers, programs, scripts and so on. Data should be stored on one of the data disks, you can run a nightly rsync job to make a copy of your data disk on one of our scratch disks, see the page on rsync in http://www.star.bris.ac.uk/local for instructions on how to do this.

Things to Check Before Running your Programs

Whenever you do anything on a computer, the main resources that you use are CPU, memory (RAM) and disk space. Here some guidelines you should bear in mind.

Before running a job, check the busyness of the machine using the "w" command, as shown below:

/home/rahm/[pol]rahm:  w
  2:39pm  up 13 days, 23:58,  1 user,  load average: 1.04, 1.05, 0.93
USER     TTY      FROM              LOGIN@   IDLE   JCPU   PCPU  WHAT
rahm     tty1     -                22Apr 1 13days  5:09m  0.01s  startx
/home/rahm/[pol]rahm:

The load average shows you the load level of the machine, over the last 1, 5 and 15 minutes. If the level is around 1 as shown above, the machine is already busy running a job. Don't run more than one job per thread, we have hyperthreading enabled on all our machines, so each physical CPU can run two programs. See our servers page to see the maximum loads our servers can take. If someone else is using a desktop computer interactively, and you want to run a program on that machine, use the "nice" command to set your process priority at a level that will not interfere with the interactive user. It would also be polite to ask the interactive user's permission before using their machine as well. See below for an example of using the nice command to lower the priority of a program:

home/rahm/sims_new[pol]rahm: nice myprogram &
[1] 23520
/home/rahm[pol]rahm:

You can check how many threads a machine has using the lscpu command, confusingly this is the same as the CPU(s) number from lscpu.
When programming, don't allocate huge amounts of memory in arrays you don't use.
Use the top program to check your CPU usage.
If you are running a job on a machine, try to use local disks on that machine, this avoids wasteful traffic across our ethernet network and your program will be faster by a factor of up to 10!
If you are planning to run C or Fortran programs that take a long time to complete, make sure you compile them with optimisation. Ask the system manager if you don't know how to do this.

Memory Usage

The Random Access Memory (RAM) in our machines varies from 8gb in older desktop to 1Tb for typhon. Be aware of this when deciding where to run your jobs. Running the top will show the installed and available memory.

Printing

Always print on both sides of the paper (duplex mode). Contrary to urban rumour, theses and reports do not have to be single sided.

Don't submit large jobs that take 20 minutes or more to print, to the printer during the day (9am to 5pm), save them for evening, or possibly lunchtimes.

Rhys Morris

Last modified: Wednesday, 09 June 2021