hp xc4000 at ssck · 2008. 9. 9. · landes hlr phases 1 and 1a landes hlr start of installation...

Scientific Supercomputing Center Karlsruhe

HP XC4000 at SSCKxc2.rz.unikarlsruhe.de

hwwxc2.hww.de

Organization – Infrastructure – Architecture

Nikolaus GeersRudolf Lohner

Rechenzentrum, SSCKUniversität Karlsruhe (TH)

[email protected]@rz.unikarlsruhe


hkzbw

» High Performance Computing Competence Center of the State of BadenWürttemberg

» Founded in 2003 by the Universities of Karlsruhe and StuttgartUniversity of Heidelberg joined in 2004

» Coordinate HPC competency to build a center that is competitive at an international level

» HPCsystem for nation wide usage HLRSHPCsystem for state wide usage SSCK

» Grid Computing across both sites

» Research activities– Cooperate with end users in development of new HPC applications

• Life sciences• Environment research• Energy research

– Grid computing


hww: Cooperation with Industry

» Höchstleistungsrechner für Wissenschaft und Wirtschaft (hww) GmbHHigh Performance Computing for Science and Industry

» Joint operation and management of HPC systems within hww GmbH– Universities of Stuttgart, Karlsruhe and Heidelberg

– TSystems SfR

– Porsche

» End user support– academic users HLRS / SSCK

– industry and research labs TSystems

» Through hww the new HP XC system will be available to customers from universities as well as from industry and research labs.


High Performance Computing Competence Center (HPTC3)

» Cooperation of SSC Karlsruhe, HP and Intel– Similar Cooperation is planned with AMD

» Extending XC system and testing of new features– Integration of XC and Lustre

– Integration of different node types into XC system

– High availability of critical resources

– Monitoring

» Training and Education– Usage of XC system

– Optimization and tuning of application codes

» Porting and tuning of ISV codes

» Program development tools


Development of HPC Systems xc1 and xc2 at SSCK

Q1/04 Q4/04 Q1/05 Q3/06 15.1.2007 Q1/07

Phase 0Landes HLR

Phases 1 and 1aLandes HLR

Start ofInstallation

Phase 2Landes HLR

Nov. 06Dec. 06

Start ofTest Operation

Phase 2Landes HLR

Start ofProd.Operation

Phase 2Landes HLR

xc1HLR of Univ,Shutdown of

IBM SP

xc1 xc2


HP XC – Installation Schedule (Phase 2)

Phase 0 (Q1 2004)» 12 2way nodes (Itanium2)» 4 file server nodes

– 2 TB shared storage

» Single rail Quadrics interconnectPhase 1 (Q4 2004)» 108 2way nodes

– Intel Itanium2

» 8 file server nodes– Approx. 11 TB storage system

» Single rail Quadrics interconnectPhase 1 (Q1 2005)

» 6 16way nodes– Intel Itanium2 – 2 partitions with 8 CPUs each

» Single rail Quadrics interconnectPhase 2 (Q3 2006)» 750 4way nodes

– two sockets – dual core AMD 2,6 GHz, 16 GB

» 10 server nodes » Infiniband DDR Interconnect» 56 TB storage system

Q1/04 Q4/04 Q1/05 Q4/06

today

» Total of 3.000 processor cores» Total of 15,6 TFlop/s peak performance» Total of 12 TB of main memory

~300 proc. | ~2 TFlop/s | ~2 TB mem.Test System

Q1/07


Time Schedule of xc2

» September 2006– delivery and assembly of racks

» October 2006– cabling of Admin network and InfiniBand interconnect– Software installation– First internal testing

» November 2006– Further internal testing– Early ‘friendly’ users– Start of acceptance test

» January 2007– End of acceptance test

» January 15, 2007– Start of production service


Challenges: Room Layout

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» 20 racks for compute nodes

» 8 racks for network switches

» Maximum cable length for IB DDR is 8 m


Challenges: Cabling

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Challenges: Cabling

» Cable ducts on top of racks

» Cable ducts under raised floor

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Challenges: Cooling

» Water cooling of each rack


Challenge: Cooling

» HP Modular Cooling System added to each rack


Challenges: Hardware Installation


HP XC4000 at a Glance

xc2.rz.unikarlsruhe.dehwwxc2.hww.de


HP XC4000@SSCK: The Key Figures

» 750 fourway compute nodes– 3000 cores

» 2 eightway login nodes

» 10 service nodes

» 10 file server nodes

» InfiniBand DDR interconnect

» 15.6 TFlop/s peak performance

» 12 TB main memory

» 56 TB shared storage

» 110 TB local storage

xc2.rz.unikarlsruhe.de


XC2 in Detail

xc2.rz.unikarlsruhe.de

hwwxc2.hww.de


Compute Nodes for MPI Applications

» 750 fourway nodes HP DL 145 G2– Two dual core CPUs

• 2.6 GHz, 5.2 GFlop/s per core• 1 MB L2 cache per core

» 16 GB main memory per node– 4 GB per core

» 146 GB local disk space

» Fast InfiniBand DDR interconnect– Latency: ~ 3 µsec– Bandwidth: 1600 MB/s at application (MPI) level

» Parallel MPI applications, up to O(1000) tasks


HP DL 145 G2 Block Diagramm

OpteronCPU 1

PC3200DDR1

PC3200DDR1

400 MHz 400 MHzOpteronCPU 2HT link

6,4 GB/s 6,4 GB/s

PCIExpress

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InfiniBand 2.0 GB/s

Peripherals


AMD dual core Opteron Processor

Core 1 Core 2

64KBICache

64KBDCache

1 MB L2 cache

System request Queue

64KBICache

64KBDCache

1 MB L2 cache

Crossbar

Integrated memory controller

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InfiniBand DDR Network

» InfiniBand DDR Network

» Full fat tree structure

» 2 GB/s peak bandwidth (bidirectional)

