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Programming Techniques For Supercomputers

This document discusses parallel distributed-memory computers and hybrid systems. It begins by introducing the basic concepts of distributed-memory parallel computers, including that each processor has exclusive local memory and communicates via message passing over a communication network. Popular network topologies like fat trees and meshes are then discussed. Finally, the document analyzes key network performance characteristics like bandwidth, latency, and bisection bandwidth, using examples from real networks like Gigabit Ethernet and InfiniBand.

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Varun Nagpal
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
121 views

Programming Techniques For Supercomputers

This document discusses parallel distributed-memory computers and hybrid systems. It begins by introducing the basic concepts of distributed-memory parallel computers, including that each processor has exclusive local memory and communicates via message passing over a communication network. Popular network topologies like fat trees and meshes are then discussed. Finally, the document analyzes key network performance characteristics like bandwidth, latency, and bisection bandwidth, using examples from real networks like Gigabit Ethernet and InfiniBand.

Uploaded by

Varun Nagpal
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Programming Techniques for Supercomputers:

Parallel Computers (2*)


Distributed-memory computers / Hybrid systems
Communication Networks

Prof. Dr. G. Wellein(a,b) , Dr. G. Hager(a) , M. Wittmann(a)


(a)HPC

Services Regionales Rechenzentrum Erlangen


fr Informatik

(b)Department

University Erlangen-Nrnberg, Sommersemester 2016


*see

lecture 7 for first part

Parallel Computers (2) - Introduction


Classification according to address space organization
Shared-Memory Architectures:
Cache-Coherent Single Address Space

Distributed-Memory Architectures
No Cache-Coherent Single Address Space

Hybrid architectures containing both concepts are state-of-the art

July 4, 2016

PTfS 2016

Distributed-memory computers & hybrid systems

Parallel distributed-memory computers: Basics


Distributed-memory parallel computer:

Each processor P is connected to exclusive


local memory (M) and a network interface (NI)
Node
A (dedicated) communication network
connects all nodes
Data exchange between nodes: Passing
messages via network (Message Passing)

Variants:

Prototype of first PC clusters:

No global (shared) address space


No Remote Memory Access (NORMA)

Node:
Network:

NON-COHENRENT shared address space


(NUMA), e.g. CRAY
PGAS languages (CoArray Fortran, UPC)

First Massively Parallel Processing


(MPP) architectures:
CRAY T3D/E, Intel Paragon

July 4, 2016

PTfS 2016

Single CPU PC
Ethernet

Parallel distributed-memory computers: Hybrid system


Standard concept of most modern large parallel computers: Hybrid/hierarchical
Compute node is a 2- or 4-socket shared memory compute nodes with a NI.
Communication network (GBit, Infiniband) connects the nodes
Price / (Peak) Performance is optimal; Network capabilities / (Peak) Perf. gets worse
Parallel Programming? Pure Message Passing is standard. Hybrid programming?
Today: GPUs / Accelerators are added to the nodes to further increase complexity

Distributed-memory parallel
July 4, 2016

PTfS 2016

Networks

What are the basic ideas and


performance characteristics of modern
networks

Networks Basic performance characteristics


Evaluate the network capabilities to transfer data
Use the same idea as for main memory access:
Total transfer time for a message of N Bytes is:

T = TL + N/B
TL is the latency (transfer setup time [sec]) and B is
asymptotic (N oo) network bandwidth [MBytes/sec]

Consider simplest case (Ping Pong)


Two processors in different nodes communicate via network
(Point-to-point)
A single message of N Bytes is sent forward and backward
Overall data transfer
is 2 N Bytes!

July 4, 2016

PTfS 2016

Networks Basic performance characteristics


Ping-Pong benchmark (schematic view)
1 myID = get_process_ID()
2 if(myID.eq.0) then
3
targetID = 1
4
S = get_walltime()
5
call Send_message(buffer,N,targetID)
6
call Receive_message(buffer,N,targetID)
7
E = get_walltime()
8
MBYTES = 2*N/(E-S)/1.d6 ! MBytes/sec rate
9
TIME = (E-S)/(2*1.d6) ! transfer time in microsecs
10 ! for single message
11 else
12
targetID = 0
13
call Receive_message(buffer,N,targetID)
14
call Send_message(buffer,N,targetID)
15 endif
July 4, 2016

PTfS 2016

Networks Basic performance characteristics


Ping-Pong benchmark for GBit-Ethernet (GigE) network
N1/2 : Message size where 50% of peak bandwidth is achieved

Beff = 2*N/(E-S)/1.d6

Asymptotic
bandwidth
B=111 Mbytes/sec
0.888 GBit/s

July 4, 2016

Latency (N 0):
Only qualitative
agreement:
44 ms vs. 76 ms

PTfS 2016

Networks Basic performance characteristics


Ping-Pong benchmark for DDR Infiniband (DDR-IB) network
Determine B and TL independently and combine them

July 4, 2016

PTfS 2016

10

Networks Basic performance characteristics


First Principles modeling of Beff(N) provides good qualitative
results but quantitative description in particular of latency
dominated region (N small) may fail because
Overhead for transmission protocols, e.g. message headers
Minimum frame size for message transmission, e.g. TCP/IP over Ethernet
does always transfer frames with N>1
Message setup/initialization involves multiple software layers and protocols;
each software layer adds to latency; hardware only latency is often small

