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 authorized_keysy. 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 at the bottom 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.
    1. You can search for text entered into the description and by project to find earlier jobs. The columns can also be sorted by clicking on the top caption for each column. Press filter to invoke a search. You can also delete unwanted jobs.
    2. When the job is finished, select an output file (normally the Gaussian log file or formatted checkpoint file) for download and inspect using eg Gaussview 6.1.1.
    3. Hint: the job description is editable. To do so, click on the Job ID on the left. You can change the project here as well as edit the description. If your project depends on computed energies (ideally the Gibbs Energy) then enter that into the description field. It then makes it much easier if you are calculating a series of molecules with the same formula and by the same method to compare them all by energy or to find all energies with a common numerical prefix.
13. If you want to follow the progress of your job, go to https://api.rcs.imperial.ac.uk/saml/acs/ Here, you can also extend the run time of your job, but only by 24 hours!
14. Once you are satisfied with a finished job, you may wish to publish all the key files to the data repository. This needs setting up here. For information about how to also publish experimental data such as NMR spectra, see here.