Uppsala Multidisciplinary Center for Advanced Computational Science

Getting started: First login to UPPMAX

N.B. You are NOT supposed to log in to any webpage with the password and username you get via uppmax support N.B.

In order to use the UPPMAX resources you must login to a dedicated login computer (or 'login node') using ssh ("secure shell"). On linux/unix computers this is done in the terminal with the 'ssh' command. On windows you can download a small freeware program called MobaXterm to connect via ssh.

The hostname used to login is:

milou.uppmax.uu.se

or

rackham.uppmax.uu.se

... depending on where you have an allocation.

Unless you know for certain that you have an allocation on milou or rackham, use tintin. All users are allowed on tintin while only members of some projects are allowed on milou and rackham.

Note: This is a "round robin" address which will direct you to one of the physical login nodes, tintin1.uppmax.uu.se or tintin2.uppmax.uu.se, etc. (If needed, you can also login directly to one of these, by using their respective hostnames.)

Specific for a Linux/Unix or a Mac computer

On unix/linux and Mac OS, start a terminal and use the ssh command, like so (substitute 'username' with your own username):

ssh username@rackham.uppmax.uu.se

  • Note: change "rackham" to the name of the machine you want to connect to.
  • In order to run graphical programs, you need to either enable X11 forwarding, i.e. use ssh -X username@rackham.uppmax.uu.se, or log in using ThinLinc.

Specific for a Windows computer

If you are running windows you could download and install a terminal program like MobaXterm.

After downloading and extracting the zip archive you will have 2 files; MobaXterm_Personal_X.X.exe and MobaXterm_Personal_Customizer_X.X.exe

I suggest you delete the Customizer file since it can only be used if you have bought a licence for the program.

Double click the MobaXterm_Personal_X.X.exe and you should see a terminal window. Use the ssh command, like so (substitute 'username' with your own username):

username@rackham.uppmax.uu.se

Common for all systems (Windows, Linux, OSX)

If it is the first time you connect, you will also need to confirm the host key by pressing 'Yes' if you get pop-up question or by typing 'yes' if you get the question on the command line.

After this, it will ask you for your password. When you type your password, it will look as if nothing is happening. This is to keep others from seeing how many characters your password has, so just keep typing and press enter when you think you have typed it correctly.

A note for people using MobaXterm: It will ask you if you want to save your password. Press 'No' and check the box 'Do not show this message again'.

Then, you are logged in! To log out again, type 'exit'.

Note: The information displayed in the welcome screen (of which only the last lines visible in the screenshot above because of the small window size) contains very important information about the usage of UPPMAX, which might affect your jobs, such as scheduled downtime etc, so please read very carefully, and look out for any announcements!

Changing your password

You should regularly change your password. This is done in the standard Linux way. Type:

passwd

The system will prompt you for your current password, after which it will ask you for a new password and a confirmation of the new password. 

Copying files from/to your UPPMAX account

From a Linux or Unix computer

Copy a file from you computer to your home directory on UPPMAX:

scp some_local_file user@rackham.uppmax.uu.se:/home/username/some-file 

Copy a file from your home directory on UPPMAX to your computer:

scp user@rackham.uppmax.uu.se:/home/username/some-file local_file_or_directory 

To place the file in the directory you are currently standing in, use a dot ('.') as the local directory:

scp user@milou.uppmax.uu.se:/home/username/some-file .

From a Windows computer

If you are running windows you could download or upload files using the file browser in MobaXterm, or the WinSCP software to upload and download files in a similar fashion to how FTP clients work.

Where are my files? (Or, what are the different file systems?)

You have access to the same home directory regardless of what cluster you have logged into. Here you store your private files.

All UPPNEX projects also have a central storage area under the /proj/[project id]/ directory path. I.e. when you first login to UPPMAX you will see your home directory, so you will have to change to the project directory if you want to transfer project data files.

Also note that UPPMAX uses different disk quotas on your home directory and other areas you have access to (like the project folder).

Example: to see who much disk space you use:

uquota

We have a page with more information about different file storages and quotas that can be good to read.

