PC-Cluster and Opti-Cluster

The PC-Cluster is a teaching facility of the LSS. It consists of 15 workstations plus one lecturer's workstation. These PC mainly are for our students. To be able to use the computer, you need to request an account at Dr. Janiga. Ideally, the local account name matches with your university account.

The room has a transponder key lock, as most of the chair's rooms and laboratories. However, only a few transponders are available for students. Let your supervisor check whether there is a transponder left unused. However, usually there are not enough available. In that case, ask in the offices down the hallway to open the room for you. During working hours there usually is someone who can be asked.

If you are using the PC cluster the first time read through these guides:

Rules of Conduct

PC Cluster

  1. Clean up regularly!
    1. Cleanup your storage regularly. Remove temporary, intermediate steps. If home is full, the whole cluster will be affected!
    2. After completing your thesis (or other work), give your data to your supervisor, and empty your home-folder
    3. Log out from your computer if your are not using it anymore.
  2. The computers are always running. You don't need to switch them on/off. In case of problems, contact Dr. Janiga (G03-233).
  3. Check whether the computer you attempt to use is already in use (top, Ganglia (only inside OVGU net))
  4. Don't use multiple computers (max. 2). Speak with your supervisor to receive time on the Opti-Cluster, or Neumann
  5. If you're the last one leaving the room:
    1. Close all windows
    2. Switch off lights
    3. Switch on the air conditioner (especially in summer)
    4. Make sure the door is closed. Lock the room if you have a transponder.
  6. Avoid drinking and eating in the room.

Opti-Cluster

  1. Exclusively for LSS employees (no self-service by students)
  2. Check whether the nodes are already in use (top, Ganglia (only inside OVGU net))
  3. If you are a student needing extra resources, speak with your supervisor or Dr. Janiga stating approx. requirements.

Let us know, if this list is incomplete, or something is incorrect.

Remote Connecting

As long as you are within the university's network, you can try to connect to machines, such as Neumann or our PC cluster. You are inside the network under one of the following circumstances:

  • your PC is connected via LAN to the network, such as Workstation in offices, RTLs and our PC cluster.
  • your computer/notebook is connected to the OvGU WLAN

If your computer is not within the university's network, you'll have to use VPN to get inside. Via VPN connection the computing machines can be accessed as you would do within the university's network. See the sketch beside. The URZ (University-IT-Service) explains how to setup a VPN connection here.

When your computer is located within the network, continue reading the Remote Connection Guide

Frequent problems

OpenFoam - No such file or directory

When you login to the PC-Cluster via ssh you may receive such a message:

Last login: Wed Nov 14 14:54:11 2018 from 141.44.232.165
-bash: /opt/OpenFOAM-2.3.0/etc/bashrc: No such file or directory 

Solution

  • It's only occuring on server
  • ignore this message

Cause

  • OpenFOAM is only installed on the workstations (~ws01)and the opticluster (~server02)
  • It's not installed on the login node server
  • the bash environment on the PC-Clusters loads a prepared bashrc in default which contains OpenFOAM links (/home/software/bashrc_mini)

No access to compute nodes

StarCCM, Fluent or manual connections complain:

mpirun: Warning one or more remote shell commands exited with non-zero
status, which may indicate a remote access problem.
error: Design STAR-CCM+ simulation completed
Server process ended unexpectedly (return code 255)
mpirun: Warning one or more remote shell commands exited with non-zero
status, which may indicate a remote access problem.

Similar symptome: Run this command on server:

ssh c001

It will ask for your password.

Solution

  • Log into the remote computer
  • Create a second keypair. Press enter three times after running this command:
    ssh-keygen
  • Add the new key to authorized_keys:
    cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys

Cause

  • Compute nodes are a subnet work from the login nodes
  • Compute nodes read authorized_keys file to self identify user
  • A required key pair is not created automatically, or might have been overwritten

Specifications

Workstations 15+1 PC with 4 CPU @ 3.3 Ghz, 8Mb Cache(Intel Xeon E3-1230 v3)
32GB RAM
NVIDIA Quadro K2000D graphics card
Intel 8 Series/C220 Series Chipset Family
GBit Ethernet
Opti-cluster 8 Nodes with 6 CPU @ 3.5 Ghz, 15Mb Cache (Intel Xeon E3-1650 v3)
32GB RAM
Intel 8 Series/C220 Series Chipset Family
GBit Ethernet
Central Storage 7.3 TB home directory
1.8 TB global directory

Available Software by Q4 2017

  • ABAQUS
  • ANSYS, v17.0, v14.0, incl. Fluent, CFX, ICEM CFD,…
  • StarCCM, most major versions
  • Matlab, R2014a
  • OpenFOAM, 3.0.x, 2.1.x, 2.3.0
  • OPAL++
  • Ensight
  • Netbeans
  • NUMECA

Presentations in Cluster room

Master PC

The usage of the projector and the master pc (lecturer pc) is not straightforward.

