Understanding living systems
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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.
New users need these two steps before moving any further:
DLS Data Archive (accessing long-term storage for scans older than 40 days; see data retrieval for more tips).
Savu is a preferred Python-based tool for reconstructing raw DLS tomography data (i.e. radiographic projections).
Before you start, please install the NoMachine NX Client.
NoMachine
and click on New ConnectionNX
nx.diamond.ac.uk
as the host (and leave 4000 as the port)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.
Alternatively, you could connect via ssh
(e.g. to run a download operation remotely: wget https…
)
$ YourFedID@nx.diamond.ac.uk
Run the following commands in a Terminal: Applications –> System Tools –> Terminal
.
$ module load hamilton $ qlogin -P i13 -l gpu=1 -l gpu_arch=Pascal -l exclusive $ 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:
module load global/cluster qlogin -q high.q@@com14 -l exclusive -l gpu=1,nvidia_tesla -P i13
Similarly, to run Avizo 2019.1 (on DLS campus only)
module load avizo/2019.1; avizo
Further details are available in the online beamline manual.
— Igor Chernyavsky, 2018/03/24 19:00 —
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.
Try either
Running the shortcut SURVOS on the Desktop (C:\Users\...\Anaconda2\envs\ccpi\Scripts\SurVos.exe)
or
[Start] --> Anaconda Prompt > activate ccpi > SuRVoS
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 —
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.
$ ssh -Y username@e-a07maat1101X.it.manchester.ac.uk
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).
Note 1: If you are using MacOS or Windows, you also need to install and run an X Server
first (see more details on X-forwarding).
Note 2: On a university-managed Linux PC, you could connect directly via a name alias, e.g. $ ssh -Y cs1
.
Ref (X) | Name | Core Count | Core Speed and Type | RAM (GiB) | Note |
---|---|---|---|---|---|
a | cs1 | 12 | 3.4 GHz (Intel Xeon E5-2643v3) | 768 | Memory-intensive |
b | cs2 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | |
c | cs3 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | |
d | cs4 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | |
e | cs5 | 12 | 2.5 GHz (Inter Xeon E5-2430v2) | 128 | |
f | cs6 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | |
g | cs7 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | |
h | cs8 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | |
i | cs9 | 16 | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | |
j | cs10 | 16 | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | |
k | cs11 | 32 | 3.0 GHz (AMD Opteron 6220) | 256 | CPU-intensive |
l | cs12 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 192 | |
citadel | 8 (x2) | 3.4 GHz (Intel Xeon E5-1680v4) | 256 | GPU-intensive (Nvidia GTX1080 8GB 1.6GHz) |
Note that all CS cores run in a single-thread mode (HT is switched off).
System info:
free -h # RAM memory (or, $sudo dmidecode -t memory) lscpu # CPU params glxinfo -B # GPU memory # further detailed info sudo lshw -short #(omit sudo for partial info)
Load info:
top (followed by pressing the [t], [1] and [m] keys)
$ module load comsol53 $ comsol &
$ module load matlab2017a $ matlab &
— Igor Chernyavsky, 2019/07/15 18:00 —
Before you start, make sure there is an empty directory (e.g. ~/Shared
) in your home
directory that you are going to mount.
sshfs UoM_USERNAME@rds-ssh.itservices.manchester.ac.uk:/mnt/eps01-rds/Placental-Biophysics-Group/ ~/Shared/RDS/ fusermount -u ~/Shared/RDS/
sudo mount -t cifs -o user=UoM_USERNAME,domain=ds.man.ac.uk,sec=ntlmsspi,uid=`id -u`,gid=`id -g` //nask.man.ac.uk/home$ ~/Shared/PDrive/ sudo umount ~/Shared/PDrive/
google-drive-ocamlfuse ~/Shared/GDrive/ fusermount -u ~/Shared/GDrive/
'-o nonempty
' option if sure; you might also need to install the following Ubuntu
packages: libfuse2 build-essential libssl-dev libffi-dev python3-pip
)dbxfs ~/Shared/Dropbox/ fusermount -u ~/Shared/Dropbox/
For uploading a large file (>~ 10GB) or multiple files, use Dropbox-Uploader script:
./dropbox_uploader -s -p upload /LOCAL_FOLDER /REMOTE_FOLDER
sshfs FedID_USERNAME@nx.diamond.ac.uk:/dls/i13/data/ ~/Shared/DLS/ fusermount -u ~/Shared/DLS/
— Igor Chernyavsky, 2019/05/24 21:12 —