Beginners Guide to CEES HPC Resources

##Getting access To register for access to CEES computer resources Please fill out this form.

Non-UiO staff: You will need a guest researcher account. Your collaborator from UiO will need to submit application for this, please check [link] (http://www.uio.no/english/for-employees/support/human-resources/payroll/hr-payrollsystem/associated-users.html)

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##Logging in

1. The cod nodes

• To log in type the following command into your command line interface:

  ssh [email protected]

• Check that you are a member of the group 'seq454' by simply typing:
  groups

  If 'seq454' is not listed, please contact Lex Nederbragt.

2. Abel

• To log in, type: ssh abel.uio.no

• qlogin:

  Notes:

• When you are on the UiO network it is enough to write, for example, ssh cod5 or ssh abel

3. Navigation

Some useful commands for moving around pwd cd ls

4. Where to work? Where to store data?

Notes: *

5. Copying data

6. Softwares

• Software installed on abel

A large number of programs is already installed on abel, and can also be used when logged in to the cod nodes. These programs have been installed and are maintained by people at USIT and are available for all users of abel (not just CEES). This software is available through the 'module' system, which is explained in more detail in this manual. If you're logged in to abel or the cod nodes, type

module avail

and you'll see a list of all the available programs (it will take a few seconds until the list is loaded).

• Software installed by CEES users

As USIT people are too busy to answer every request for software installation on abel, an increasing amount of software has been installed by CEES users. This software lives in /projects/cees/bin, and in order to keep things organized, we also follow the module system. If you have properly set up your environment (see above), this type of software also shows up in the list that you see when typing module avail

You'll see it at the top of the list, under the heading '--- /projects/cees/bin/modules ---', while the modules maintained by USIT appear below, under heading '--- /cluster/etc/modulefiles ---'. Some software in /projects/cees/bin is not yet accessible through modules, but only cause we haven't gotten around to that yet. If you need to use software that's installed in /projects/cees/bin, but has no module associated with it, please contact Lex or Micha, and we'll prepare one.

• Software not installed yet

If you need to use software that's not installed on abel and the cod nodes yet, there are two ways to make it available. If you're not the only one who needs this software and it is likely to be used by many researchers, it might be worth asking people at USIT whether they could install it for you. To do so, send an email to [email protected] with a polite request, and they'll see what they can do. If you seem to be the only one interested in this software, or if USIT people are too busy to care, you can install the program yourself, in /projects/cees/bin/, and with the corresponding module. To do so, please see the instructions given here.

7. Submit jobs

• abel SLURM
• cod nodes

Useful tip

1. screen command

If you are starting a long running job you cannot close the terminal window because the job will be cancelled. Instead create a 'screen' in the terminal window from which you start to run the job: type

screen

You now started a 'new' terminal. Start your job in this new window. After you have started your job you can detach from this screen by pressing ctrl-a-d (The CTRL key with the 'a' key, followed by the 'd' key). Now you're back in the terminal where you started. You can close this terminal or even the computer and the 'new' terminal will still exist and continue to run your job. You can start multiple hidden windows by just repeating this procedure. If you want to get back into the now hidden screen type

screen -rd

If you have multiple hidden windows this command will give you a list of the windows available. To choose one of the windows just add the window-number after the command.

screen -rd 45142.pts-15.cod5

When your job is finished you need to close the hidden window by typing exit instead of ctrl-a-d

2. Jobscripts

You can use a job script: collect a bunch of commands and put them in an executable file. Run the command with

source yourcommands.sh

3. Sample SLURM script

Here is a sample slurm script that you can modify based on your needs!