Your private files

When you log in to UPPMAX for the first time you only have the following files created by the system:

ls -la
total 68
drwxr-x---  7 user     uppmax 4096 Jun  2 23:11 .
drwxr-xr-x 19 root     root      0 Jun  9 13:16 ..
-rw-r--r--  1 user     uppmax   24 Jan  9  2008 .bash_logout
-rw-r--r--  1 user     uppmax  435 Apr 21  2008 .bash_profile
-rw-r--r--  1 user     uppmax  446 Jan  9  2008 .bashrc
drwxr-xr-x  2 user     uppmax 4096 Jan  9  2008 bin
-rw-r--r--  1 user     uppmax  385 Jan  9  2008 .cshrc
-rw-r--r--  1 user     uppmax  237 Jan  9  2008 .emacs
drwxrwxrwx  1 user     uppmax   14 Jun  2 11:05 glob
-rw-r--r--  1 user     uppmax  120 Jan  9  2008 .gtkrc
-rw-r--r--  1 user     uppmax  279 Apr 21  2008 .login
drwx--S---  2 user     uppmax 4096 May  2  2008 private
-rw-r--r--  1 user     uppmax  307 Apr 21  2008 .profile
-rw-r--r--  1 user     uppmax  220 Jan  9  2008 .zshrc

The files starting with a "." are hidden files — startup scripts or configuration files. 

The default permission of your home directory is 750, i.e. you can do everything, people belonging to the same group can read and execute your files and other people can not do anything. For more info on file permissions see here.

Also note the private sub-folder. Here you can put files that you want only you, and no one else, to be able to access. Each day we have a job that ensures that all users's private folders still can't be accessed by anyone else, even if the permissions somehow accidentally would happen to be changed by yourself.

Creating and editing files

The nano text editor

There are several editors installed at UPPMAX. The one that is considered easiest to use for new users without graphics is nano.

Example: how to use nano:

nano filename

Save and exit the file with:

Control-O, Control-X

(You might need to answer "y" or "n" on some questions, and/or press "Enter" to confirm.)

Exit without saving with:

Control-X

You can get more help with nano by pressing (inside nano):

Control-G

The Emacs text editor

Another very common editor, with more features (but a little harder to use), is emacs.

Example: how to use emacs:

emacs filename

Do the editing you want, then save with:

Control-x, Control-s 

Exit emacs with:

Control-x, Control-c

You can read a tutorial in emacs by doing:

Control-h t

For a tutorial on emacs: http://www.gnu.org/software/emacs/tour/

The Gedit text editor

If you have logged in with X11-forwarding (i.e. with ssh -X username@rackham.uppmax.uu.se), then you can run gedit, a program that feels very similar to the Windows program Wordpad. 

Example: how to run gedit:

gedit &

The ampersand (&) keeps gedit from taking over your terminal session. You can navigate files and exit the program with the mouse.

Bash, bourne-again shell

Bash is the default Unix shell, a command-line interpreter and script host that provides a traditional user interface for the linux operating system at UPPMAX. Users direct the operation of the computer by entering command input as text for a command line interpreter to execute or by creating text scripts of one or more such commands.

The .bash_profile file is run whenever you login or when you start a login shell (as in starting a job in the queue).

The .bashrc file is run when an interactive shell that is not a login shell is started, or if it is called from the .bash_profile (as it is in the default configuration).

The .bash_logout file is run when you log out.

Modules

In order to make running installed programs easier you should use the module command. The different module that are installed sets the correct environments that are needed for the programs to run, like PATH, LD_LIBRARY_PATH and MANPATH.

Example: checking what modules are available:

module avail

Example: checking what modules you have loaded:

module list

Example: loading a compiler and the openmpi module:

module load pgi openmpi

Example, if you want to unload a module

module unload pgi

How to run jobs

All jobs should be run using the batch queues. Read more for milou and rackham, and the SLURM queue system.

UPPMAX homepage

Please check our homepage regularly for information, news and announcements. We will announce maintenance stops and down time there. Subscribe to the RSS newsfeeds!