Annual Report 2009

CSC annual report 2009

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YEAR OF THE ENVIRONMENT 2009

At CSC 2009 was chosen as “the Year of

the Environment”. CSC strives for eco-

logically sustainable activities. CSC a-

dopted green electricity from the begin-

ning of 2009. At the end of the year CSC

also adopted the eco-energy label of the

Finnish Association for Nature Conserva-

tion (FANC). This means that the money

used to pay the company's electricity

bills supports environmentally friendly

electricity production instead of the use

of fossil fuels. The environmental theme

is also reflected in this Annual Report,

with the illustrations consisting mostly

of photos taken by CSC employees who

participated in a nature photography

contest.

2 C S C A N N U A L R E P O R T 2 0 0 9

In Finland the computational services needed by science are

provided by CSC – IT center for science, administered by the Min-

istry of Education. CSC is a non-profit company located at Keilanie-

mi, Espoo.

CSC provides Finland's widest selection of scientific software and

databases and Finland's most powerful supercomputers and data

storage systems that researchers can use via the Funet network.

CSC’s customers also have access to the most powerful computing

and data resources in Europe.

CSC’s mission is to improve the possibilities for research, teach-

ing and product development conducted in Finnish higher educa-

tion institutions, research institutes, and industry. CSC’s operational

sphere includes national and international collaboration, enhancing

interdisciplinary interaction, and providing computation based on

distributed data processing and international data communications

connections. The staff totals almost 200 employees and the turn-

over is EUR 21.9 million. Competitive external funding represents

more than a fifth of CSC’s budget.

CSC started its operation at the Finnish State Computer Center in

1971, as the technical support unit for Univac, which was the first

academic mainframe in Finland. The Funet data communication

connections were established in 1985 and in 1988 the universities

were the first institutions in Finland to join the global Internet net-

work. CSC’s operations were incorporated in 1993, and the Ministry

of Education was assigned as the shareholder.

CSC’s resources are exploited in, for example, climate change

modeling, research on catalytic properties of metal oxides, turbulence

models, research on gene interaction, and molecular modeling of

plasma membranes. Researchers also use computer modeling and

CSC software to investigate strong geophysical processes, such as the

function of a fusion reactor and reactor materials. Modeling oceanic

currents and celestial activities require large computing power.

The rapid expansion and reliable archiving of research data rep-

resent enormous challenges requiring a great deal of work in data

processing and analysis. CSC’s storage systems’ disk capacity is more

than 1 petabyte, which roughly equals the contents of 1.5 million

compact disks. The storage capacity is used for archiving Finnish

television and radio programs for the National Audiovisual Archive,

and storing the measurement data produced by radio-astronomical

test laboratories and CERN’s LHC particle collider devices.

Researchers save time by utilizing CSC resources, because failure

to use CSC services would delay the required results by months. The

transfer of data and computing results takes place at equal speed, re-

gardless of the location of the research site. Compared with many of

its international sister centers, CSC’s IT services for science cover not

only supercomputing but also other related necessary needs, such as

powerful data processing, development of scientific programs, ultra-

fast data transfer, and specialist support. This facilitates the handling

and administration of extensive and inter-disciplinary projects.

DATA NETwORkS AND DATA HANDLINg

CSC maintains and develops the Finnish research and education

network Funet, an extremely reliable high-capacity network. Fu-

net has approximately 350,000 users. It is one of the most advanced

and reliable research networks in the world. Funet CERT (Computer

Emergency Response Team) safeguards data security of Funet, col-

laborating with member organizations and the Finnish Communica-

tions Regulatory Authority.

High-capacity data networks make it possible for the physical

storage site to be geographically remote from the user. New optical

fiber networks enable transmission of large data amounts at a rea-

sonable price.

A researcher submerged in a flood of information needs effec-

tive high-quality tools for managing the entire life span of materials.

CSC offers abundant possibilities to meet the demanding needs

of data processing. The offering includes short- and long-term

storage services, reliable backup and archiving systems that guaran-

tee data preservation and accessibility.

