Maxwell siuc hpc_description_tutorial

High–Performance Computing
(HPC)
Prepared By:
Abdussamad Muntahi
Muhammad Rahman
1

Introduction to High–Performance Computing
(HPC)
2

Introduction
• High-speed computing. Originally pertaining only to
supercomputers for scientific research
• Tools and systems used to implement and create high
performance computing systems
• Used for scientific research or computational science
• Main area of discipline is developing parallel
processing algorithms and software so that programs
can be divided into small parts and can be executed
simultaneously by separate processors
• HPC systems have shifted from supercomputing to
computing clusters
3

What is Cluster?
• Cluster is a group of machines interconnected in a way that they
work together as a single system
• Used for better speed and capacity
• Types of Cluster
o High-availability (HA) clusters
o Load-balancing clusters
o Grid computing
• Terminology
o Node – individual machine in a cluster
o Head node – connected to both the private network of the cluster
and a public network and are used to access a given cluster.
Responsible for providing user an environment to work and
distributing task among other nodes
o Computer nodes – connected to only the private network of the
cluster and are generally used for running jobs assigned to them by
the head node(s)
4

Benefits of Cluster
• Reduced Cost
o The price of off-the-shelf consumer desktops has plummeted in recent
years, and this drop in price has corresponded with a vast increase in
their processing power and performance. The average desktop PC
today is many times more powerful than the first mainframe
computers.
• Processing Power
o The parallel processing power of a high-performance cluster can, in
many cases, prove more cost effective than a mainframe with similar
power. This reduced price-per-unit of power enables enterprises to get
a greater ROI (Return On Investment) from their IT budget.
• Scalability
o Perhaps the greatest advantage of computer clusters is the scalability
they offer. While mainframe computers have a fixed processing
capacity, computer clusters can be easily expanded as requirements
change by adding additional nodes to the network.
5

Benefits of Cluster
• Improved Network Technology
o Driving the development of computer clusters has been a vast
improvement in the technology related to networking, along
with a reduction in the price of such technology.
o In clusters, computers are typically connected via a single virtual
local area network (VLAN), and the network treats each
computer as a separate node. Information can be passed
throughout these networks with very little lag, ensuring that
data doesn’t bottleneck between nodes.
• Availability
o When a mainframe computer fails, the entire system fails.
However, if a node in a computer cluster fails, its operations can
be simply transferred to another node within the cluster,
ensuring that there is no interruption in service.
6

Application of HPC
• Used to solve complex modeling problems in a spectrum of
disciplines
• Topics include:
• HPC is currently applied to business uses as well
o data warehouses
o line-of-business (LOB) applications
o transaction processing
7
o Artificial intelligence
o Climate modeling
o Cryptographic analysis
o Geophysics
o Molecular biology
o Molecular dynamics
o Nuclear physics
o Physical oceanography
o Plasma physics
o Quantum physics
o Quantum chemistry
o Solid state physics
o Structural dynamics.

Top 10 Supercomputers for HPC
June 2011
8
Copyright (c) 2000-2009 TOP500.Org | All trademarks and copyrights on this page are owned by their respective owners

Fastest Supercomputer in USA:
Jaguar @ Oak Ridge National Lab
10
http://computing.ornl.gov

Hardware and Our Cluster
SIHPCI (maxwell)
11

Cluster Architecture: Typical
12

Cluster Architecture: Maxwell
13

The Cluster: maxwell
Tech Specs:
 No. of nodes: 106
 Each node is a Intel dual CPU
Quad Core 2.3 GHz Processor
 Total No. of cores: 848
 RAM per node: 8 GB
 Storage Memory: 90 TB
14

Hardware: Master/Head Node
• Head node is responsible for providing user an environment
to work and distributing task among other nodes
• Minimum Specification
o CPU of i586 or above
o A network interface card that supports a TCP/IP stack
o At least 4GB total free space – 2GB under and 2GB under /var
o A Floppy Drive
o A CD-Rom Drive
15
Front End
Back End

Hardware: Master/Head Node
• Maxwell Specification
o Server format Rack
o CPU family Intel Xeon
o CPU nominal frequency 2.26GHz
o Processor Model Xeon E5520
o Processors supplied 2 Quad core
o Memory RAM capacity 24GB Memory (6x4GB),
o Memory type DDR3
o Memory frequency 1066MHz Quad Ranked RDIMMs
o Storage HDD 146GB 15K RPM Serial-Attach SCSI
o RAID module PERC 6/i SAS RAID Controller 2x4 Connectors
o Gigabit LAN ports 2
o Power supply rating 480W
o Idle power consumption 150W
o Peak power consumption 270W
o OS Red Hat Enterprise Linux 53AP x32 And x64
16
Front End

