Running Interactive jobs on the HPC Clusters
(i.e. iceberg or ShARC)
- Having logged onto iceberg or ShARC you will normally be on one of two head-nodes that are designated for logging in only.
- To do any useful computing you should next connect to one of the HPC worker nodes.
- You can do this interactively by using the qsh or qrsh commands.
- Or alternatively you can submit batch work to the worker nodes by using the qsub command.
NOTES: HPC head-nodes can only be used for light work such as editing files, viewing results or transferring files.
Almost all the main applications are available only on the worker nodes.
The command prompt on the interactive shell will indicate the name of the worker you are using. If it is iceberg-login1, iceberg-login2, sharc-login1 or sharc-login2 you are on the head-node and should next type qsh or qrsh to use a worker-node.
When to use qsh when to use qrsh?
Use qsh, if you have connected to iceberg or ShARC by using a graphics capable (X11) terminal emulator, such as:
If you have connected to iceberg or ShARC without the graphics (X11) capabilities then you can only use the qrsh command to get to a worker node.
This is because the qsh command requires X11 capabilities to open up a new window, whereas the qrsh command connects you to a worker by using the same window you already have to iceberg or ShARC. Both qsh and qrsh accept the same set of extra SGE parameters.
Size of the fonts on the terminal window
If some terminal emulators, in combination with the display resolution and characteristics of the workstations use undesirably small or strange fonts we recommend you resort to following methods of solution:
- use Qsh instead of qsh ( this will attempt to use a larger font for the new new window ).
- on the terminal window work area press and hold-down the Ctrl key and click the Right-hand Mouse button. This should display a menu which will have an option to change the font size.
What about memory and time-limit requests for the interactive jobs?
Qsh command will accept the -l h_rt= and -l rmem= parameters as normal but currently no interactive job will be allowed to run for more than 8 hours. If the -l h_rt=hours:minutes:seconds is not specified, it will be assumed to be the maximum allowed, i.e. 8 hours. Therefore it is unnecessary to specify it for interactive jobs unless you really want your interactive job to terminate after a given period.
Am I restricted to a single window for an interactive session?
Absolutely NO. You can have as many windows as you can handle.
Once you started a qsh session on a worker node, you can use the commands such as Xterm , uterm or xterm& to open multiple windows and perform different tasks in each of them. All these tasks will be running under the same interactive session on the same worker.
Alternatively you can use Qsh to open new interactive sessions. This will also allow you to work on multiple windows but your interactive sessions are likely to be on different worker nodes.
Batch Processing on Iceberg and ShARC
Use the qsub command. This command can be issued from any one of the head-nodes or worker-nodes for submitting batch jobs to the HPC cluster.
- Long-running applications on the head-nodes may be killed by the system administrator.
- Both batch and interactive usage of iceberg and ShARC is controlled by the "Sun Grid Engine" job scheduling system.
- Refer to section on submitting jobs to iceberg and ShARC for further details of the qsub command.