POwERFUL COMPUTERS IN FINLAND AND IN EUROPE

To meet research and product development needs, CSC provides

computing capacity of the highest European quality level. The

most powerful computer in Finland, Louhi is able to handle an in-

credible more than 100,000 billion (1012) calculations per second.

The multi-faceted computing environment also embraces the most

CSC – IT CenTer for SCIenCe In brIef

3C S C A N N U A L R E P O R T 2 0 0 9

important software applications and scientific databases. A third of

the computing time on CSC’s machines is used by the Academy of

Finland Centres of Excellence. More than 600 computing projects a

year use a total of 60 million cpu hours. Through CSC, Finnish re-

searchers have access also to the most powerful Grid computing re-

sources in Europe. Grid technology is used to amass the necessary

computing and data storage capacity. The Grid is a network of com-

puting resources or other services where computing centers pro-

vide data storage and computing resources for access by virtual or-

ganizations. It is rather similar to a power grid, through which power

plants provide consumers with electricity.

ExTENSIVE DATAbASES AND SOFTwARE

CSC’s computers run the widest range of scientific software in

Finland. Our computing environment contains more than 200 dif-

ferent ready-to-use programs. Licenses have been acquired for

software in chemistry, biosciences, geosciences, physics, statistics,

computational fluid dynamics, structural analysis, and mathemat-

ics, to mention just a few areas. CSC administrates 70 scientific data-

bases and a broad-based spatial data content. Our server environ-

ment also hosts the academic library systems for universities of ap-

plied sciences, and the Linnea system for Finnish universities. Addi-

tionally, CSC develops scientific software and coordinates national

software consortia on behalf of the Finnish higher education insti-

tutions.

INFORMATION MANAgEMENT

CSC maintains centralized data systems for administration of

education and science and participates in their development.

The purpose of the RAKETTI project is to create a shared data ware-

house for higher education institutions that will make it simpler to

monitor academic operations and facilitate the related reporting.

Haka is a shared user identification system of higher education in-

stitutions and research institutes in Finland. Haka enables the stu-

dents and staff of its member organizations to use the user identi-

fication issued by their home organization when they roam for ser-

vices of other organizations in Finland and the Nordic countries.

500,000 logins are registered per month. CSC also participated in

the planning of an identity federation for the state administration.

The Virtu federation is planned to be compatible with the Haka fed-

eration. This shared academic identification and authentication net-

work can reach roughly 800,000 users.

TRAININg

CSC provides training and system support in various disciplines.

CSC trains its customers in HPC programming and application soft-

ware use.

Recognizing the importance of developing and updating re-

searchers' skills, CSC is an active organizer of science and technolo-

gy events. Course activities touched over two thousand representa-

tives of our interest groups at a personal level. CSC relies on its own

specialists as well as outsourced lecturers. In practice, all lecturers

have a doctoral degree and most of them hold also the title of ad-

junct professor (docent). Most of the courses were arranged in Eng-

lish to provide maximum benefits for the increasingly international

universities. The overall feedback from customers was good.


ConTenTS1. MANAGING DIRECTOR´S REVIEW ................................................. 7

2. SOCIETAL IMPACT

• ThestrategyofPARADEcompleted .......................................... 11

• CSCjoinedtheAllianceforPermanentAccess(APA)................. 11

• Apreparatoryprojectonremoteuseofrecordsinformation .. 12

• CSCconductedasurveyontheresearchdataenvironment .... 12

• CSCcoordinatedResearche-InfrastructureinFinland ............. 12

• WebpagesopenedfortheResearchDataEnvironmentproject 12

• GÈANT3:Anew-generationEuropeanresearchand education networks .................................................................. 13

• CSCjoinedT&HSHOKLtd,thestrategiccentreof excellence for health and well-being ........................................ 13

• Ice2sea:CSCjoinedasea-levelresearchprogram .................... 14

• JanneKannertochairTERENA .................................................. 14

• CSC’sPerÖsterelectedChairmanofEGICouncil ...................... 14

• LetterofinterestsignedbetweenCSCandRussian T-Platforms ............................................................................... 14

