C2115 Practical introduction to supercomputing -1-organization
C2115
Practical introduction to
supercomputing
Petr Kulhánek
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science,
Masaryk University, Kamenice 5, CZ-62500 Brno
organization
Revision 1
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Content
➢ Teaching organization
schedule, block teaching, course completion
➢ WOLF cluster
structure, rules of use, administrators, classroom 1.18
➢ Prerequisites
accounts
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Teaching organization
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Semester schedule
about 15 hours per day during
5-day block teaching :-)
Self-study.
Teaching: October 5, 2020 - January 15, 2021
Examination period: January 18, 2021 - February 26, 2021
Total number of lectures: 13 x 2 hours = 26 hours
Termination: colloquium (2 + 1 credits)
Total hourly load of the subject:
1 ECTS credit -> 26 hours of study load
3 credits -> 3x 26 hours = 78 hours of study load
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Block teaching - 8.-12.2. 2021
Monday - Thursday: teaching
start at 9:00, end at 16:00
lunch and breaks according to the subject
Friday: teaching
start at 9:00, end at 10:00
final test: start at 10:00
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Block teaching - 8.-12.2. 2021
Monday - Friday: online consultation
starting at 9:00
starting at 13:00
or by prior arrangement
Assesment method:
- final test (1 hour, 50 questions) 50 points
- summary protocol from exercises
====================================================
Total: 50 points
Succeeded: >= 30 points
The test will be open in the IS from 12.2. 12:00 to 26.2. 12:00.
You will insert the report to the "Protocols" Homework Vault no later than 26.2. 12:00.
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Protocol - requirements
➢ state your full name and date of preparation
➢ protocol will be contained in one file
➢ number the pages
➢ state the assignment of the task (it can be abbreviated) including its number (see below)
and then your solution; provide only relevant information so that the result presented by
you can be reproduced
➢ the graphs will be correctly described, i.e., will include key of the axes, the description of
the data series, in case of interpolation by the curve the measured or calculated data points
will be highlighted by a cross; I recommend to script graphs in gnuplot
➢ if the quantity has a unit, always state it; a space is typed between the value and the unit,
except for angular units (degree, minute, second), where the space is not typed
➢ if the result of the exercise is not a quantitative result, then briefly describe what you did
➢ submit the report in pdf format no later than Friday, February 26, 2021 12:00 to the
Homework Vault "Protocols"; the file name will be SurnameNameC2115.pdf
L.E.T.
lesson number
exercise number
task number
Task numbering:
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Teamwork
Teamwork is essential. It allows you to
blame someone else.
Teamwork is allowed, but…
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WOLF cluster
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Rules of use
WOLF cluster is intended exclusively for teaching purposes or for scientific work
within the National Center for Biomolecular Research.
Rules for using computer network of Masaryk University:
https://is.muni.cz/auth/do/mu/Uredni_deska/Predpisy_MU/Masarykova_univerzita/Smernice_MU/SM10-17/
It is expressly prohibited to WOLF cluster use WOLF cluster for:
➢ downloading illegal content (copyrighted works, etc.)
➢ sending viruses, spam and similar materials
➢ breaking the protection of other computers
➢ read, delete, or change the unprotected contents of other users' files
The login name and password form the identity of the user and therefore
are not shared with third parties by us, we do not store or send them (e.g.,
by e-mail) in unencrypted form!
C2115 Practical introduction to supercomputing
WOLF cluster structure
wolf wolf03 wolf23wolf02 wolfsr
university
network
workstations (computing nodes)
server/front
node
Operating system: Ubuntu 18.04 (Bionic) LTS
(http://www.ubuntu.com/)
0.18 1.18 2.11
wolf32 wolf40wolf31wolf30
0.18
wolf01
switch
computing nodes
Rooms:
0.18 Server room C04/UKB
1.18 Computer room C04/UKB
2.11 Seminar room C04/UKB
0.57 Seminar room (library) C04/UKB
All nodes are accessible directly from public network.
Domain: ncbr.muni.cz
wolflr
0.57
forbidden to log in
temporarily out of order
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Cluster administrators
Before contacting the administrator, consult your problem with your colleague, teacher or
supervisor. If you do not resolve the issue, report the problem to the administrators by
sending an e-mail to
support@lcc.ncbr.muni.cz
In the report, indicate
➢ Problem description, command name
➢ User name, machine
➢ Copy of error output (complete from command entry)
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Classroom 1.18
➢Classroom with 23 PCs
➢Arranged into a
computing cluster
The classroom is freely accessible to students studying at the NCBR and also to
students who have lectures in the classroom during given semester.
Safety!
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Prerequisites
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Prerequisites - accounts
➢ Who doesn't have an account in MetaCentrum – applies now!
➢ Account on the WOLF cluster
https://wolf.ncbr.muni.cz
▪ create an account
▪ resetting password, account renewal
▪ classroom occupancy
▪ documentation
➢ Account in a virtual organization MetaCentrum
http://metavo.metacentrum.cz
▪ application
▪ account management
▪ resetting password, account renewal
▪ overview of computing resources and data repositories
▪ documentation