Introduction to servers, HPC, and Cloud Computing

1. Computing Hardware
Jeff Allen
Quantitative Biomedical Research Center
UT Southwestern Medical Center
BSCI5096 - 3.26.2013

2. Outline
• Servers
• Clusters
• The Cloud

3. Outline
• Servers
– Concepts & Definitions
– Novel properties of servers
• Clusters
• The Cloud

4. Servers – Concepts & Definitions
“A computer or program that
supplies data or resources to other
machines on a network.”
• File Server • Email Server
• Database Server • iTunes Server
• Web Server • Computing Server
server. (n.d.). Collins English Dictionary - Complete & Unabridged 10th Edition. Retrieved March 25, 2013,
from Dictionary.com website: http://dictionary.reference.com/browse/server

5. Servers – Concepts & Definitions
• Same hardware
components as your
Personal Computer
– Processor, Memory, Pow
er Supply, Hard Drive
• Often stacked in a rack
Image from: http://www.stealth.com/industrial_rackmounts_sr1501datasheet.htm

6. Servers – Concepts & Definitions
• Same hardware
components as your
Personal Computer
– Processor, Memory, Pow
er Supply, Hard Drive
• Often stacked in a rack
http://www.daystarinc.com/hosting-facility

7. Is this a server?
Image from: http://www.stealth.com/industrial_rackmounts_sr1501datasheet.htm

8. Is this a server?
Image from: http://mediapool.getthespec.com/media.jpg?m=gBLSSTJ6IbHLuZD1JNnmyw%3D%3D&v=HR

9. Is this a server?
Image from: http://www.maximumpc.com/articles/reviews/hardware

10. Is this a server?
Image from: http://www.phonearena.com/image.php?m=Articles.Images&f=name&id=28259&name=GT-
I8520_1.jpg&caption=&title=Image+from+%22UPDATED%3A+Samsung+I8520+is+an+Android+phone+with+built-in+projector%22&kw=&popup=1

11. Is this a server?

12. Common Attributes of a Server
• Often runs an Operating System geared
towards servers.
• Primarily accessed remotely
– Often “headless” (no monitor)
• Runs 24/7, minimize downtime
• May be kept in a data center
– Superior cooling, increased security, etc.
• Redundancy (Power, Disk Storage)
• More powerful and expensive

13. Operating System
Client PCs Servers
• Windows (XP, Vista, 7, 8) • Linux (Red Hat, Suse
• Mac OS Enterprise, Ubuntu
• Linux Server)
(Ubuntu, Mint, openSUS • Windows (Windows
E) Server 2003, 2008, 2012)
• Non-Linux Unix
(BSD, Solaris, AIX)

14. Remote Access & the Shell
• Typically don’t have
physical access to the
server, must access
over a network
• Windows is heavily
graphical, access
using “Remote
Desktop”
Image from http://www.softsalad.com/software/remote-desktop-control.html

15. Remote Access & the Shell
• Typically don’t have
physical access to the
server, must access
over a network
• Windows is heavily
graphical, access
using “Remote
Desktop”
• Linux is less
graphical, access via
a “Shell”
Image from http://www.softsalad.com/software/remote-desktop-control.html

16. Shell Access
1. User logs in
2. User types command
3. Computer executes Shell
command and prints
output
4. User types another
command
5. …
6. User logs off
Modified from http://software-carpentry.org/4_0/shell/intro.html

17. Shell Comparison
Windows (Graphical) Linux (Shell)
Image from http://www.dedoimedo.com/computers/windows-7.html

18. Shell Comparison
Windows (Graphical) Linux (Shell)

19. Shell Comparison
Windows (Graphical) Linux (Shell)

20. Shell Access
• Slow learning curve
• Can often be confusing at first, requires a new way
of thinking
• Ultimately very powerful and efficient
• Three reasons to use:
1. It’s your only choice for remote access on some non-
graphical systems
2. Many software tools only offer Command Line
interfaces
3. Allows for powerful new combinations of tools
Modified from http://software-carpentry.org/4_0/shell/intro.html

21. Data Centers
• Redundant, independent power feeds
– Diesel generator backup
• Redundant Internet connections
• Redundant cooling
• 24/7/365 staffing, restricted access