• FinnishresearchersandCSChaveakeyroleinprocessing measurement data from the Planck satellite ............................ 15

• PRACEimplementingapersistentresearchplatform ............... 16

• PRACEprototypetestingstarted .............................................. 16

• CSCacquiredanewsupercomputerfortheFinnish Meteorological Institute ............................................................ 16

• CSC’sstoragecapacityexceededonepetabyte ........................ 16

• Commonrecommendationontheuseofsmart cards with certificates for universities ...................................... 17

• CSCnowusingtheFANCeco-energylabel ............................... 17

• GreenrenewalsatCSC .............................................................. 17

3. DATA SERVICES FOR SCIENCE AND CULTURE

• NationalDigitalLibrary .............................................................. 19

• TestrunsofCERN’sparticlecolliderstarted ............................. 20

• DigitalarchivingofradioandTVprogramsstarted .................. 20

• CSCopenedadatabaseservice ................................................. 21

• PaITulispatialdataserviceforresearchandteachingat higher education institutions ................................................... 21

• TheFinnishNationalGallerychoseCSCastheirinformation system maintainer .................................................................... 21

• PairsDBproteinsequencealignmentdatabaseupdated .......... 22

• Reviseddigitalmorphologyarchiveslaunched ........................ 22

• ResearchmaterialonendangeredlanguagesinCSC’s LanguageBankofFinland ......................................................... 22

4. APPLICATION SERVICES

• ElmersoftwareavailableforLinuxoperatingsystem ............... 25

• Newsolutionmethodsforinherentlycoupledproblems of acoustics ............................................................................... 25

• ElmerchosenasanapplicationprogramforPRACE ................. 26

• SOMA2modelingenvironmentwasupdated ........................... 26

• Chipsterenablesgeneactivitystudiesalsoatthe protein level .............................................................................. 26

5. INFORMATION MANAGEMENT SERVICES

• RAKETTIprojectreachingfullspeed ......................................... 29

• Datawarehousingservicetosupportknowledge management ............................................................................ 29

• ExperimentallearningintheOhaTVpilot ................................. 30

• Highereducationinstitutionsagreedonbuildinga common basic e-Administration system .................................. 30

• RAKETTIsupplementedwithasubprojecttocoverIT support for research administration ......................................... 30

• Workonoverallacademicarchitecturestarted ......................... 31

• CSCstartedastheoperatorforthegovernment’sVirtu federation ................................................................................. 31

• TheKalmarUnionenablesaccesstoNordichighereducation institutions with one username ................................................ 31

• EduuniservicesplatformprovidesITservicesforthe Ministry of Education administrative field ................................ 31

• CSCservicesplatformfortheuniversities’personneland finance administration .............................................................. 31

6. COMPUTING SERVICES

• Hippu,CSC’snewapplicationserver ......................................... 33

• FinalreportofFinHPCpublished .............................................. 33

• MorepowertoPRACEprototype .............................................. 34

• GrandChallenges ...................................................................... 34

• Amethodforvirtualdrugscreening ......................................... 34

• Large-scalesimulationoncytochromefunction ...................... 34

• Irradiationeffectsincarbonandboronnitride nanostructures ......................................................................... 35

• Computationalimputationofthegenome-wide information of 30,000 Finns ..................................................... 35

• Biopolymerdynamicsinnanopitgeometries ........................... 35

• ThreeFinnishresearchprojectsgrantedaccesstoDEISA resources .................................................................................. 36

• Adaptiveestimationofclimatemodelclosureparameters ...... 37

• SimulationsofbeyondtheStandardModeltheories ................ 37

• PlasmasimulationswithELMFIRE ............................................. 37

7. FUNET NETWORK SERVICES

• RoamingintheFunetnetworkextended ................................. 39

• LightpathreachedOulu............................................................39

• Highereducationinstituteswantcentralizedservices on video communications ........................................................ 40

