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Cloud Computingat Amazon’s EC2
Grid Computing
Shared resources – many computer clusters transferring data and running jobs.
Geographically distributed.Cross-grid collaboration.Idea is analogous to electric power network
(grid), where power generators are distributed, but users access electric power without bothering about the source of energy and its location.
LHC Computing Grid (LCG)
Cloud Computing
What if I don’t have my own cluster?Cloud computing refers to a cluster that invites
users to send jobs. (SaaS –Software as a Service)Computation, software, data access, and storage
services that do not require user knowledge of the location or configuration of the system.
Term comes from the cloud drawing used in the past to represent the telephone network, later represents the internet.
Cloud Computing
Cloud Computing
Private companies large data centers.When considering operational costs, 50k servers
are cheaper per cpu then 1k servers (5 to 7 times cheaper).
Amazon: • $0.085/cpu-hour• No minimum, maximum• No contract
Amazon E2
aws.amazon.comComputing cluster – create an account and
provide a credit card.Let Amazon take care of the hardware.
Cloud BioLinux
JCVI (J. Craig Venter Institute) created cloud version of NERC BioLinux VM.
An Ubuntu machine with over 100 NEBC software packages. Image stored at EC2, is available to be copied at no charge, by EC2 users.
http://aws.amazon.com
Create a new account
Enter your information
Sign up for an EC2 account
Click on “Sign up for Amazon EC2”
EC2 Account
• Signing up for EC2 automatically signs you up for Amazon Simple Storage Service, and Amazon Virtual Private Cloud.
• Requires credit card information.• No charges until you start using the services.• Amazon will email with Access Identifiers, and
instructions for your first log in.
Click on “AWS Management Console”
Click the EC2 Tab
Launch an Instance
I recommend biolinux
Click “Select”
Pricing
• Amazon has a variety of VM sizes available – pricing is at: http://aws.amazon.com/ec2/pricing/
• You are charged for CPU usage, for data storage, and for data transferred to or from Amazon. Charges continue until a VM is “Terminated”.
• You can set up a small test VM for free – select “Micro” for the size.
Kernel defaults are fine
Create a Key Pair
Create security group
Launch
Machine info
“Terminate” to end charges
ssh to the machine
A window opens, telling you how to connect to your new VM, eg,:
“ssh -i key_pair_name.pem [email protected]”
However, for biolinux, do:ssh –i key_pair_name.pem ubuntu@ec2-76-202-
01-919.compute-1.amazonaws.com
NX
Use NX for the graphical display (built in to biolinux already). Open source, can be found at http://www.nomachine.com/
Must ssh into VM FIRST, using the key pair.>adduser <username>>groups >usermod -G <grp1>,<grp2>,ssh <username>
Start NX
“Configure”
BioLinux over NX
Data Stored at Amazon
There are large datasets stored at Amazon, available for use – free of charge (mostly). You are charged for any data you copy.
http://aws.amazon.com/datasetsto search through them.
http://aws.amazon.com/datasets
DatasetsHuman DNA sequences: • 1000 Genomes Project (7,300 GB) • Ensembl Annotated Human Genome - FASTA (115 GB)• Ensembl Annotated Human Genome - MySQL (200 GB) • GenBank (200 GB) • Human Liver Cohort (Sage Bionetworks) (0.6 GB) • Illumina - Jay Flatley's Human Genome Data Set. (350 GB) • YRI Trio Data - complete genome sequence for three individuals (700 GB)
Other (might include some human data): • Ensembl - FASTA DB (100 GB) • Influenza Virus (including Swine Flu) - from NCBI (1 GB) • UniGene - from NCBI (10 GB) •
PubChem Library - from NCBI (230 GB)
Public Snapshots
Select “Volumes”
Create a Volume
Instance Information
Attach it to your Instance
Mount the Volume
From your VM:>sudo mkfs –t ext3 /dev/sdf>sudo mkdir /mnt/datasets>sudo mount –t ext3 /dev/sdf /mnt/datasets
200GB of genbank data are now in /mnt/datasets