Troubleshooting

Occasionally tasks will fail. Grid Engine provides some tools and logging information for debugging such tasks.

When tasks begin running they generate two files, jobname.ojobid (e.g. feat.o12345) (referred to as the .o file) and jobname.ejobid (referred to as the .e file), which by default are created in the folder from which fsl_sub was run. The .o file contains any text that the program writes to the console whilst running, for example: 

fsl_sub ls my_fo​​lder

outputs the job id ''12345''. The task would generate a file ls.o12345 containing the folder listing for my_folder. If your command produces a running commentary of its progress you could monitor this with the tail command:

tail -f command.o12345

This will continue displaying the contents of command.o12345, adding new content as it arrives until you exit (type CTRL-c). The .e file contains any error messages the command produced. If you still need help then please contact the IT Team.

​​​KILLING JOBS

If, after submitting a job you realise that you have made a mistake or that the job can't complete (perhaps you have insufficient disk space), you can kill the job with the command:

qdel job_id

If the job is currently running there may be a short pause whilst the task is terminated.