• Scienceprograms24hoursadayfromFunet Antenna .................................................................................... 40

• CSCchoseJuniperrouters ........................................................ 40

• Funetlinkedtonewtrans-Atlanticpolarnetwork connections .............................................................................. 40

• FunetopticalfibercircuitandFICIX3pointtoOulu .................. 42

• CSCconnectedRussianresearchnetworktoNORDUnet with fiber technology ................................................................ 42

• IPv6intheFunetnetwork ......................................................... 42

AnnUAL rePorT 2009

ConTenTS


• Thefutureinternetisalreadyhere ........................................... 42

• TheFunetcertificateserviceopened ........................................ 43

8.CUSTOMERSANDCOLLABORATIONS

• Murskacomputingclusterwasthemostpopular ..................... 45

• Theheaviestuseinnanoscienceandphysics ........................... 45

• CSC’sopensourceGPAWthemostpopularapplication software .................................................................................... 46

• TheAcademyofFinlandCentresofExcellenceusinga third of computing time ........................................................... 46

• CSC’sHelpdeskreformed ......................................................... 46

• Customercommunication ........................................................ 46

• Trainingcoursesandevents ..................................................... 47

• AnewstandardforMPIcreatedinHelsinki ............................... 48

• Updatedtrainingroomsupportsnewstyleteachingin computing ................................................................................ 48

• Customersurvey2009forcustomersusingcomputing, software and data storage services ........................................... 48

• GrowthinHakausermanagementservices .............................. 49

• Thenewapplicationserverandautomaticcleaning software into use ...................................................................... 49

• IntrusionintoCSC’scomputingenvironment .......................... 49

• UserlogforChipsterandPaITuliincreasing .............................. 50

• Collaborationprojects .............................................................. 50

9. ORGANIZATION

• Personnel .................................................................................. 53

• PersonnelrepresentativetoCSCmanagementgroup .............. 54

• Organizationcharts .................................................................. 56

10. ADMINISTRATION

• BoardofDirectors ..................................................................... 58

• CompanyGovernance .............................................................. 59

• Managementgroup .................................................................. 60

• Balancesheet ............................................................................ 67

11. CSC IN STATISTICS ................................................................... 78

12. RESEARCHRESULTSOBTAINEDWITHCSCRESOURCES

• Solarmagneticfieldgenerationverifiedbymodeling .............. 87

• Dissertationonthereliabilityofmethodsusedin modeling of shell structures ..................................................... 87

• Xenonusedasaspybroughtnewinformationonmaterials’ properties ................................................................................. 88

• Brightedgesofpotassiumislandsongraphitearecaused by the measurement device ..................................................... 89

• Whatmakesnanoparticlesabletocausecelldeath? ................ 89

• Pre-historicclimatecontrolledthedevelopmentof mammal communities.............................................................. 90

• Mathematicalmodelingofwavepropagation .......................... 91

• Dissertationoncoarse-grainedmethods .................................. 91

• Dissertationonenzymemodeling ............................................ 92

• Researchtestingthevalidityoftechnicolortheories ................ 92

• Dissertation:modelinggivesnewinformationfor preventing the breast cancer .................................................... 93

• Dissertation:Preparationandstructuralcharacterization of chalcogenoether complexes of platinum, palladium, rhodium, rutherium, and mercury ........................................................... 93

• Anewpromisingnanomaterialfromboronandnitride ........... 94

• Waveloadscausespringingvibrationofships .......................... 94

• Increasinghydroelectricpowerbyimprovingtheaccuracyof inflow forecasting ..................................................................... 95

• Studiesaboutchiralcomplexesandenantiodifferentiation ..... 96

• Dissertation:LHCandRIB–twofrontlineprojectsinnuclear and particle physics .................................................................. 96

• Dissertationongeneexpression:frommicroarraysto functional genomics ................................................................. 97

• Dissertation:Anewgrapheneedgefoundinadditionto zigzag and armchair ................................................................. 97

• Dissertation:Developmentofbeamandplatefiniteelements based on the absolute nodal coordinate formulation ............... 97

