1. Creating an AMI at Amazon’s EC2 Joe Steele jrsteele@unomaha.edu

2. 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.

3. Cloud Computing

4. Amazon E2 aws.amazon.com Computing cluster – create an account and provide a credit card. Let Amazon take care of the hardware.

5. 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.

6. http://aws.amazon.com

7. Create a new account

8. Enter your information

9. Sign up for an EC2 account

10. Click on “Sign up for Amazon EC2”

11. 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.

12. Click on “AWS Management Console”

13. Click the EC2 Tab

14. Launch an Instance

15. I recommend biolinux

16. Click “Select”

17. Pricing Amazon has a variety of VM sizes available – pricing is at: http://aws.amazon.com/ec2/pricing/ 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.

18. Kernel defaults are fine

19. Key files For biolinux, you don’t need to add “User Data”. For VipDac (on the Back-Up slides) the Amazon key IS needed. When you create a Key Pair (next slide), save the *.pem file to a safe place.

20. Create a Key Pair

21. PEM file Save the *.pem file to a safe place. Linux: the *.pem file has to be protected: >chmod 400.pem Windows: Download PuTTYgen, and use it to change the *.pem file to a *.ppk file.

22. Create security group

23. Launch

24. Machine info

25. “Terminate” to end charges

26. First connection to Biolinux A window opens, telling you how to connect to your new VM, eg,: “ssh -i key_pair_name.pem root@ec2-76-202-01- 919.compute-1.amazonaws.com”root@ec2-76-202-01- 919.compute-1.amazonaws.com However, for biolinux, or any unbuntu VM, do: ssh –i key_pair_name.pem ubuntu@ec2-76-202-01- 919.compute-1.amazonaws.comubuntu@ec2-76-202-01- 919.compute-1.amazonaws.com from a Linux machine, make sure the key_pair_name.pem is set to read only for the user only.

27. First Connection From Windows: Use PuTTYgen to change key_pair_name.pem to key_pair_name.ppk. Use PuTTY to connect, and put key_pair_name.ppk under “SSH” -> “Auth”. When connected to biolinux, you will be asked to set a password for ubuntu. If not, you need to start NX client: >./configure_freenx.sh

28. NX Use NX for the graphical display (built in to biolinux already). Open source, can be found at http://www.nomachine.com/http://www.nomachine.com/ Must ssh into VM FIRST, using the key pair. You can stick with the ubuntu user, or add new users: >adduser >groups >usermod -G,,ssh

29. Start NX

30. “Configure”

31. Configure NX Note the use of “GNOME” and “LAN”. The Host should be “ec2-72-…amazonaws.com”. Also, the “Key…” works with the default key.

32. BioLinux over NX

36. 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/datasets to search through them. Datasets that might be of interest in bioinformatics are listed at: http://biodoc.ist.unomaha.edu/wiki/Inventory_ of_amazon_data

37. http://aws.amazon.com/datasets

38. Datasets Human 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)

39. Public Snapshots

41. Select “Volumes”

42. Create a Volume

43. Instance Information

44. Attach it to your Instance

45. 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

46. Test Usage for the First Year

47. CPU charges

48. Data Transfer charges

49. Data storage charges

50. Back Up slides

51. VipDac Tutorial