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Academic year 2021-2022 1
Jean-Christophe SOETENS
Department of Chemistry
University of Bordeaux
jean-christophe.soetens@u-bordeaux.fr
Academic year 2021-2022
About using computers
J-C. Soetens (U Bordeaux )
ANYWHEREPersonal laptop, pc, mac…
Local resourcesoperating system : macOS
Windows, linux…
Connexion tocomputing center
Gaudi operating system : Unix
2Academic year 2021-2022 2
Map
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
LAVOISIERiMac Apple
Local resourcesoperating system : macOS
Connexion tocomputing center
Gaudi operating system : Unix
“ Pôle modélisation ” of ISM/A12
computer gaudi ( gaudi.ism.u-bordeaux.fr )
For all sizes of calculations of a wide range of applicationsusing home programs or various softwares
Softwares :
terminal or X11
Apple / macOS or
TurboVNC
PuTTY (a free telnet/SSH client )
PC / windows and
TurboVNC (Virtual Network Computing)
Softwares : terminal or X11
Command :
$ ssh -Y login@gaudi.ism.u-bordeaux.fr
3Academic year 2021-2022 3
Computer center - Gaudi
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
“ Pôle modélisation ” of ISM/A12
computer gaudi ( gaudi.ism.u-bordeaux.fr )
For all sizes of calculations of a wide range of applicationsusing home programs or various softwares
The gaudi cluster comprises about 700 CPU-cores spread across 40 compute nodes with 32 to 256 GB of RAM and GPU.All the nodes are interconnected by Infiniband (scratch space of 6 To). The storage capacity is about 20 To (RAID5) and anincremental backup (30 To) is performed daily.
front behind
4Academic year 2021-2022 4
Computer center - Gaudi
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
The gaudi cluster comprises about 700 CPU-cores spread across 40 compute nodes with 32 to 256 GB of RAM and GPU.All the nodes are interconnected by Infiniband (scratch space of 6 To). The storage capacity is about 20 To (RAID5) and anincremental backup (30 To) is performed daily.
“ Pôle modélisation ” of ISM/A12
computer gaudi ( gaudi.ism.u-bordeaux.fr )
For all sizes of calculations of a wide range of applicationsusing home programs or various softwares
5Academic year 2021-2022 5
Computer center - Gaudi
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
The gaudi cluster comprises about 700 CPU-cores spread across 40 compute nodes with 32 to 256 GB of RAM and GPU.All the nodes are interconnected by Infiniband (scratch space of 6 To). The storage capacity is about 20 To (RAID5) and anincremental backup (30 To) is performed daily.
“ Pôle modélisation ” of ISM/A12
computer gaudi ( gaudi.ism.u-bordeaux.fr )
For all sizes of calculations of a wide range of applicationsusing home programs or various softwares
http://theo.ism.u-bordeaux.fr
6Academic year 2021-2022 6
Tools
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
Softwares :
PC / windows PuTTY (a free telnet/SSH client )
TurboVNC (Virtual Network Computing)
Windows
PuTTY
and
https://www.putty.org/ https://www.turbovnc.org/
Softwares : terminal or X11
Command :
$ ssh -Y login@gaudi.ism.u-bordeaux.fr
macOS
terminal X11
or
7Academic year 2021-2022 7
Tools
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
Windows : upload and install these two softwares
https://www.putty.org/
https://www.turbovnc.org/
macOS : upload and install only TurboVNC
https://www.turbovnc.org/
8Academic year 2021-2022 8
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
Windows : configuration of and
PuTTY
First time :
1) Configure PuTTY for an SSH connection with Gaudi2) Log on Gaudi with PuTTY / SSH
- start vnc server and define a password- get the display number
3) Configure PuTTY for a « SSH Tunnel » with Gaudi
Each time :
4) Log on Gaudi through the « SSH Tunnel » 5) Lunch turbovnc and log on
9Academic year 2021-2022 9
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
First time :
1) Configure PuTTY for an SSH connection with Gaudi
Windows : configuration of and
PuTTY
10Academic year 2021-2022 10
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
First time :
2) Log on Gaudi with PuTTY / SSH- start vnc server : command « vncserver », define a vnc password if this is
requested- get the display number : command « vncserver –list »
Windows : configuration of and
PuTTY
ENT login/password
11Academic year 2021-2022 11
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
First time :
3) Configure PuTTY for a SSH Tunnel with Gaudi
5900 + display number
Windows : configuration of and
PuTTY
12Academic year 2021-2022 12
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
Each time :
4) Log on Gaudi through the SSH Tunnel5) Lunch TurboVNC and log on using the vnc password
Windows : configuration of and
PuTTY
ENT login/password
13Academic year 2021-2022 13
Configuration ( Windows )
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
If everything is ok, you access to an environment like this :
14Academic year 2021-2022 14
Configuration ( macOS)
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
macOS: configuration of
First time :
1) Log on Gaudi with terminal or X11- start vnc server : command « vncserver », define a vnc password if this is
requested- get the display number : command « vncserver –list »
Each time :
2) Start Turbo VNC3) Prepare the connection4) Connect through SSH5) Connect to vnc server
ENT login/password
15Academic year 2021-2022 15
Configuration ( macOS)
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
macOS: configuration of
First time :
1) Log on Gaudi with terminal or X11- start vnc server : command « vncserver », define a vnc password if this is
requested- get the display number : command « vncserver –list »
ENT login/password
16Academic year 2021-2022 16
Configuration ( macOS)
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
macOS: configuration of
Each time :
2) Start Turbo VNC3) Prepare the connection
17Academic year 2021-2022 17
Configuration ( macOS)
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
macOS: configuration of
Each time :
4) Connect through SSH
5) Connect to vnc server
ENT login/password
vnc passworddisplay number
18Academic year 2021-2022 18
Configuration ( macOS)
Statistical Mechanics & SimulationsJ-C. Soetens (U Bordeaux )
If everything is ok, you access to an environment like this :
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