juhan kim, the kias cac january 23, 2011. to build linux cluster from the commodity hardware like...

How to Build Parallel Computers in a Lab

Juhan Kim, The KIAS CAC

January 23, 2011

Moor’s Law

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The Cheapest Way to Get a Super Computer To build linux cluster

from the commodity hardware like cpu (x-eon,amd), network (gi-gabit,infiniband), etc

Overview of the TOP500.org http://www.top500.org/ Top 500 supercomputers from 1993 –

now Lists in order of LINPACK test (double

precision) Rpeak, Rmax

Top500 : Countries

Top500 : processor types

Top500 : network

Top500 : Operating systems

Top500: Applications

Top500: # of CPU cores

Cluster Hardware CPU

AMD Opteron Pentium (Xeon) Itanium2 benchmark test: http://www.spec.org/cpu/

12 integer benchmarks Video compression, quantum computing, path-finding, combinartorial optimization,

discrete event simulation, etc. 17 floating-point benchmarks

Fluid dynamics, quantum chemistry, general relativity, ray tracing, quantum chem-istry, weather prediction, biochemestry, etc.

mean of 12/17 resulting speeds/throughputs of integer/floating-point calculation No I/O & No network communication Spec[xx]2006 : to measure the speed of a core Spec[xx]2006_rate : to measure the throughput of a chip/chips

Network Commodity 1G/10G Infiniband

Intel X86

Most widely used processor

EM64T : 64bit sup-ported

Fastest integer arithmetic process

Fastest floating point arithmetic process

AMD Opteron

x86_64 architec-ture

Good performance/cost in floating-point & integer arithmetic process

Itanum2

First released in 2001

Impressive Linpack efficiecy: ~90%

SpecFP2006_rate

W300,000

W500,000

SpecFP2006 rate

W1,000,000

$700

Processor GHz Cores SPECint2006

SPECfp2006 Price

Xeon E5620 2.4 4 31.6 37 0.5 MW

Opteron 4184 2.8 6 25.2 34.2 350 USD

Opteron 6174 2.2 12 21.5 30.7 1.5 MW

Intel Core i7-940 2.9 4 30.8 31.3 0.8 MW

Intel Itanium2(18MB)

1.6 2 11.5 17.7 700 USD

IBM Power7 (780)

- 16 44 (4.14GHz) 71.5 (3.86GHz) ???

Processor Summary (Processor Speed)

•Performance: • IBM Power >> Xeon > Opteron 4184 > Core i7 > Opteron 6174 > Ita-nium2

•Performance/cost :• Xeon > Opteron 4184 > Core i7 > Opteron 6174 > Itanium2

Processor GHz (Gflops)

Ncore Nthread

SPECint2006_rate/core

SPECfp2006_rate/core

Xeon E5620 2.4(38.4) 4 2 27.8 21.1(84.8/chip)

Opteron 4184 2.8(67.2) 6 1 19.8 15.1(90.6/chip)

Opteron 6174 2.2 (105.6) 12 1 16.1 13.0(156/chip)

Intel Core i7-940 2.9 (46.4) 4 2 29 21.5(86/chip)

Intel Itanium2(18MB)

1.6 (12.8) 2 1 11.7 7.25(14.5/chip)

IBM Power7 (780)

3.72 (89.3 (?))

6 4 40 35.5(142/chip)

Processor Summary (multi processing speed)

200

400

600

800

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1200

1400

1600

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2000

0

20

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120

140

SpecColumn1

Performance(thoughput)/cost

I7-860/920: best perf/costOpteron series: show a good performance/costI7-940, x5670: poor ratio

E5620I7-940

X5670

I7-860

Opteron6172Opteron6136

E5630x5550

I7-920

8cores

12cores

Off-the-self computer boxes Dell PowerEdge R610

1U rack mount 2-way Xeon E5620

(2.4Ghz, 4cores) 24GB Memory 160GB HardDisk 3,075 USD (5.38MWon) Specfp2006: 37 Specfp2006_rate: 169 Xeon E5620 vs. E5506

(2.13Ghz) 20 % cheaper 30% slower

Dell Opteron server

Dell PowerEdge R815 1U rack mount 2-way Opteron 6128

(2Ghz, 8cores) 32GB Memory 250GB disk 4,556 USD Specfp2006: 28 Specfp2006_rate: 233 Opteron 6128 vs. 6136

(2.4Ghz) 40% more expensive 20 % faster

IBM Xeon Server

IBM x3650 M3 2-way Xeon E5620

(2.4Ghz, 4cores) 2U rack mount 24GB mem 146GB Disk 5,958 USD Specfp2006: 37 Specfp2006_rate:

169

IBM Opteron server

IBM x3755 M3 3U rack mount 2-way Opteron 6128

(2Ghz, 8cores) 24GB Memory 300GB disk 7,729 USD Specfp2006: 28 Specfp2006_rate: 233 Opteron 6128 vs. 6136

(2.4Ghz) 10% more expensive 20 % faster

IBM Power7 server IBM Power 710 Express

1-way socket Power7/ 3.Ghz (4cores) 4GB memory 150GB disk Specfp2006_rate: ??? 5,852 USD 8,120 USD (6cores,3.7Ghz;