As the message size increases the software may switch to different


protocol, e.g. from eager to rendezvous

Typical message sizes in applications are neither small nor large


N1/2 value is also important: N1/2 = B * TL
Network balance: Relate network bandwidth (B or Beff(N1/2)) to
computer power (or main memory bandwidth) of the nodes
July 4, 2016

PTfS 2016

11

Networks: Topologies & Bisection bandwidth


Network bisection bandwidth Bb is a general metric for the data
transfer capability of a system:
Minimum sum of the bandwidths of all connections cut when
splitting the system into two equal parts
More meaningful metric in terms of
system scalability:
Bisection BW per node: Bb/Nnodes
Bisection BW depends on
Bandwidth per link
Network topology

Uni- or Bi-directional bandwidth?!


July 4, 2016

PTfS 2016

12

Network topologies: Bus


Bus can be used by one
connection at a time
Bandwidth is shared among
all devices
Bisection BW is constant Bb/Nnodes ~ 1/Nnodes
Collision detection, bus arbitration protocols must be in place
Examples: PCI bus, diagnostic buses
Advantages
Low latency
Easy to implement

Disadvantages
Shared bandwidth, not scalable
Problems with failure resiliency (one defective agent may block bus)
Fast buses for large N require large signal power
July 4, 2016

PTfS 2016

13

Non-blocking crossbar
A non-blocking
crossbar can mediate
a number of connections
between a group of
input and a group of
output elements

This can be used as a


4-port non-blocking
switch (fold at the secondary diagonal)
2x2
switching
element

Switches can be cascaded to form


hierarchies (common case)
Allows scalable communication at high hardware/energy costs
Crossbars can be used as interconnects in computer systems
NEC SX9 vector system (IXS)
July 4, 2016

PTfS 2016

14

Network topologies: Switches and Fat-Trees


Standard clusters are built with switched networks
Compute nodes (devices) are split up in groups each group is
connected to single (non-blocking crossbar-)switch (leaf switches)

Leaf switches are connected with each other using an additional


switch hierarchy (spine switches) or directly (for small configs.)
Switched networks: Distance between any two devices is
heterogeneous (number of hops in switch hierarchy)
Diameter of network: The maximum number of hops required to connect two
arbitrary devices, e.g. diameter of bus=1

Perfect world: Fully non-blocking, i.e. any choice of Nnodes/2


disjoint node (device) pairs can communicate at full speed
July 4, 2016

PTfS 2016

15

Fat tree switch hierarchies


Fully non-blocking
Nnodes/2 end-to-end connections with full bandwidth
B
Bb = B * Nnodes/2
Bb/Nnodes = const. = B/2
Sounds good, but see next B
slide

Oversubscribed
Spine does not support Nnodes/2

spine switch

full BW end-to-end connections


k=3

Bb/Nnodes = const. = B/(2k),


with k oversubscription factor

Resource management
(job placement) is crucial
July 4, 2016

node
PTfS 2016

leaf switch
16

Fat trees and static routing


If all end-to-end data paths are preconfigured (static routing),
not all possible combinations of N agents will get full bandwidth
Example:
is a collision-free pattern here (15, 26,37, 48)
Change 26, 37 to 27, 36:
has collisions if no other
connections are
re-routed at the
same time

Static routing:
Quasi-standard in
commodity interconnects

However, things are


starting to improve
slowly
July 4, 2016

PTfS 2016

17

Full fat-tree: Single 288-port IB DDR-Switch


SPINE switch level: 12 switches

Basic
building
blocks:
24-port
switches
S = 12+24
switches
LEAF switch level: 24 switches with 24*12 ports to devices
288 ports
July 4, 2016

PTfS 2016

18

Fat tree networks Examples


Ethernet
1 Gbit/s &10 &100 Gbit/s variants

InfiniBand
Dominant high-performance commodity interconnect
DDR: 20 Gbit/s per link and direction (Building blocks: 24-port switches)
QDR: 40 Gbit/s per link and direction
QDR IB is used in the RRZEs LiMa and Emmy clusters
Building blocks: 36 port switches Large 36*18=648-port switches
FDR-10 / FDR: 40/56 Gbit/s per link and direction
EDR: 100 Gbit/s per link and direction

Intel OmniPath
Up to 100 Gbit/s per link & 48-port baseline switches
Will be used in RRZE next generation cluster

Expensive & complex to scale to very high node counts


July 4, 2016

PTfS 2016

19

Meshes
Fat trees can become prohibitively expensive in large systems
Compromise: Meshes
n-dimensional Hypercubes
Toruses (2D / 3D)
Many others (including hybrids)

Each node is a router

Example: 2D
torus mesh

Direct connections only between


direct neighbors
This is not a non-blocking corossbar!
Intelligent resource management and
routing algorithms are essential

Toruses at very large systems: Cray XE/XK series, IBM Blue Gene
Bb ~ Nnodes(d-1)/d Bb/Nnodes0 for large Nnodes
Sounds bad, but those machines show good scaling for many codes
Well-defined and predictable bandwidth behavior!
July 4, 2016

PTfS 2016

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