22. RAID
Disk 1
• “Redundant Array of
Disk 2 Independent Disks”
RAID
• Store information
Disk 3
Array redundantly
Disk 4 • Support failure of
one or more hard
Disk 5
drives without losing
data

23. Server Computing Power
• Often very expensive machines
• Hardware designed to support more resources
than a PC
– May have dozens or hundreds of GB of RAM
– Very expensive powerful processor, or even
multiple processors

24. Outline
• Servers
• Clusters
– Motivation & Concept
– Job submission
– Example
• The Cloud

25. Example Problem
• Group of 10
researchers
• Too many concurrent
users, runs slowly
• Have some very large
jobs

26. Naïve Solution
• Buy more independent
servers!
• Let people connect to
whichever server they
want
• Problems:
– Not sure which servers
are busiest
– Still takes weeks to run
big simulations

27. Clustered Solution
• Servers are “nodes” in a
cluster
• Log in via head node
• Head node manages
requested jobs
– Submits them to “worker”
or “slave” nodes
– Intelligently calculates
available resources on
each worker node
• Multiple nodes can work
on a single task

28. Job Submission
• Prepare a script to be executed (“myjob.sh”)
– Include specifications on resources required
• (“-l nodes=2:ppn=4”)
– Or what queue it should be submitted to
• Different queues have different priorities and permissions
• Submit that job to the head node (“qsub
myjob.sh”)
• Head node will begin executing as soon as it
has sufficient resources

29. Clustered Solution

30. Clustered Solution
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

31. Clustered Solution
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

32. Clustered Solution
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

33. Clustered Solution
Job #2
Job #1
User: User9
User: User4
Nodes Req’d: 1 Nodes Req’d: 1
Program: align.sh Program:
simul.sh

34. Clustered Solution
Job #2
User: User9
Nodes Req’d: 1
Program: simul.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

35. Clustered Solution
Job #2
User: User9
Nodes Req’d: 1
Program: simul.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

36. Clustered Solution
Job #2
User: User9
Nodes Req’d: 1
Program: simul.sh
Job #3
Job #1 User: User2
User: User4
Nodes Req’d: 1 Nodes Req’d: 2
Program: align.sh Program:
splice.sh

37. Clustered Solution
Queued
Job #3
Job #2 User: User2
User: User9 Nodes Req’d: 2
Nodes Req’d: 1 Program:
Program: simul.sh splice.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

38. Clustered Solution
Queued
Job #3
Job #2 User: User2
User: User9 Nodes Req’d: 2
Nodes Req’d: 1 Program:
Program: simul.sh splice.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

39. Clustered Solution
Queued
Job #3
User: User2
Nodes Req’d: 2
Program:
splice.sh
Job #2
Job #1
User: User9
User: User4
Nodes Req’d: 1
Nodes Req’d: 1
Program: simul.sh
Program: align.sh

40. Clustered Solution
Queued
Job #3
User: User2
Nodes Req’d: 2
Program:
splice.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

41. Clustered Solution
Queued
Job #3
User: User2
Nodes Req’d: 2
Program: splice.sh
Job #1
User: User4
Nodes Req’d: 1
Program: align.sh

42. Clusters
• Solve problem of sharing resources
• Allow multiple nodes to collaborate on a single
job
– Programs must be specifically designed to run in
this fashion
• Can solve very large problems by combining
hundreds of nodes together
– Global weather forecasting, particle collisions at
CERN, etc.

43. HPC at UT Southwestern
• QBRC manages an 18 node cluster on-
campus.
• Have access to Texas Advanced Computing
Center (TACC) at UT Austin
– 6,400 node cluster with > 100k cores
– Attracts many users, often a queue before your
jobs will run.

44. Outline
• Servers
• Clusters
• The Cloud

45. Cloud Computing
• Vendors with access to massive computing
resources began leasing their servers out
– Amazon, Microsoft, Google, Rackspace
– Charge per hour of use, usually just a few cents.

46. Cloud Computing - Advantages
• No up-front purchase/cost
• No hardware to manage
• 100 servers in parallel is the same cost as a
single server running for 100 hours
– Can get parallel jobs done much more quickly

47. Cloud Computing - Disadvantages
• Data must be transferred over the Internet
– Can take hours to upload a large sequencing
experiment.
• Can be more expensive than internal clusters