16GB) 14,620 USD (8cores,

3.55Ghz; 16GB) Specfp2006_rate

213 (6core, 3.72Ghz, 8,120 USD)

248 (8cores, 3.55Ghz, 14,620 USD)

Comparisons

Throughput/cost1. Dell PowerEdge Xeon R610 : 0.055/$2. Dell PowerEdge Opteron R815 : 0.051/$3. IBM Opteron x3755 : 0.03/$4. IBM Xeon x3650 : 0.028/$5. IBM Power7 6-core : 0.026/$

Network

Myrinet

http://www.myri.com/myrinet/prod-uct_list.html

Throughput : 800 MB/s Latency: 2.7μs Cost: 20,000 USD for 16port

1,250 USD/port ~ 1.4 Mwon/port

Infiniband network (latency: 0.1 μsecond)

•Throughput (QDR): 40Gbps•Infiniband Chassis: 50MWon•Leaf (18port) : 10MW•Adapter card: 1MW•Cable: 0.8MW

•64nodes: 255MW•32nodes : 130MW (?)•Cost/port = 4MW/port

Quadrics

No more available Closed in 2009

System Monitoring Tool Ganglia

Using lm_sensors CPU load, network usage,

Disk usage, temperature Providing statistics (daily,

weekly, monthly usages) How to install: http://

blog.naver.com/PostView.nhn?blogId=me2you2&logNo=100037667623&redirect=Dlog&widgetTypeCall=true

Adding temperature monitoring script to Ganglia# cat > /etc/

cron.d/cputemp

0-59/1 * * * * root /pack-ages/exam-ples/cputemp

^D#

#!/bin/bash# author: Mike Snitzer <msnitzer@plogic.com># desc: used to make lm_sensors metrics available to ganglia# /etc/sysconfig/ganglia is used to specify INTERFACECONFIG=/etc/sysconfig/ganglia[ -f $CONFIG ] && . $CONFIG

#default to eth0if [ -z "$MCAST_IF" ]; then MCAST_IF=eth0fiGMETRIC_BIN=/usr/bin/gmetric# establish a base commandline#GMETRIC="$GMETRIC_BIN -i $MCAST_IF"GMETRIC="$GMETRIC_BIN”SENSORS=/usr/bin/sensors# load the lm_sensors modulesmodule=`/sbin/lsmod | awk '{print $1}' | grep i2c-piix4`if [ -z "$module" ]; then /sbin/modprobe i2c-piix4 # lm87 is for supermicro P3TDLE, replace when appropriate /sbin/modprobe lm87 /sbin/modprobe coretempfi# send cpu temps if gmond is running`/sbin/service gmond status > /dev/null`if [ $? -eq 0 ]; then # send cpu temperatures let count=0 for temp in `${SENSORS} | grep Core | cut -b 8-18`; do $GMETRIC -t float -n "cpu${count}_temp" -u "C" -v $temp let count+=1 done

# send cpu fan speed let count=0 for fan in `${SENSORS} | grep fan1 | cut -b 9-17`; do $GMETRIC -t uint32 -n "cpu${count}_fan" -u "RPM" -v $fan let count+=1 donefi

Research Funds available in Ko-rea

http://www.nrf.re.kr/html/kr/busi-ness/business_01_01_02.html

Danawa Linux CPU Cluster (33n-odes)

Installation: Jan. 2010 Intel i7 Bloomfield 920 Single socket, 8GB memory 1G network SpecFP2006_rate= 78.9/4cores 4 cabinets (44U) 4 X 3kW UPS Danawa price: 51MWon (

http://www.danawa.com/) Company-proposed price:

150MWon 1month assembling by one per-

son 1month system installing by one

person Need a lot of man power

GPU Cluster @ CAC 25 sets of CPU+GPU

machines Peak performance ~

10x64(dual socket, quad core) node CPU clusters

Total cost ~ 1.5 x 64 node CPU cluster

CPU nodes: IBM x3550 (dual Xeon E3640, 24 GB, 3x1Gbps)

20KWatt power

Fund vs. Cluster size

1. 32node Danawa cluster (SPecfp2006_rate: 2560)2. 64node IBM Xeon cluster (8960) + 3year warranty3. 32node Dell Opteron cluster (7488)4. 64node Dell Opteron cluster (14976)5. 24node Nvidia S2050 + IBM Xeon cluster (10x#2)

1 23 4 4i2i3i

5

Conclusion

Spec2006/Rpeak Xeon E5620> i7-940 > Power7 >

Opteron >> Itanium Spec2006/cost

i7 series>Xeon E-series>Opteron>Xeon X-series>>Itanium

Cost IBM > Dell >> Danawa

Conclusion 2/ Discussion

Interconnection Infiniband/Myrinet:

40/20% of total cost based on the IBM/Dell Cluster 80/60 % of total cost based on the Danawa Cluster

Disk Storage Lustre File System: a few 10s Mwon for 10TB

one (a few?) MDS (Meta Data Server) + many OSS (Object Storage Server)

SAN : very expensive