1. The Applications list shows that the software I need is installed but when I type the command I'm told "command not found".
2. How do I set up my account so that modules I always require are loaded automatically?
3. Attempts to log in with NX fail. Why?
   
4. My interactive processes were killed after a couple of hours. What went wrong?
5. My job fails to run! There is no output and no errors are reported. What's gone wrong?
6. My job started but only ran for a minute. What's gone wrong?
7. My job is shown as Blocked or Deferred.  What's gone wrong?
8. How should I acknowledge use of the HPC facilities in research publications?
   

The Applications page says that the software I need is installed but when I type the command I'm told "command not found".

This is probably because you've not loaded the module which sets up your environment correctly for this software. There is further documentation about how to use Modules which explains this in more detail.

How do I set up my account so that modules I always require are loaded automatically?

You can edit the file

~/.bashrc

adding entries at the end of this file to always load the modules you need. If you haven't made any other modifications to this file and you always wish to use R version 2.13.0, your .bashrc file would become:

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions

module load R/2.13.0

Attempts to log in with NX fail. Why?

Usually a failure to log in with NX is due to your account having gone over quota. The NX server session on ALICE and SPECTRE stores some state files within your home directory; if you have reached or exceeded your  file quota, these cannot be created and NX fails.

If this happens it is still possible to log in via SSH (i.e. with PuTTY). Log in, check your quota with the quotacheck command, and if necessary delete any unwanted files, or move them to your scratch directory. Once some space has been cleared, it will be possible to log in with NX again.

My interactive processes were killed after a couple of hours. What went wrong?

The login nodes on SPECTRE have a hard limit of two hours of CPU time usage per process. If this is exceeded, the process will be killed. For further information see the page about Interactive vs Batch jobs.

My job fails to run! There is no output and no errors are reported. What's gone wrong?

Almost certainly this is because you have not specified a value for pvmem, or have a value which is too low. Increase the value requested and resubmit your job.

My job started but only ran for a minute. What's gone wrong?

It's likely that you've not requested the walltime for a job. This is required to ensure that jobs can be scheduled effectively and that the system can be emptied for service days. If it's not specified, the default value is one minute. There is more information in the page about Submitting Jobs

My job is shown as Blocked or Deferred.  What's gone wrong?

Jobs can be placed in the deferred state for several reasons. 

1. You have too much outstanding work (i.e. a large number of running and/or idle jobs)
2. A back-end service was experiencing problems when you submited your job
   
3. There is something wrong in your job submission script

In the first two cases you don't need to do anything as the scheduler will re-assess Deferred jobs after an hour to see if the condition that lead to them being deferred has gone away.  If so, your jobs will be moved to the running or idle state as normal.  The command

> checkjob -v <jobid>

will give you more information about why a job has been deferred.

How should I acknowledge use of the HPC facilities in research publications?

 One of the following statements should be used:

This research used the ALICE High Performance Computing Facility at the University of Leicester.

or

This research used the SPECTRE High Performance Computing Facility at the University of Leicester