Mod:HPC-add

Configuring the Imperial College HPC Resource to run Gaussian Calculations using an ELN

1. 
   Go to https://portal.hpc.imperial.ac.uk and login using your college user name and password
2. 
   Select Pools and complete the section All Pool as shown (queue name of your choice, Host = login.cx1.hpc.ic.ac.uk and path = /apps/scan-scripts/pqchem and click Add
3. 
   You should get Pool added successfully and the instructions shown.
   1. In particular, download the key, which should have the name portalkey.rsa-7.pubkey
   2. Open this file in a non-wrapping text editor such as WordPad, and copy the single line to the clipboard
4. To complete the next step you will have to install an SFTP client. The below is appropriate for Windows 10 (for which you have admin rights to install programs).
   1. An example of an sftp client is WInSCP, which can be downloaded from https://winscp.net/eng/download.php
   2. Launch WinSCP and log in to an SFTP session using Hostname login.cx1.hpc.ic.ac.uk, your College user name and password.
   3. On the left panel of the resulting screen you will see folders on your local computer; on the right panel are folders on the remote server. You need to find the directory .ssh on the remote server which is normally hidden, so first you need to reveal hidden files. To do this, in the “Options” menu at the top, choose Preferences and then Panels. Tick the box “Show Hidden Files”, then OK. You should then see the .ssh directory in the path /rdsgpfs/general/user/yourusername/home
   4. In the .ssh directory, you will find a file called portalkey.rsa-7.pubkey. Still in WinSCP, Double click on this file to open it in an editor, then paste in the line you copied to the clipboard above, save and close the file.
5. You will now need permissions to join the Gaussian users group on the HPC system. You should email Mike Bearpark with a request. This may take ~24 hours to propagate.
6. Log in again to https://portal.hpc.imperial.ac.uk, click on Pools and then in the line for your created pool, click on Applications/view. It should show a list of authorised applications. If the list is empty, click on Refresh application list and if all the appropriate permissions have been set, the list should appear (if the list is blank you do not have these permissions).
7. To submit a job, you first have to prepare the Gaussian input file. Do not add any  % commands, start immediately with the keywords line.
8. First, create a new project by clicking Projects. You can have as many of these as you wish
9. Click on New job and select your newly added pool followed by continue
10. Select Application type. Recommended are the three types labelled Gaussian g16-c01-avx 8px 22GB and the 16px and 20px versions, then continue
    1. The scheduling of the job is controlled by the resources you request. The 8px job will run more quickly than the 20px job (which may pend for several days). Try testing the job input with a short queue first.
11. Select a Gaussian input file (ignore the Formatted checkpoint file) and enter a good description (one you are likely to understand when you write your paper up a year or so later!)
12. 
    Click on job list It will show pending or running. If it shows Finished it has probably failed with a Gaussian error.