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Why are my jobs waiting for so long to start?

  • Check gnodes and priority.

  • Check how many cores you are asking for.

  • Check how much memory you are asing for.

  • Check how much time you are asking for.

Why is the partition I chose being ignored?

Unless you specify a partition other that short/normal, like fat2 or express, the partition parameter is largely ignored and your jobs are actually submitted to both partitions. When they start, they are moved to a single partition, in which they are started. This is done to avoid waiting in the short queue if normal nodes are empty.

Long story short: don’t worry, just submit the job asking for an appropriate time limit and it will start in an appropriate place. Unless you want fat2 or express, you can forget about the partition parameter.

How do I open images/PDFs?

Use eog for images and evince for PDF. For these to work you will need to SSH to the cluster with X-forwarding enabled.

How can I avoid losing my session when I close my laptop?

Use a terminal multiplexer like tmux or screen.

How do I prevent accidental changes to my important data?

Put the data in a separate folder and run:

[fe1]$ chmod -R a-w datafolder

Now you can’t change, add or remove files in that folder or any of its subfolders.

Why can’t I connect?

We only allow incoming connections from a whitelisted set of IPs, so if you get a connection refused you should try sending us an email with the IP you are connecting from. You can see what your IP is on http://myip.dk.

Contact us if you need your IP address to be whitelisted.

I have a collaborator that would like to upload some data, how do we do that?

We have a special upload user so just send us their email and we will set them up. Once the data is uploaded we will move it to a folder you have access to.

I am in a closed zone, how do I export files?

If you have many files you should pack them up in a tar/zip. Use gdk-export on the file to be exported and then send an email to Anders Børglum and CC us so we can see when he approves it.

I am in a closed zone, how do I import files?

Importing and exporting data is done through an intermediate server for security reasons. Transferring data into the cluster isn’t restricted, but we still have to go through the intermediate step, so the first thing you do is upload the data to ipsych.genome.au.dk with scp.

[local]$ scp my-file me@ipsych.genome.au.dk:
me@ipsych.genome.au.dk's password:
my-file                                   100% 4387     4.3KB/s   00:00

Now we can import it into the actual cluster, by running the gdk-import command from a session on fe2.

[fe2]$ gdk-import my-file my-file
my-file                                   100% 4387     4.3KB/s   00:00

Now the file is available to your user from all machines, just like any other file in your home directory.

I am in a closed zone, why is NoMachine acting up?

We have seen cases where the keyboard (or just some buttons) stop working and some other mysterious bugs like this.

You should try closing NoMachine completely (not just the window with the current session) and reconnecting - if that doesn’t work the only thing we can do is to kill your session so shoot us an email if you need that.