View source for Mod:HPC-add

= Breaking news.  The configuration mechanism has changed =
Whilst we wait for new instructions, please do not attempt the below. Currently, it will not work.

== Configuring the  Imperial College HPC Resource to run  Gaussian Calculations using an ELN ==
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#Chemistry department users  need  to be registered to use the  HPC. If a PG, ask  your supervisor to use https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/support/getting-started/  to make a request for you. You also need permissions to join the '''Gaussian users group''' and '''pqchem''' queue on the  HPC system.  You should email Mike Bearpark with a request for these. This may take ~24 hours to propagate.
#[[File:Screenshot_103.jpg|400px|right]]Once registered, go to  https://portal.hpc.imperial.ac.uk and login using your college user name and password (if connecting from outside the College network, you may require to [https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communicate/remote-access/virtual-private-network-vpn/ setup a VPN] to have access).
#[[File:Screenshot_104.jpg|450px|right]]Select Pools and complete the section '''Add Pool''' as shown (queue name of your choice, Host  = '''login.cx1.hpc.ic.ac.uk''' and path = '''/apps/scan-scripts/pqchem''' and click  '''Add'''
#[[File:Screenshot_105.jpg|500px|right]]You should get '''Pool added successfully''' and the instructions shown.
##In particular, '''download the key''', which should have the name '''portalkey.rsa-7.pubkey'''
##Open this file in a non-wrapping text editor such as  WordPad, and copy the single line to the clipboard
#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).
##An example of an sftp client is '''WInSCP''', which can be downloaded from [https://winscp.net/eng/download.php https://winscp.net/eng/download.php]
##Launch WinSCP and log in to an SFTP session using Hostname '''login.cx1.hpc.ic.ac.uk''', your College user name and password.
##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''' 
##*If you are a new user, this directory may not yet exist, and you should create it.
##In the''' .ssh''' directory, you will find a file called '''authorized_keys'''. 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. If the file does not exist, create it.
#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).
#To submit a job, you first have to prepare the  Gaussian input file.  Do not add any  % commands, start immediately with the keywords line.
#First, create a new project by clicking '''Projects'''. You can have as many of these as you wish
#Click on '''New job''' and select your newly added pool followed by '''continue'''.
#Select '''Application type'''. Recommended are the three types labelled '''Gaussian g16-c01-avx 8px 22GB''' and the 16px and 20px versions,  select a project then '''continue'''
##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.
#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!)
#[[File:Screenshot_106.jpg|700px|right]]Click on  '''job list'''.  It will show '''pending''' or '''running'''.  If it immediately shows '''Finished''' it has probably failed with a  Gaussian error. It the system is misbehaving it will show '''Failed''' and ICT need to fix it (rare).
##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.
##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'''.
##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.
#If you want to follow the progress of your job, go to https://api.rcs.imperial.ac.uk/jobs/qstat Here, you can also extend the run time of your job, but only by 24 hours!
#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 [[Orcid|here]]. For information about how to also publish experimental data such as  NMR spectra, see [[rdm:synthesis-lab|here]].
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