Part 1: Connecting to UPPMAX

Before moving on to the exercises, you will first need to connect to Milou on Uppmax through ssh.

Instructions for mac
If you have a Mac, first check if you will be able to use X forwarding. It is included in older macs but was removed in the latest releases where you need to install it (see: http://support.apple.com/en-us/HT201341). Then start the terminal (black screen icon).

Instructions for PC
If you work on a PC, download and start MobaXterm (you can download it here: http://mobaxterm.mobatek.net/).

You will be using half a node (8 cores) per person. This means you will end up sharing one node for two people as one node consists of 16 cores. It is essential to log in with X forwarding (-X) option to be able to display graphical interfaces across remote computers. Type the following command but replace username with your login name.

Connect to Uppmax:

ssh -X username@milou.uppmax.uu.se

The next command will reserve a compute node for the next 8 hours.

The following command should be run only once a day otherwise you will be using more than 8 cores and others might not be able to connect.
Go to the next step if you already run step 2 today

salloc -A g2015028 -t 08:00:00 -p core -n 8 --no-shell --qos=interact &

Type the following command to see the node you are affected to:

squeue -u username

The nodelist column gives you the name of the node that has been reserved for you.

To log in to compute node run the following command (replace mXX with the actual compute node you are assigned to)

ssh -X mXX

Make sure that you can launch graphical tools in your node by typing this command:

xclock

If you see the clock then you should be able to launch GUI-based tools such as MEGAN or Artemis remotely. Close the clock.

Load all necessary softwares to complete all exercices

source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

Now we can check that all softwares have been correctly loaded, please type the following command in your terminal and check that all element of the list below is listed.

module list

Please contact the teachers if one of those softwares do not appear in your list.

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