UKCA Training: Logging in and Setting up

You will be using the machines in the G30 computer lab in the Department of Chemistry.

In G30

You will be using MCS Linux on the G30 workstations during this course.

1. Boot to MCS Linux
   • If the machine is powered-off, please turn it on.
   • If machine is on the Windows login screen, press Ctrl-Alt-Del and the press the drop-down menu on the red power-off button (bottom right) and select Restart.
2. On the BIOS boot screen, select MCS Linux
3. Software updates may need to be applied - this may take some time.
   • If the workstation needs to reboot after updates, should boot back into MCS Linux automatically.
4. Note: the workstations will power-down in the evenings. DO NOT stay logged-in. You should also remember to save your work regularly.
5. To log-in, use the conference username and password provided in the white envelope. These details are unique to you - do not share them with others.

PUMA and ARCHER

You should use your personal PUMA account during this course.

1. Log in to PUMA using your personal account details: ssh -X userid@puma.nerc.ac.uk
2. Log in to ARCHER using the provided training account username and password: ssh -X ncastrXX@login.archer.ac.uk

• Note: Please type your ARCHER password carefully - if it is typed incorrectly too many times you may find that you are locked out of the account
• When password-less logins have been set-up, you will be able to login to ARCHER directly from PUMA

3. If you have NOT already done so, generate your SSH-key:
puma$ ssh-keygen -f ~/.ssh/id_dsa -C " userid@puma.nerc.ac.uk" Generating public/private rsa key pair. Enter passphrase(empty for no passphrase): TYPE_YOUR_PASSPHRASE Enter same passphrase again: TYPE_YOUR_PASSPHRASE Your identification has been saved in ~/.ssh/id_dsa. Your public key has been saved in ~/.ssh/id_dsa.pub. The key fingerprint is: md5 1024 String of characters userid@puma.nerc.ac.uk

• TYPE-YOUR-PASSPHRASE needs to be a fairly complicated and unguessable passphrase. You can use spaces in the pass phrase if it helps you to remember it more readily. It is recommended that you don't use your password just in case this is hacked. Note: Please DO NOT use an empty passphrase as this presents a security issue.

4. Add the public key to the ~/.ssh/authorized_keys file on ARCHER.

• To achieve this in a secure manner, do the following:

puma$ cat ~/.ssh/id_dsa.pub | ssh ncastrXX@login.archer.ac.uk 'mkdir -p .ssh ; cat - >> ~/.ssh/authorized_keys' Enter the password of your ARCHER training account

• Sometimes, even though the file is copied across successfully, the above command will hang. In which case, do a Cntl-C to exit, and login to the remote platform and verify the file .ssh.authorized_keys has arrived safely

8a) Follow the instructions at https://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/sshAgent 8b) setup script can be copied from: /home/ukca/TutorialSetup

9) When logged into ARCHER, a .profile can be copied from: /home/n02/n02/ukca/TutorialSetup

10) Modify the UMUI to use the ARCHER training account username

11a) If you are having problems compiling (i.e. the job is taking a lot longer than 10 minutes) you should manually compile the job on the login node. 11b) To do this, you need to include the hand-edit: ~ukca/hand_edits/VN8.4/manual_comp_ARCHER.ed 11c) Save, process, and submit in the usual way 11d) Then, on ARCHER you will find that the job has not been submitted to the serial queue. To compile the job you should first

cd
ls -ltr ./umui_runs 
./umui_runs/jobid-XXXXXXXX/umuisubmit_compile

where jobid-XXXXXXXX is the most recent directory. 11e) After the job has compiled, you should then

qsub -q course1 ./umui_runs/jobid-XXXXXXXX/umuisubmit_rcf

followed by

qsub -q course1 ./umui_runs/jobid-XXXXXXXX/umuisubmit_run