• Fullerenestructuredeterminedonsilversurface ..................... 98

• Dissertation:Computationalscreeningfornewdrugs ............. 99

• Geometryofnanosizedclustersexplainsdifferencesin reactivity ................................................................................. 100

• Reductionsinindustrialprocesses’energyconsumption .......101

• Dissertation:Novelrobotsolutionsforconstructing fusion reactors .........................................................................101

• Nuclearmagneticresonance(NMR)parametersofgraphene fragments evaluated computationally .................................... 102

• Dissertation:Environmentcausesgoldennanoparticles to transform ........................................................................... 103

• Inhibitor’sroutestoproteinPOP ............................................ 103

• Dissertation:Simulationsofwetfibernetworkscanimprove paper production methods .................................................... 103

• Dissertation:ModellingborealforestCO2exchangeand seasonality .............................................................................. 104

• Dissertation:Identificationofhadronicallydecayingtau leptons in searches for heavy MSSM Higgs bosons with the CMS detector at the CERN LHC ................................................ 104

• Dissertation:Genomicprofilingofgastriccancer ................... 105

• Dissertation:Preparation,structureandbondingofnovel chalcogen-nitrogen ring systems ........................................... 105

• Adissertationonthesimulationoffreesurfaceflows ............ 105

• Dissertationonstaticanddynamicalpropertiesoftwo dimensional lattices ................................................................ 106

• Dissertationonunlimited-vocabularyspeech recognition ............................................................................. 106

• Dissertation:Computationalmodelsofcrumplingofthin sheets and membranes .......................................................... 106

www.CSC.FI

ConTenTS

AnnUAL rePorT 2009



CSC has an established position as an active player in the European

IT environment. We have increased our operations especially in ser-

vices relating to information management, data storage and distri-

bution. Our clientele has become more broad-based and use of our

services has increased. We have started new development projects

to be able to meet the needs of our customers better than ever. Ex-

amples of these efforts include the projects on spatial data systems,

user identification, green machine room technology, and develop-

ment of data infrastructure.

During 2009 we made special efforts to improve our environ-

mental awareness and eco-efficiency. Sustainable development and

environmental aspects were taken into account when the new ma-

chine room facilities were being planned and in planning for future

computer systems. CSC is striving to create the most eco-efficient

data center concept in the world. Ecological values are taken into

consideration in everything we do. Since 2009, environmentally

friendly energy has been used in both of our service centers. Last

year the Finnish Association for Nature Conservation (FANC) granted

CSC the right to use the FANC eco-energy label, which may only be

associated with renewable energy meeting strict environmental cri-

teria. We also founded the GreenCSC committee to promote green

perspectives, with representatives from different employee groups.

CSC’s staff have welcomed all these initiatives, even the ones that

require personal efforts, with an extremely positive attitude.

COMPREHENSIVE SERVICES

The disk capacity of CSC’s storage systems exceeded 1 petabyte in

April. The capacity growth has been strong, for at the turn of the

millennium our disk volume was less than 10 terabytes. We need

storage capacity because extensive national collaboration in data

storage management is important. There was strong growth in data

services, too. CSC was chosen to conduct a national-level survey on

the research data environment, the CSC-steered strategy on Euro-

pean data infrastructure was completed in November, and major ef-

forts have been made in the work on long-term preservation of in-

formation. CSC opened the PaITuli spatial data service for use at

Finnish higher education institutions. The service provides spatial

data services free of charge to be employed by research and teach-

ing staff at higher education institutions. CSC is taking an increas-

ingly active role in the field of culture. CSC and the Finnish National

Gallery signed a four-year contract on system services. As part of

this contract CSC provides the Finnish National Gallery with an inte-

grated virtualization and server platform as well as disk system ser-

vices.

For Oodi, a data system to support academic administration, CSC

worked on a common concepts model to form the basis for an aca-

demic data warehouse. The idea is to standardize methods for stor-

ing information on such things as teaching and degrees in order to

make it possible to exchange data from different quarters and facili-

tate uniform reporting.

