Main Page

# _________  # ___   ___     # ______      # ___ __ __     #  # _______     # ______       # ______      # __  __      # ______    #
#/________/\ #/__/\ /__/\    #/_____/\     #/__//_//_/\    #  #/______/\    #/_____/\      #/_____/\     #/_/\/_/\     #/_____/\   #
#\__.::.__\/ #\::\ \\  \ \   #\:::_ \ \    #\::\| \| \ \   #  #\::::__\/__  #\:::_ \ \     #\:::_ \ \    #\:\ \:\ \    #\:::_ \ \  #
#   \::\ \   # \::\/_\ .\ \  # \:\ \ \ \   # \:.      \ \  #  # \:\ /____/\ # \:(_) ) )_   # \:\ \ \ \   # \:\ \:\ \   # \:(_) \ \ #
#    \::\ \  #  \:: ___::\ \ #  \:\ \ \ \  #  \:.\-/\  \ \ #  #  \:\\_  _\/ #  \: __ `\ \  #  \:\ \ \ \  #  \:\ \:\ \  #  \: ___\/ #
#     \::\ \ #   \: \ \\::\ \#   \:\_\ \ \ #   \. \  \  \ \#  #   \:\_\ \ \ #   \ \ `\ \ \ #   \:\_\ \ \ #   \:\_\:\ \ #   \ \ \   #
#      \__\/ #    \__\/ \::\/#    \_____\/ #    \__\/ \__\/#  #    \_____\/ #    \_\/ \_\/ #    \_____\/ #    \_____\/ #    \_\/   #
#            #               #             #               #  #             #              #             #             #           #

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

Group Calendar

https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

Group Meetings

Past Group Meetings here. Group Meetings take place every other Monday at 3.30pm.

Michaelmas 2022

Date	Talk	Cake
10th October	Yi Sun	Kripa
24th October	Chiara	Andreea
7th November	Lila	Eline
21st November	Moritz	Alex (Mince Pies)

Journal Club

12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs here.

2022-23

Date	Contributor	Paper
5 Oct 2022	Chiara	Quantum theory based on real numbers can be experimentally falsified
2 Nov 2022	Daniel	The role of references and the elusive nature of the chemical bond
28 Nov 2022	Andreea	} Summer 'Interns' Past Summer Interns here. Group List The full timeline of all current and past group members is available here. NB autogenerated by `thom-fs-common/old-ifs-thom/cbh31/groupwiki` An up to date list of group members is also available here. Thom Group photo Summer 2022 Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021 Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019 Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017 Computing Resources - Group computers available. - Clusters available. - Storage available. Computing Setup Guide Anaconda takes up a lot of space on /home so it's worth running mv ~/.conda /scratch/$USER/.conda ln -s /scratch/$USER/.conda ~/.conda Introduction to basic shell commands - There are a number of tutorials available which document basic operations that are useful including: General bash commands Setting up cygwin Setting up ssh keys and general bash commands what are helpful Setting up ssh config files using GIT The Ten Git-mmandments Useful cerebro queue commands Some vim tidbits Currently undergoing construction. How to connect to department machines On Mac/WSL: Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service In the terminal run the command ssh -X crsid@citadel.ch.cam.ac.uk When prompted input your Admitto username (crsid) and password Once this has worked run the command ssh -X crsid@machinename in the terminal to log into a particular machine Set up logging in without a password: Generate an ssh key by running the command ssh-keygen in the terminal, as described in detail in the section "Introduction to basic shell commands" Use cd ~/.ssh to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key Log into the department citadel machine, and create / navigate to a directory called .ssh Use chmod 700 .ssh to set permissions for the directory Input vi authorized_keys to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type :wq and press enter to write and quit the editor Log into the particular machine you want to ssh to, and repeat steps 3 to 5 Exit back to your machine and navigate to the home directory Input vi .ssh/config to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given: Host citadel User crsid Hostname citadel.ch.cam.ac.uk ForwardAgent yes ProxyCommand none Host machinename Hostname machinename ProxyCommand ssh citadel -W %h:%p User crsid ForwardAgent yes ServerAliveInterval 60 ServerAliveCountMax 10 Press escape, then input :wq followed by enter to exit the editor. You can now log straight into citadel with ssh citadel or straight into your machine with ssh machinename. The last two commands stop the ssh being killed if you are idle for too long. The ServerAliveInterval is how many seconds to ping a null packet, and the ServerAliveCountMax are how many consecutive times it needs to fail for the ssh to be killed. File Transfer Protocol : You may want to transfer files between department machines and your computer. The standard way is to scp via the terminal with commands : UPLOAD : scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath DOWNLOAD : scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer. ON WINDOWS: I recommend the WinSCP software. You can download it from here. Once installed, click New Session, and choose SFTP protocol with : Hostname = machinename Port number = 22 Username = crsid Leave 'Password' entry empty. Then click on Advanced..., Tunnel tab, check the Connect through SSH tunnel tickbox and enter: Hostname = citadel.ch.cam.ac.uk Port number = 22 Username = crsid Leave 'Password' entry empty. Click OK and click Save, and finally Login. Enter your admitto password twice. You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy ! ON MAC\LINUX: You can download FileZilla for MacOS or linux. The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY. On MacOS please follow this guide. On Linux you can do : sudo apt-get install -y putty Open it by typing putty on the terminal. The interface should open. Type the following entries : in the SSH/Tunnels tab : Source Port = 3111 Destination = machinename:22 local auto and click Add. (source port can be any number > 1024) in the session tab : Host Name = citadel.ch.cam.ac.uk port = 22 connection type = SSH Enter a name for this connection in the saved sessions entry, and click Save. Now click Open. A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine). Now open FileZilla, and enter : Host = sftp://localhost username = crsid password = admitto password port = 3111 and click Quickconnect. (port needs to be the same as source port in puTTY). A window will open (Unknown host key), click OK. Hopefully the connection is successful. You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy ! Useful Software Using QChem Using QCMagic SimpleDMC MRCC GAMESS Useful Information Guidelines on Code Review How to do things relating to HANDE How to run PySCF or other Python software on Archer How to run QChem on darwin Where to get Travel Money Backed-up Storage How to get IQMol to run a local version of Q-Chem via SSH Slow ubuntu dash Persistent X sessions for remote working Paper submission Getting Started with cerebro Things to do before leaving The Ten Git-mmandments: what NOT to do Archiving data for the university repository To-do list for the Thom Group Website Group Activities To-do list for the Wiki - A pretty picture - A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful - A "How to:" page on using qchem - A Pretty picture for the $wgLogo