Thom Group Wiki - User contributions [en]

Computer and Storage List

2020-09-03T12:32:38Z

Fa381:

{| class="wikitable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Hardware requests
|-
|carpathia
|379
|Alex
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 18.04.5
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 18.04.5
|-
|hypatia
|
|
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 16.04
|-
|serenity
|378
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 16.04
|
|
|2 x monitors
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 16.04.7
|-
|gritstone
|
|Hang, Jimin
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 16.04.4
|-
|moonraker
|
|Nick Lee
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 16.04.7
|-
|obsidian
|
|Hugh
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04
|-
|hylas
|378
|Fabio
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04.7
|
|
|1 x monitor, 1 x keyboard
|-
|cerberus
|
|Alex
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|
|David
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|chesterian
|
|Bang
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|nemesis
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 16.04.7
|-
|cerebro
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9)
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

Computer and Storage List

2020-09-03T09:55:45Z

Fa381:

{| class="wikitable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Hardware requests
|-
|carpathia
|379
|Alex
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 18.04.5
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 18.04.5
|-
|hypatia
|
|
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 16.04
|-
|serenity
|378
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 16.04
|
|
|2 x monitors
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 16.04.7
|-
|gritstone
|
|Hang, Jimin
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 16.04.4
|-
|moonraker
|
|Nick Lee
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 16.04.7
|-
|obsidian
|
|Hugh
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04
|-
|hylas
|378
|Fabio
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04
|
|
|1 x monitor, 1 x keyboard
|-
|cerberus
|
|Alex
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|
|David
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|chesterian
|
|Bang
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|nemesis
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 16.04.7
|-
|cerebro
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9)
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

Ssh session with X-forwarding

2020-05-01T12:04:09Z

Fa381:

==Config files==

In order to set up a quick link to an ssh session through citadel with X-forwarding the following code has to be added to a </code>~/.ssh/config</code> file

</code>
ForwardX11 yes
ForwardX11Trusted yes

Host $machine
User $crsid
Hostname $machine.ch.private.cam.ac.uk
ProxyCommand ssh -Y $crsid@citadel.ch.cam.ac.uk -W $machine.ch.private.cam.ac.uk:22

Host citadel
User $crsid
Hostname citadel.ch.cam.ac.uk
</code>

where </code>$machine</code> is the local host you would like to connect to (cerebro/sandstone/hylas ...)

Ssh session with X-forwarding

2020-05-01T12:00:51Z

Fa381:

In order to set up a quick link to an ssh session through citadel with X-forwarding the following code has to be added to a </code>~/.ssh/config</code> file

</code>
ForwardX11 yes
ForwardX11Trusted yes

Host $machine
User $crsid
Hostname $machine.ch.private.cam.ac.uk
ProxyCommand ssh -Y $crsid@citadel.ch.cam.ac.uk -W $machine.ch.private.cam.ac.uk:22

Host citadel
User $crsid
Hostname citadel.ch.cam.ac.uk
</code>

where </code>$machine</code> is the local host you would like to connect to (cerebro/sandstone/hylas ...)

Ssh session with X-forwarding

2020-05-01T11:59:28Z

Fa381:

In order to set up a quick link to an ssh session through citadel with X-forwarding the following code has to be added to a </code>~/.ssh/config</code> file

<syntaxhighlight lang="bash">
ForwardX11 yes
ForwardX11Trusted yes

Host $machine
User $crsid
Hostname $machine.ch.private.cam.ac.uk
ProxyCommand ssh -Y $crsid@citadel.ch.cam.ac.uk -W $machine.ch.private.cam.ac.uk:22

Host citadel
User $crsid
Hostname citadel.ch.cam.ac.uk
</syntaxhighlight>

where </code>$machine</code> is the local host you would like to connect to (cerebro/sandstone/hylas ...)

Ssh session with X-forwarding

2020-05-01T11:52:21Z

Fa381:

Ssh session with X-forwarding

2020-05-01T11:51:27Z

Fa381: Created page with "In order to set up a quick link to an ssh session through citadel with X-forwarding the following code has to be added to a `~/.ssh/config` file ``` ForwardX11 yes ForwardX11T..."

In order to set up a quick link to an ssh session through citadel with X-forwarding the following code has to be added to a `~/.ssh/config` file
```
ForwardX11 yes
ForwardX11Trusted yes

Host $machine
User $crsid
Hostname $machine.ch.private.cam.ac.uk
ProxyCommand ssh -Y $crsid@citadel.ch.cam.ac.uk -W $machine.ch.private.cam.ac.uk:22

Host citadel
User $crsid
Hostname citadel.ch.cam.ac.uk
```
where `$machine` is the local host you would like to connect to (cerebro/sandstone/hylas ...)

Shell Introduction

2020-05-01T11:46:56Z

Fa381:

# [[GIT | Using a GIT repository]]
# [http://ss64.com/bash/top.html Using the ''top'' function to see running functions]
# [http://www.tecmint.com/screen-command-examples-to-manage-linux-terminals/ The Screen program.] Useful for running processes without getting DC'd. See also nohup.
# [[Background | Jobs in the background]] Doing other stuff while your computer is outputting data.
# [[.bashrc | .bashrc - creating an alias]] bespoke functions and the $PATH statement.
# [[Mounting | Mounting]] and symbolic links
# [[Queuing | Queuing]] Queue information for cerebro
# [[ssh session with X-forwarding | ssh session with X-forwarding]]
# [[Persistent X | Persistent X Sessions]]

Main Page

2020-05-01T11:42:44Z

Fa381: /* Introduction to basic shell commands */

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

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]].

===Easter 2020===

{| class="wikitable"
! style="width: 25ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David ||
|-
|1st June 2020 || Hugh ||
|-
|15 June 2020|| Bang ||
|}

=Summer 'Interns' 2019=
{| class="wikitable"
! style="width: 25ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 18ex;" | '''Project'''
|-
|Kripa Panchagnula || 12th August - 27th September || Astrochemistry
|-
|Tiger Zhang || 2nd August - 20th September || Frustrated Lewis Pairs
|-
|David Kovacs || 29th July - 27th September (ex 20-26th Aug)|| Solid-state Coupled Cluster
|-
|Nicholas Lee || 29th July - 27th September (ex 4-9th Aug)|| Singlet-Triplet Fission
|}

= [[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.

= 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]]
# [[IFS Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]

= [[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