Hardware: Computing Node (Client)
• Dedicated for Computation
o CPU of i586 or above
o A disk on each client node, at least 2GB in size
o A network interface card that supports a TCP/IP stack
o All clients must have the same architecture (e.g., ia32 vs. ia64)
o Monitors and keyboards may be helpful, but are not required
o Floppy or PXE enable BIOS
o A CD-Rom Drive
17
Two Quad Core
processors
Memory slot
Memory slot

Hardware: Computing Node (Client)
o CPU family Intel Xeon
o CPU nominal frequency 2.13GHz
o Processors supplied 2 quad core
o Memory RAM capacity 8GB Memory (4x2GB)
o Memory type DDR3
o Memory frequency 1333MHz Dual Ranked UDIMMs
o storage HDD 160GB 7.2K RPM SATA
o Gigabit LAN ports 2
o Power supply rating 480W
o Idle power consumption 115W
o Peak power consumption 188W
o OS Red Hat Linux 5 HPC
18
Front End

Hardware: Switch
– The switch is necessary for communication between the nodes
– Each node (including the head node) should have its own port on the
switch. In other words, if there are one head node and 8 client nodes,
you need at a minimum a 9-port switch
19
Switch

Hardware: Switch
o Model: Power Connect 6248
o Port: 48 10/100/1000BASE-T auto-sensing Gigabit Ethernet switching ports
o 48 GbE(giga bit ethernet) Port Managed Switch, two 10GbE and Stacking
Capable
20
Power Connect 6248 Switch Stack

Hardware: Power Distribution Unit
• APC Switched Rack Power Distribution Units (PDUs) place rack equipment
power control in the hands of the IT Manager. Remote outlet level controls
allow power on/off functionality for power recycling to reboot locked-up
equipment and to avoid unauthorized use of individual outlets. Power
sequencing delays allow users to define the order in which to power up or
down attached equipment. Avoid circuit overload during power recovery
and extend uptime of critical equipment by prioritizing the load shedding.
o PDU plug type L6-30P
o PDU ModelAPC AP7541
o PDU Max Amperage Load 30
21

Hardware: External Storage Array
• Minimum Specification:
o Model Power Vault MD1000 Hard Drive
o Max Supported Capacity 1.1 TB
o Host Channels 2
o Data Transfer Rate 300 MBPs
o Supported Devices Hard drive , Disk array (RAID)
o Spindle Speed 15000 RPM
o Total storage array 6
o In Each Storage Array 15 HDD
o Each HDD has 1*1 TB
o Total Storage Capacity 6*15*1.1 TB
22
Front Side
Back Side

Hardware: KVM Switch
• KVM (Keyboard Video Mouse) Switch is a device used to connect a
keyboard, mouse and monitor to two or more computers. KVM switches
save money, time, space, equipment and power. These switches are also
widely deployed to control pools of servers in data centers. Some KVM
switches support user terminals at both ends that allow local and remote
access to all the computers or servers.
23

Hardware: Networking
• Clusters are interconnected with both GigE (Dell PowerConnect 6248 and 48 GbE
PortManaged
• Switch, 2xDell PowerConnect 3424 24 Port FE with 2 GbE Copper Ports and 2 GbE
Fiber SFP
• Ports and Infiniband (Dell 24-Port Internally Managed 9024 DDR InfiniBand Edge
Switch)
• Switches and cards
24
Switch Ports Cable connectivity

Software for High–Performance Computing
(HPC)
27

Software for HPC
• For effective use of cluster for HPC the following
tools are at our disposal
– Remote hardware management
 Remote power on/off
 Monitoring CPU (for temperature etc.)
– Cluster management
 Monitoring programs, system administration etc.
– Job scheduling
– Libraries/languages for parallel programming
 Massage Passing Interface (MPI)
28

Cluster Management
• Cluster management software offers
– Easy-to-use interface for managing clusters
– Automates the process of queuing jobs
– Matching the requirements of a job and the
resources available to the cluster
– Migrating jobs across the cluster
• Maxwell uses Red Hat Enterprise Linux
29

Cluster Management
• Red Hat Enterprise Linux
– Specially for the scientific computing purpose to
deploy clusters of systems that work together
– Excellent hardware detection and monitoring
capabilities
– Centralized authentication and logging services
– Fast IO (Input/Output)
30

