H3ABioNet

Pan African Bioinformatics Network for H3Africa

H3ABioNet Advanced Systems Administration Workshop - Bioinformatics and Computational Biology Unit, University of Pretoria 2nd to 11th Feb 2015

Workshop training materials are available at: http://training.h3abionet.org/technical_workshop_2015/

Venue of workshop: Bioinformatics and Computational Biology Unit, University of Pretoria

Dates for the workshop: 2nd February to 11th February, 2015

Workshop organisers: H3ABioNet and the Bioinformatics and Computational Biology Units, Universities of Pretoria and the Witwatersrand H3ABioNet Nodes

Link to registration form:http://surveys.h3abionet.org/sysadmincourse2/

Participation: Participation is by nomination of individuals from their H3ABioNet Node or H3Africa projects’ Principal Investigators.

Workshop Sponsors: H3ABioNet.

Workshop Overview: In keeping with the H3ABioNet Consortium's mandate to build and develop bioinformatics capacity in Africa, the Infrastructure Working Group (ISWG) is organizing an H3ABioNet-Funded Technical-Training workshop for System Administrators of the various Nodes and H3Africa projects. This is a follow up to the initial systems administration workshop run in Pretoria, 2013 to enhance the capacity of newly hired personnel.
The aim of the workshop is to train newly hired System Administrators and/or their representatives on systems administration of Unix type servers/infrastructure relevant for data management and storage for H3Africa affiliated projects and subsequent bioinformatics research.

Intended Audience: Newly hired System Administrators and previous attendees of the systems administration workshop in Pretoria who work on systems administration of UNIX type servers and infrastructure relevant for data management and storage for H3ABioNet Nodes and H3Africa affiliated projects engaged in bioinformatics research.

Syllabus and Tools: Participants will learn about the command line, Linux file management, basic process management, network fundamentals, program installation, job scheduling, backups, encryption, virtualisation, server management and automation using Puppet and Server Configuration, scripts for configuration of multiple machines, setting up compute clusters.

Trainers: Professor Fourie Joubert (University of Pretoria), Professor Scott Hazelhurst (University of the Witwatersrand), Mohamed Alibi (Institut Pasteur de Tunis), Peter van Huesden (South African National Bioinformatics Institute), Ayton Mentjies (University of Cape Town).
 
Prerequisites: Remote access and administer privileges to install software programmes on a serve in your Institute is a must. Good working knowledge of Unix, provision of systems administration support within your Institution. Those unfamiliar with Unix are encouraged to work through the following resources to enable them to gain the most from the workshop:
H3ABioNet Systems Administration Documentation Level 1 and Level 2 and http://www.washington.edu/R870/

Objectives: After this workshop participants should be able to:

  • Install Linux on a server from scratch,
  • Create basic and advanced bash shell scripts
  • Implement basic Linux file management and manage physical storage partitions,
  • Perform user and group management, and use standard Linux permissions
  • Perform basic network and firewall configuration,
  • Use standard encryption and compression techniques
  • Install software from source and using a package management
  • Remotely access systems and perform large-scale data transfer
  • Automate system setup and configuration
  • Set up compute clusters
  • Follow H3ABioNet Standard Operating Procedures

Workshop limitations: This workshop will provide an introduction and foundation for continued learning within a user group of your peers who will attend the H3ABioNet Advanced Systems Administration Workshop and participation within the H3ABioNet Infrastructure Working Group.

Workshop costs: H3ABioNet will cover the costs of the a return economy air ticket to South Africa, accommodation from the night before the portion of the workshop you are attending starts (either the 1st of February or the 5th of February 2015) till the night the workshop ends on 11th of February at the Brooklyn Guesthouse (http://www.brooklynguesthouses.co.za).

H3ABioNet will not cover the costs of the meal for the first evening of your arrival on the 1st of February 2015, vaccinations, visa fees or airport transfers from your local area which will be borne by your home Institution.

Please note if a participant is unable to attend this workshop after acceptance due to a last minute cancellation, the costs of the air tickets, accommodation and catering will be borne by their home Institution.

Workshop Program:

Systems Administration for Beginners

Time

Topic

2nd February 2015

8:00

Registration and Introductions

8:30

Pre-workshop evaluation

9:00

Introduction to Linux, CLI, basics of file system

10:45

Tea break

11:15

Process management

1:00

Lunch

2:00

Text editors and key utilities

3:30

Tea Break

4:00

Introduction to scripting and bash

5:30

Workshop End

3rd February 2015

9:00

User and group management

Physical storage and file systems

10:45

Tea Break

11:15

Network fundamentals and firewalls

1:00

Lunch

2:00

Security overview

ssh (client and server)

3:30

Tea Break

4:00

Encryption, compression, tar, md5sum etc

5:30

Workshop End

4th February 2015

9:00

Installing Scientific Linux from scratch

10:45

Tea Break

11:15

Scientific Linux package management

1:00

Lunch

2:00

Updates and mirrors

3:30

Tea Break

4:00

Backup strategies

5:30

Workshop End

5th February 2015

9:00

Installing packages from source and Symbolic Link usage

10:45

Tea Break

11:15

Job scheduling

1:00

Lunch

2:00

Setting up Globus Connect Personal and Server – transfer of a standard dataset amongst H3ABioNet Nodes

3:30

Tea Break

4:00

Automating administration

5:30

Workshop End

 

Systems Administration for Experts

Time

Topic

6th February 2015

9:00

Bash programming

10:45

Tea Break

11:15

Scripting for management (Expect, Spawn and practicals)

1:00

Lunch

2:00

Virtualisation I

3:30

Tea Break

4:00

Virtualisation II

5:30

Workshop End

7th February 2015

9:00

Overview of advanced storage options

RAID

10:45

Tea Break

11:15

NFS

1:00

Lunch

2:00

LVM practice

3:30

Tea Break

4:00

LVM practice

5:30

Workshop End

8th February 2015

Free Day

Time

Topic

9th February 2015

9:00

H3ABioNet SOPs

10:45

Tea Break

11:15

Puppet Installation

1:00

Lunch

2:00

Puppet Usage

3:30

Tea Break

4:00

Puppet Usage

5:30

Workshop End

10th February 2015

9:00

Cluster setup

10:45

Tea Break

11:15

Cluster management

1:00

Lunch

2:00

Cluster monitoring (Nagios, Icinga)

3:30

Tea Break

4:00

Run example of  MPI programs on Cluster

6:00

Workshop End

11th February 2015

9:00

Gluster

10:45

Tea Break

11:15

Overview of grid computing

Certificate management

1:00

Lunch

2:00

GridFTP

3:30

Tea Break

4:00

H3ABioNet NetMap Project and installation practical

6:00

Workshop End