Thom Group Wiki - User contributions [en]

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2020-09-23T10:50:40Z

Ij251: /* How to connect to department machines */

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

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

{{Special:IframePage}}

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]].

===Michaelmas 2020===

{| class="wikitable"
! style="width: 25ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Fabio ||
|-
|26th October 2020 || Andreea ||
|-
|9th November 2020 || David/Kripa||
|-
|23rd November 2020|| Arta ||
|}

=Summer 'Interns' 2020=
Past Summer Interns [[Past Summer Interns|here]].

{| class="wikitable"
! style="width: 25ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 18ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || || Astrochemistry || hypatia
|-
|Hang Xu || || EOM-CC || gritstone
|-
|Jimin Li || || holoHubbard || gritstone
|-
|Constance Kraay || || Embedded NOCI || nemesis
|-
|Toby Antipaas || || SMM || sandstone
|-
|Tiger Zhang || || TM Symmetry || sandstone
|-
|Nicholas Lee || || Singlet Fission || moonraker
|}

= [[Group_List | Group List]] =
An up to date list of group members is also available here: http://www.ch.cam.ac.uk/group/thom.

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_List | Computer List]] =
- Group computers available.

= [[Introduction | 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 [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

'''On Mac:'''

# 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 authorised_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

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''

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]

= 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

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | 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

Main Page

2020-09-18T14:47:53Z

Ij251: Adding a page with instructions on how to connect to a department machine from Mac for the first time

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

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

{{Special:IframePage}}

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]].

===Summer 2020===

{| class="wikitable"
! style="width: 25ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

=Summer 'Interns' 2020=
Past Summer Interns [[Past Summer Interns|here]].

{| class="wikitable"
! style="width: 25ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 18ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || || Astrochemistry || hypatia
|-
|Hang Xu || || EOM-CC || gritstone
|-
|Jimin Li || || holoHubbard || gritstone
|-
|Constance Kraay || || Embedded NOCI || nemesis
|-
|Toby Antipaas || || SMM || sandstone
|-
|Tiger Zhang || || TM Symmetry || sandstone
|-
|Nicholas Lee || || Singlet Fission || moonraker
|}

= [[Group_List | Group List]] =
An up to date list of group members is also available here: http://www.ch.cam.ac.uk/group/thom.

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_List | Computer List]] =
- Group computers available.

= [[Introduction | 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 [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

On Mac:

# 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"
# 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

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]

= 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

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | 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