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Data Access, Imaging Tools & Protocols

Remote Access to Diamond Light Source (DLS) Data Servers

The details below refer to accessing the Beamline i13 (Coherence X-ray Imaging).

Please note that all data created in /dls/tmp/ will be deleted after 30 days, so make sure you transfer it to Dropbox or other online storage at least weekly.

Setting-up and Connecting

Before you start, please install the NoMachine NX Client.

  1. Run NoMachine and click on New Connection
  2. Leave protocol as NX
  3. Enter nx.diamond.ac.uk as the host (and leave 4000 as the port)
  4. Leave default Password Authentication method and No Proxy options
  5. Tick Create a Desktop Link to get a handy shortcut

From now on, all you need to do is to double-click on the desktop NoMachine link and enter your Federal User ID and password. Note that you will need to select (or create a new) Virtual Desktop.

Remote SuRVoS operation

Run the following commands in a Terminal: Applications –> System Tools –> Terminal.

$ module load global/cluster
$ qlogin -q high.q@@com14 -l exclusive -l gpu_arch=Pascal -P i13
$ module load survos
$ survos &

See also SuRVoS Tutorial Materials.



Technical info useful for troubleshooting: Linux Imaging Workstation [i13-ws010.diamond.ac.uk] 172.23.113.76 (NX port 4000)
List of Compute Nodes: qhost
Other possible graphical options for high GPU / Memory Usage:

qlogin -q high.q@@com14 -l exclusive -l gpu=1,nvidia_tesla -P i13

Further details are available in the online beamline manual.

Igor Chernyavsky, 2018/03/24 19:00

X-ray Imaging Centre at Alan Turing Bldg

Please book PC1 in advance of your session. And please make sure to save your data to an external HDD before the end of the session.

Running SuRVoS

Try either

  Running the shortcut SURVOS on the Desktop (C:\Users\...\Anaconda2\envs\ccpi\Scripts\SurVos.exe)

or

  [Start] --> Anaconda Prompt
  > activate ccpi
  > SuRVoS

Running Avizo

Note that there are Light and Full versions. One 'full' licence takes 4 'light' ones (out of a total of 32), so a 'full' version is not always available.

Igor Chernyavsky, 2018/03/26 18:00

Maths Compute Servers at Alan Turing Bldg

You need a a Maths Linux account to access the servers. If you do not have one, please contact Chris Paul, stating your UoM username and reason for access.

  • On Linux or MacOS: open a Terminal emulator and run
    $ ssh -Y username@e-a07maat1101X.it.manchester.ac.uk
  • On Windows: install and run PuTTY. Enter e-a07maat1101X.it.manchester.ac.uk as the Host Name, SSH as the Connection Type and hit [Open].

Here username is your UoM username, and X is the reference letter ('a' to 'l') from the Table below (if unsure, use a for CS1 as a starting point).

Ref (X) Name Core Count Core Speed and Type RAM (GB) Note
a cs1 12 3.4 GHz (Intel Xeon E5-2643v3) 792 Memory-intensive
b cs2 8 3.3 GHz (Intel Xeon E5-2643) 131
c cs3 8 3.3 GHz (Intel Xeon E5-2643) 131
d cs4 8 3.3 GHz (Intel Xeon E5-2643) 131
e cs5 12 2.5 GHz (Inter Xeon E5-2430v2) 131
f cs6 12 2.5 GHz (Intel Xeon E5-2430v2) 131
g cs7 12 2.5 GHz (Intel Xeon E5-2430v2) 131
h cs8 12 2.5 GHz (Intel Xeon E5-2430v2) 131
i cs9 16 3.0 GHz (Intel Xeon E5-2623v3) 263
j cs10 16 3.0 GHz (Intel Xeon E5-2623v3) 263
k cs11 32 3.0 GHz (AMD Opteron 6220) 263 CPU-intensive
l cs12 12 2.5 GHz (Intel Xeon E5-2430v2) 198

System info:

free -h --si
lscpu

Load info:

top (followed by pressing the [t], [1] and [m] keys)

Running COMSOL

$ module load comsol53
$ comsol &

Igor Chernyavsky, 2018/06/19 18:00

MRC Behind-the-Scenes

i/placenta/data.1534446950.txt.gz · Last modified: 2018/08/16 19:15 by Igor Chernyavsky
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