The projector in the cluster room grew quite old. Together with the available linux distribution the following command has to be run in a terminal.

$ /usr/bin/kcmshell4 display

This can be added to your .bashrc by:

$ echo "alias display=/usr/bin/kcmshell4 display" >> ~./bashrc
$ source ~./bashrc

Now, you can run the following command in a terminal:

$ display

Display opens a KDE menu which sets the screen resolution for the video interfaces (dvi sockets). Here select the following screen resolutions.

FIXME add picture of dvi vga converter

Your own pc

FIXME

VGA

HDMI possible?

Desktop Sharing - wsxx to wsxx

Section is adapted from Sources: Krfb and Krdc
licensed with CC-BY-SA.

Broadcasting with krfb

  • Start Krfb via the Start Menu: → Applications → Internet → Desktop Sharing (Krfb)
    alternatively, open a terminal and run:
    krfb
  • Click the “New Personal Invitation” button
  • Foward the ip adress including the port, and the password
  • When the guest tries to connect, you will see a popup window in which you can approve the connection by clicking appropriate button.

Receiving with krdc

  • Start Krdc via the Start Menu: → Applications → Internet → Krdc
    alternatively, open a terminal and run:
    krdc
  • Type in the name or ip address of the remote computer (this is a VNC protocol).
    An example: 192.168.1.102:5900 (identify the port after the colon)
  • Select the vnc protocol, not the rdp protocol.
  • On the Sending computer, accept the new connection.
  • Type in your user name and then the login password that the remote computer requires.
  • When your mouse is within the window limits of the host's desktop, you can control the remote computer.

Desktop Sharing - WS to personal computer

Sometimes it would been convenient to get a peak on your desktop from home when you can't come to the PC-Cluster, such as late hours. Sharing the desktop to a remote computer, such as your own PC at home takes some preparation. This setup needs physical access to the workstations in the PC-Cluster room. Setting this connection up on weekends/holidays is impossible.

activate Broadcasting with krfb

  • Start Krfb via the Start Menu: → Applications → Internet → Desktop Sharing (Krfb)
    alternatively, open a terminal and run: krfb
  • Click the “Configure” button
  • Go to Security Tab
  • Check Allow uninvited connections
  • Uncheck Ask before accepting an uninvented connection
  • Set a good password!
  • Press Apply, then return with OK
  • krfb can now be closed.

<WRAP center round important 60%> Remember to re-open krfb and reset to defaults if you don't need desktop sharing anymore! So that you close the vnc server/port.

Opening an SSH Tunnel

  • Install and set up PuTTY according to this Guide.
  • Load the settings for the PC-Cluster
  • Open the Category: Connection → SSH → Tunnels
  • In Source Port type a number, such as 9999, and remember it
  • set the radio button to Dynamic
  • Press Add. In the a field above D9999 should appear.
  • Return to the Category: Session
  • Save the new configuration
  • Open the connection to the PC-Cluster

Using VNC from your computer through SOCKS proxy

You'll need a VNC client which is capable to connect to a remote computer using a socks proxy server.

  • Windows users: download RealVNC viewer, not RealVNC Connect. It's free, and does not need any account.
  • Install it.
  • Take care to select all options to not send any anonymous reports/data.
  • In the preferences, navigate to proxy.
  • Set the protocoll to SOCKS instead of HTTP
  • Enter the proxy address 192.168.1.1xx:5900 Replace the xx with the number of the workstation. For example: a vnc connection on ws07 needs the proxy address 192.168.1.107:5900
  • Save and Connect and enter the previously set password. Ignore possible warnings on unencrypted desktop sharing. Only if you work on sensitive data, such as patient data, don't use this desktop sharing method.
  • Enjoy.

Other OS, you may try: https://serverfault.com/questions/216991/vnc-connection-via-ssh-proxy-machine#

guide/pccluster.txt · Last modified: 2019/11/02 16:45 by seengel
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