Cloud Computing
Mick Watson
Director of ARK-Genomics
The Roslin Institute
Structure
• What is a computer
– Desktops / servers / clusters
– Clients / servers
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Virtualisation
The Cloud
Accessing the Amazon cloud
Costs etc
What is a computer?
What is a server?
What is a cluster?
• A cluster is a connected set of computers (nodes)
• Any job can be run on any of the nodes
• A server may be a single PC, it may be cluster
An operating system?
• An OS is the software that runs the computer:
– E.g. Windows
– E.g. Linux
– E.g. Mac OSX
– E.g. Android
– E.g. Solaris
– E.g. iOS
Virtualisation
• You can run an entire computer inside a computer
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Take OS and data and all running processes
Create an “image”
Recreate that image inside another PC
Access it as if it was a (physical) normal PC
• http://en.wikipedia.org/wiki/Virtualization
What is “the cloud”?
• There is not just one!
– Amazon EC2
– Rackspace
– Etc
• “The Cloud” refers to a large cluster of
computers, in which you can create, for a fee,
as many virtual computers as you like
AMAZON EC2
We will use Amazon EC2
• Terminology:
– EC = “Elastic Compute”
– Image – a preconfigured computer image. Like a template.
– Instance – an virtual version of an image that you can log in to and use
• Select a pre-configured Amazon Machine Image (AMI) to get up and
running immediately.
• Or create an AMI containing your applications, libraries, data, and
associated configuration settings.
• Configure security and network access
• Choose which instance type(s) you want, then start, terminate, and
monitor as many instances as you like.
• Pay only for the resources that you actually consume, like instancehours or data transfer
• Close down the image(s) when finished
Linux
• Linux refers to an entire family of operating systems:
– Red Hat
– Ubuntu
– Debian etc
• Linux is free
• Many of the computers that power the internet run
Linux
• Almost all bioinformaticians use it
• Powerful, extendable and open
The power is the command line
• Don’t panic!
BioLinux
• http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0
• A Linux operating system designed for bioinformatics
• More than 500 bioinformatics software programs
installed on top of Ubuntu 10.4 base
• There are BioLinux AMIs
on EC2 – CloudBioLinux
• We have created our own
AMI based on
CloudBioLinux
How powerful?
• Once you have selected the “type” of computer (AMI) you
must then select the size and power
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M1 Small Instance (Default) 1.7 GiB of memory, 1 EC2 Compute Unit (1 virtual core with 1
EC2 Compute Unit), 160 GB of local instance storage, 32-bit or 64-bit platform
M1 Medium Instance 3.75 GiB of memory, 2 EC2 Compute Units (1 virtual core with 2 EC2
Compute Units each), 410 GB of local instance storage, 32-bit or 64-bit platform
M1 Large Instance 7.5 GiB of memory, 4 EC2 Compute Units (2 virtual cores with 2 EC2
Compute Units each), 850 GB of local instance storage, 64-bit platform
M1 Extra Large Instance 15 GiB of memory, 8 EC2 Compute Units (4 virtual cores with 2 EC2
Compute Units each), 1690 GB of local instance storage, 64-bit platform
M3 Extra Large Instance 15 GiB of memory, 13 EC2 Compute Units (4 virtual cores with 3.25
EC2 Compute Units each), EBS storage only, 64-bit platform
M3 Double Extra Large Instance 30 GiB of memory, 26 EC2 Compute Units (8 virtual cores
with 3.25 EC2 Compute Units each), EBS storage only, 64-bit platform
How powerful?
• Once you have selected the “type” of computer (AMI) you
must then select the size and power
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Micro Instance 613 MiB of memory, up to 2 ECUs (for short periodic bursts), EBS storage only,
32-bit or 64-bit platform (free)
High-Memory Extra Large Instance 17.1 GiB memory, 6.5 ECU (2 virtual cores with 3.25 EC2
Compute Units each), 420 GB of local instance storage, 64-bit platform
High-Memory Double Extra Large Instance 34.2 GiB of memory, 13 EC2 Compute Units (4
virtual cores with 3.25 EC2 Compute Units each), 850 GB of local instance storage, 64-bit
platform
High-Memory Quadruple Extra Large Instance 68.4 GiB of memory, 26 EC2 Compute Units (8
virtual cores with 3.25 EC2 Compute Units each), 1690 GB of local instance storage, 64-bit
platform
High-CPU Medium Instance 1.7 GiB of memory, 5 EC2 Compute Units (2 virtual cores with 2.5
EC2 Compute Units each), 350 GB of local instance storage, 32-bit or 64-bit platform
High-CPU Extra Large Instance 7 GiB of memory, 20 EC2 Compute Units (8 virtual cores with
2.5 EC2 Compute Units each), 1690 GB of local instance storage, 64-bit platform
How powerful?
• Once you have selected the “type” of computer (AMI) you
must then select the size and power
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Cluster Compute Quadruple Extra Large 23 GiB memory, 33.5 EC2 Compute Units, 1690 GB of
local instance storage, 64-bit platform, 10 Gigabit Ethernet
Cluster Compute Eight Extra Large 60.5 GiB memory, 88 EC2 Compute Units, 3370 GB of local
instance storage, 64-bit platform, 10 Gigabit Ethernet
Cluster GPU Quadruple Extra Large 22 GiB memory, 33.5 EC2 Compute Units, 2 x NVIDIA Tesla
“Fermi” M2050 GPUs, 1690 GB of local instance storage, 64-bit platform, 10 Gigabit Ethernet
High I/O Quadruple Extra Large 60.5 GiB memory, 35 EC2 Compute Units, 2 * 1024 GB of SSDbased local instance storage, 64-bit platform, 10 Gigabit Ethernet
THE PRACTICAL
• http://www.ark-genomics.org/events-online-training/eu-training-course
• In this course you will start a new Amazon EC2 instance and
begin to learn some of the essentials of the linux commandline
• Don’t panic.