Document 6504838

CUBRIC IT system
How to find your way around CUBRIC digital maze
Tuesday, 1 October 13
CUBRIC IT
Our goal is to create a reliable and evolving infrastructure and support system that
satisfies the diverse and changing technology requirement of CUBRIC
•
•
The MSc Room: 57 Park Place
CUBRIC IT:
•
•
Tuesday, 1 October 13
Spiro: spiro@cardiff.ac.uk
Cyril: charronc@cardiff.ac.uk
•
INSRV - INformation SeRVices
•
•
•
Library help desks
40 - 41 Park Place
insrvConnect@cardiff.ac.uk
Cardiff University Brain Research
Imaging Centre
•
•
Tuesday, 1 October 13
Big data : MEG and MRI generate vast
amount of data
Complex analysis : signal
processing, statistical analysis
•
Sensitive and precious data
•
Data needs to be protected against
identification, loss, corruption, must be
retrievable, re-usable, ...
•
Expensive information (£500 per hour
for MRI, £350 per hour for MEG)
•
Medical nature of the data
The cluster
The computing core of CUBRIC
• Cluster of computer nodes
• 1296 nodes (Central Processing Units,
CPUs)
•
Tuesday, 1 October 13
16GB of memory per node
• Scheduling system
• analysis can be divided in smaller jobs
• submit analyses to the scheduler
which dispatches them to the nodes
The storage
The CUBRIC vault
• 90 TB of highly resistant and fast storage
• Corruption of the data (data rot, i.e.
silent corruption of the data)
• Expensive, use responsibly
• Losing sensitive data (stolen laptop)
• Perils :
• The storage system is protected
against those (Contact us in case of
• Hardware failure
mishap).
• User mishap
• Water or fire damage
Tuesday, 1 October 13
How to access it?
•
Tuesday, 1 October 13
Workstation or Virtual Machine (aka
NoMachine)
•
on one of the PAWS (workstation in
the MSc room) using your username
and password
•
•
using NoMachine from anywhere else
it’s all Linux, you won’t see (much of) a
difference
•
NoMachine is a service that allows you
to connect to a virtual machine hosted
in CUBRIC computing facilities
•
requires to install a client (OpenNX,
available on Windows, Linux and
Mac OS X, you can google it)
•
see CUBRIC user website for
parameters
How to use it?
• Your Home folder
• your Home folder: 10GB (very
secure, comes back quick)
Tuesday, 1 October 13
•
your Data folder: 400GB (very secure,
comes back later)
•
your Scratch folder: unlimited but
reclaimed (there is no free lunch)
• Analysis software
• fMRI: SPM, FSL, AFNI
• structural MRI: ExploreDTI, McDespot
• MEG: SAMstatistics, MRIviewer
• Generic Tools: MATLAB, Python,
various scripting languages
CUBRIC user website
• sites.cardiff.ac.uk/cubric
• Log in with your username and
password
•
Tuesday, 1 October 13
information of MRI and MEG analysis
pipelines (how to get your data from the
repository, how to extract your data,
how to compensate for field
inhomogeneities in your fMRI
sequences) and experiment setups
•
information on how to use Linux
(commands)
•
information on MATLAB
CUBRIC studies database
https://studies.cubric.cf.ac.uk
•
View the planning for fMRI, MEG,
seminars
•
retrieve your experiment data using
the cart
Tuesday, 1 October 13
Cardiff University IT (INSRV)
•
portal.cardiff.ac.uk
•
•
•
where can I register?
•
•
•
•
networked storage
links to
Voyager Library Catalogue
electronic journal
password management
Wireless access: eduroam
•
email
•
•
•
Tuesday, 1 October 13
•
•
•
Julian Hodge Study Centre
Libraries
40 - 41 Park Place (INSRV)
how to: www.cf.ac.uk/insrv/wireless
antivirus: www.cf.ac.uk/insrv/it/antivirus
mobile website: m.cardiff.ac.uk