Getting help
The login nodes on Iridis run a Linux operating system. Googling for things like
How to change directory in Linux
is likely to point you to a useful webpage. The terminal is called bash. So googling for how to do things in bash can also be useful.
Most linux command do have a man page that can be shown with
man <name_of_command>
You can navigate the man page similar to navigation in vi or more (see below).
Working with the file system
Changing the directory
The command to change directories is
cd <name_of_folder>
The filesystem on Iridis4 has two main parts:
/home- This filesystem should hold all your “valuable” files. It is regularly backed up./scratch- This filesystem is meant to store temporary files from your calculations and is not backed up.
The /home filesystem has a default quota of 100GB per user. On \scratch, the quota 1000GB.
There are a few handy tricks:
- You can use
~(tilde) as a shortcut to the home directory - Absolute paths start with
/ - You can use auto-complete by pressing
<tab>
Listing directory content
The command to list the content of a directory is
ls <name_of_folder>
If ls is evoked without an argument, it shows the content of the current directory.
The most useful switches for ls are:
| Switch | Meaning |
|---|---|
| -a | Shows all files including hidden files |
| -l | Shows dates and file sizes as well |
| -h | Uses output formats that are ‘human-readable’ |
Looking at files
There are a number of commands useful to print the content of files.
| Command | Meaning |
|---|---|
cat <filename> |
Prints the entire content of a file to the terminal |
more <filename> |
Prints the content of a file one page after another. |
| “Space” advances a full screen; Return advances line-by-line | |
| “q” exits from displaying the file | |
head <filename> |
Only displays the first couple lines in a file |
tail <filename> |
Only displays the last couple of lines in a file |
Working with the job scheduler
Most calculations on Iridis4 will be done in ‘batch-mode’ (non-interactive). The cluster uses a batch scheduler called TORQUE. The most important commands are
| Command | Meaning |
|---|---|
qsub |
Submits a new job to the queue |
qstat |
Shows the status of submitted jobs |
qdel |
Deletes a scheduled job |
There are also a number of convenience scripts to submit standard jobs for the most often used programs. These generate a job script automatically. You can use
| Command | Meaning |
|---|---|
vsub |
Generate a job running VASP |
csub |
Generate a job running CRYSTAL14 |
The -h switch shows options for both scripts.
Submitting a vasp job
vsub -q test -w 01:00:00 -j O2_dimer
would generate a vasp job to be run on the ‘test’ queue asking for one hour of walltime (after which the job will be killed), and gives the job a name ‘O2_dimer’. If successful, the commands will show the requested resources and a job id that can be used to interact with the job:
Submitting job O2_dimer in folder /home/dk2u09/zhengxu/scratch/tutorial/O2_dimer
Requesting 1 nodes a 16 CPUs, 10gb memory, and 01:00:00 walltime
Submitted job O2_dimer with id 3557693.blue101
The qstat command allows to check the status of jobs in the queue. It shows a table with id, name, the queue, and the status of a job. The status is indicated by a single letter
| Status | Meaning |
|---|---|
| Q | The job is queued and will execute later |
| R | The job is currently running |
| C | The job has completed |
| E | The job is in error and needs attention |
| H | The job is on hold. It will retain its position in the queue, but not execute |
Copying things to/from Iridis4
The way to copy files from/to Iridis depends on your computer and operating system. If you use Putty (Windows), you find a tutorial here How to use putty. Mac OS and Linux have native support for copying files using the ssh protocol:
scp <username>@iridis4_a.soton.ac.uk:<path_and_filename_on_iridis> <local_filename>