Parallel Computing
• Form of computation in which many calculations are carried out
simultaneously, operating on the principle that large problems can
often be divided into smaller ones, which are then solved
concurrently i.e. "in parallel"
• Different forms of parallel computing
– Bit-level parallelism
– Instruction level parallelism
– Data parallelism
– Task parallelism
• Parallel Computer classification
– Multiple processing elements (multi-core and multi-processor) within
a single machine
– Using multiple computers to work on the same task - clusters, MPPs
(Massive Parallel Processing), and grids
31

Parallel Programming
• Parallel computer programs are more difficult to write than
sequential programs
• Potential problems
– Race condition (output depending on sequence or timing of
other events)
– Communication and synchronization between the different
subtasks
• HPC Parallel Programming Models associated with different
computing technology
– Single Instruction Multiple Data (SIMD) on Single Processors
– Multi-Process and Multi-Threading on SMP (symmetric
multiprocessing) Computers
– Message Passing Interface (MPI) on Clusters
32

Parallel Programming
• Message Passing Interface (MPI)
– An application programming interface (API) specification
that allows processes to communicate with one another by
sending and receiving messages
– Now a de facto standard for parallel programs running on
distributed memory systems in computer clusters and
supercomputers
– A massage passing API with language-independent
protocol and semantic specifications
– Support both point-to-point and collective communication
– Goals are high performance, scalability, and portability
– Consists of a specific set of routines (i.e. APIs) directly
callable from C, C++, Fortran and any language able to
interface with such libraries, including C#, Java or Python
33

Maxwell: A Brief Introduction
35
Tech Specs:
 No. of nodes: 106
 Each node is a Intel dual CPU
Quad Core 2.3 GHz Processor
 Total No. of cores: 848
 RAM per node: 8 GB
 Storage Memory: 90 TB

How to create an account?
• Send an email to
– Nancy Beasley nancyj0@siu.edu or
– Dr. Shaikh Ahmed ahmed@siu.edu
• Provide the following information
– Name
– Affiliation
– IP address of the computer(s) on SIUC network from which you
would access Maxwell
• Will receive an email with Log In information
36

• IP address look-up
37
Go to Start

38
Type in ‘cmd’ to go to
command prompt

39

40
Type in ‘ipconfig’ to
get the IP Address

41
IP Address

Login Procedure
• Download ‘Putty’
– Web addresses
• http://www.putty.org/
• http://download.cnet.com/PuTTY/3000-7240_4-
10808581.html
– Run ‘Putty’
• Use Host Name or IP address of Maxwell
– Host Name: maxwell.ecehpc.siuc.edu
• Enable X11
42

Login Procedure
• Run ‘Putty’
– Start ‘Session’
43
Type in Host Name:
“maxwell.ecehpc.siuc.edu”

Login Procedure
• Run ‘Putty’
– Enable X11
• Connection > SSH > X11
44
Check ‘Enable X11
Forwarding’

Login Procedure
• Run ‘Putty’
– Enable X11
• Connection > SSH > X11
– Open
45
Press Open to start
the session

Login Procedure
46
Type in Your Login
ID
Example ‘nanoSIUC’

Login Procedure
47
Type in
Password

Login Procedure
48
Prompt with
your Login ID.
Interface for
User to use
Maxwell

MPI Test
• Copy “mpi_test” directory to your “home” directory
– Type in the following command
• cp –r /home/nanoSIUC/mpi_test .
49

Run MPI
50
Type in ‘ls’ to view
the content of your
account

Run MPI
51
Folder containing
files to test MPI

Run MPI
52
Change Directory
and view the files in
‘mpi_test’
Open to see the
content of these files

Run MPI
• File: ‘bsub.sh’
53
job_name
output_file
run_limit
memory_limit
processor_use
run_time
to run a
parallel
program
by MPI
Change this
(nanoSIUC) to
your login ID

Run MPI
54
• File: ‘submit_script.sh’
Creates a new directory to generate
output.
Directory name:
cpi_test_<number of nodes used>

Run MPI
• Script to Run MPI
– ./submit_script.sh bsub.sh <# of Processors> <input file>
– <# of Processors> is an integer
– <input file> is optional.
• If in different directory, use the path of the input file as well
55

Run MPI
• Script to Run MPI
56
Running MPI Program
<# of processors>
Output Directory

Run MPI
57
• Viewing Output
Output File
Content of Output
Directory

Run MPI
58
• Viewing Output
Content of Output
File

Maxwell siuc hpc_description_tutorial

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