» 3 µsec latency


InfiniBand DDR Network

750 compute nodes

10 service nodes

10 file server nodes 65 leaf switches 3 core switches


InfiniBand DDR NetworkSKAMPI: nonduplex pingpong

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InfiniBand DDR NetworkSKAMPI: nonduplex pingpong

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InfiniBand DDR NetworkSKAMPI: duplex pingpong

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Login Nodes

» 2 eightway nodes HP DL 545 G2– Four dual core CPUs

• 2.6 GHz, 5.2 GFlop/s per core• 1 MB L2 cache per core

» 32 GB main memory per node– 4 GB per core

» 292 GB local disk space

» Interactive access– File management, job submission– Program development (compilation, short test runs etc.)– Debugging– Pre and Postprocessing


Parallel File System HP SFS

» Shared storage for all nodes of XC system

» 10 file server nodes– 2 MDS / Admin– 2 OSS for $HOME– 6 OSS for $WORK

» 56 TB file space– 8 TB $HOME– 48 TB $WORK

» Expected bandwidth– Read / write from one node: 340 MB/s / 340 MB/s– Total read / write bandwidth of $HOME: 600 MB/s / 360 MB/s– Total read / write bandwidth of $WORK: 3600 MB/s / 2200 MB/s


File Systems of XC2

$WORK$HOME$TMP

$TMP $TMP $TMP


Characteristics of File Systems

» $HOME– shared, i.e. identical view on all nodes– permanent files– regular backup– files space limited by quotas– used for many small files

» $WORK– shared, i.e. identical view on all nodes– semi permanent files, one week lifetime of files– best used by large files, sequential files access

» $TMP– local, nodes on different nodes see different $TMP– temporary files, will be discarded at job end– best used by temporary scratch files


Software Environment

» HP XC version 3.0 software stack– HP XC Linux for HPC (based on Red Hat Enterprise Linux Advanced

Server Version 3.0– nagios, syslogng, …– SLURM, local addon JMS (job_submit … )– HP MPI– Modules package (module add … )

» HP SFS file system (based on lustre)» Compilers

– gnu, Intel, PGI, PathScale

» Debuggers– gdb, ddt

» Profilers» Applications


XC2 in Comparison with XC1

» Identical software environment

» Different processor architecture

» 4way nodes instead of 2way nodes

» Similar ratio of– Memory size : floating point performance– Communication bandwidth : floating point performance

» Number of CPUs (cores) increased by factor of 10– Much larger jobs O(1000) MPI processes

• Fine grain parallelization• Finer resolution

– More jobs in parallel


XC2 in Comparison with XC1

1,21

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1,07

3,44

1,10

SPARC

PLESOCC

IMDMETRAS

FDEM/LINSOL


Early ‘friendly’ users

» You will help us to stabilize and improve the system.

» You may get a lot of CPU cycles for your research work.

» But– We cannot guarantee the high stability of a production system.– We may have to shut down the system without warning.– Not all software components may work as desired.– Scalability of some tools may be a problem.

» If you can work with these restrictions and want to become an early user of the xc2, please send an email to

[email protected]


Thank You


Compilers on XC2

» GNU Compilers and third party compilers


Compilers and module command

» module add compilerwhere compiler stands for: gnu/3, gnu/4, intel, pgi or pathscale

» Environment variables modified by this command:– PATH– LD_LIBRARY_PATH– MANPATH– FC, F77, CC F90, CXX– MPI_F77, MPI_F90, MPI_CC MPI_CXX– CFLAGS, FFLAGS– ACMLPATH

– Some compiler specific variables, i.e. LM_LICENSE_FILE etc.

» By default the command module add intelis executed during login.


module add intel

» Environment variables modified by this command:– PATH, LD_LIBRARY_PATH and MANPATH:

correspondig subdirctories of compiler installation directories are added– FC = ifort– F77 = ifort MPI_F77 = ifort– F90 = ifort MPI_F90 = ifort– CC = icc MPI_CC = icc– CXX = icpc MPI_CXX = icpc– CFLAGS = – FFLAGS = – ACMLPATH =


module add pgi


correspondig subdirctories of compiler installation directories are added– FC = pgf77– F77 = pgf77 MPI_F77 = pgf77– F90 = pgf90 MPI_F90 = pgf90– CC = pgcc MPI_CC = pgcc– CXX = pgcc MPI_CXX = pgcc– CFLAGS = – FFLAGS = – ACMLPATH =


module add pathscale


correspondig subdirctories of compiler installation directories are added– FC = pathf77– F77 = pathf77 MPI_F77 = pathf77– F90 = pathf90 MPI_F90 = pathf90– CC = pathcc MPI_CC = pathcc– CXX = pathcc MPI_CXX = pathcc– CFLAGS = – FFLAGS = – ACMLPATH =


module add gnu/3


correspondig subdirctories of compiler installation directories are added– FC = gf77– F77 = gf77 MPI_F77 = gf77– F90 = MPI_F90 = – CC = gcc MPI_CC = gcc– CXX = g++ MPI_CXX = g++– CFLAGS = – FFLAGS = – ACMLPATH =


module add gnu/4 or module add gnu


correspondig subdirctories of compiler installation directories are added– FC = gfortran– F77 = gfortran MPI_F77 = gfortran– F90 = gfortran MPI_F90 = gfortran– CC = gcc MPI_CC = gcc– CXX = g++ MPI_CXX = g++– CFLAGS = – FFLAGS = – ACMLPATH =

hp xc4000 at ssck · 2008. 9. 9. · landes hlr phases 1 and 1a landes hlr start of installation...

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