Troubleshooting


Here you can find solutions to some common problems encounter by our users.

1. When trying to submit a job I get “qsub: script is written in DOS/Windows text format“.

This is a known problem. The batch job scripts are simple text files, but there are different convention about text files formats in Windows and UNIX environment. So if you happened to modify the job script on a windows machine, or in any case if you encounter this error message, just login to any HPC nodes, and run the command dos2unix followed by your job script, i.e.:

dos2unix batch_job.sh

This should fix everything.

 

2. I cannot access /work1, /SCRATCH/ directory after log-in via thinlinc.

/SCRATCH/ is only mounted/accessible from the application nodes, the hpc-interactive nodes and the transfer.gbar.dtu.dk node, dedicated to file transfer to and from the cluster. It is not directly accessible from the “local” terminal on the thinlinc machines. If the prompt of your terminal starts with th you are on the wrong machine, these should only be used via thinlinc and not interactively. To get access to one of the application nodes type

linuxsh

To get access to one of the interactive nodes type

qrsh

In both cases, you can add the -X option to allow for X11 forwarding (graphics).