CSC integrated the Haka user authentication system of Finnish

higher education institutions to the corresponding Nordic systems.

This project stands unique in the world. CSC offers a national Funet

network roaming service for students and staff of Funet member

organizations. Organizations that have acquired a roaming license

can access each other’s networks using their own their own identifi-

cation codes. Hence, visiting researchers and students are allowed

fast and convenient network access with the user IDs supplied for

SUSTAInAbLe DeVeLoPMenT IS A TrUMP CArD In CoMPeTITIon

MAnAgIng DIreCTor'S reVIew


MAnAgIng DIreCTor'S reVIew

their home organizations. In December CSC signed a contract that

provides Funet member organizations with an opportunity to join

the certificate service supplied by TERENA. The service is included in

the Funet fee, which will reduce our customers’ certification costs.

ACTIVE CLIENTELE

Our 2009 customer statistics are impressive. The logins and batch

jobs on CSC’s computers totaled more than two million, which is

more than twice the total for the previous year. Our computing ca-

pacity was used by 643 projects with a total of 1,561 users. The big-

gest user groups were from the fields of biosciences, physics and

chemistry. Nanoscience researchers were the heaviest users of pro-

cessor time. Our major customers (project usage more than 20,000

processor hours) ran over 18 percent of our customer projects. They

used almost 99 percent of the computing time, which indicates that

the profile of our computer usage is appropriate. More than 22 mil-

lion processor hours of our application software were used. The

highest number of new projects was in the fields of biosciences, lin-

guistics, and grid use. The Academy of Finland Centres of Excellence

used 32 percent of CSC’s computing time, which is more than twice

the computing volume of the previous year.

The Funet network usage figures continued to grow in 2009, es-

pecially concerning international traffic. The amount of internation-

al traffic on the NORDUnet line grew by an average of 47 percent

from the previous year. The growth in domestic traffic was slower,

but even for that, the growth of inbound traffic from other networks

to Funet was more than 15 percent. The usage of the Haka Federa-

tion grew by 43 percent. The number of logins during the past year

was 5.45 million. Almost all higher education institutions, 98.8 per-

cent altogether, are already covered by the Haka contract.

The Scientist’s interface was in active use by researchers who

used CSC’s services by downloading an average of 32,300 pages per

week, i.e. 6,200 more than the number downloaded in 2008. Data

were downloaded from the PaITuli spatial data system over 10,000

times and more than 25,000 jobs were sent to the Chipster bioinfor-

maticsservice.CSCwasalsoanactivetrainingprovider:130training

days with 2,020 participants.

Alex Bunker’s group studied in their Grand Challenge project prolyl oligopeptidase protein (POP) by molecular dynamics simulations. POP is a very important protein involved in a wide range of metabolic and neurological functions. Figure shows a visualization of one of the strongest bonds between the two halves of POP protein..

© C

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INTERNATIONAL RECOgNITION

CSC successfully continued its active role in Europe. During the past

year, CSC was able to fill two internationally significant chairman-

ships. Our expertise was recognized when the Director of Funet

Network Services, Janne Kanner,waselectedonJune12thtochair

the Board of Directors of TERENA (Trans-European Research and

Education Networking Association) for the following three year

period (2009–2011) and the Director of Application Services, Per

Öster, was elected to chair EGI (European Grid Initiative). Of the pre-

vious nominations, Leif Laaksonen continues as the chairman of

e-IRG (e-infrastructure Reflection Group) and Janne Kanner as the

chairman of NORDUnet. Additionally, CSC employees have partici-

pated in several national and international working groups.

Participating in several European projects has helped CSC’s inter-

nationalization. We have actively participated in the PRACE (Partner-

ship for Advanced Computing in Europe) and DEISA (Distributed Eu-

ropean Infrastructure for Supercomputing Applications) projects, as

well as in the EGI and EGEE projects promoting grid collaboration.

CSC’s computers have had several foreign users and correspond-

ingly, Finnish researchers have gained access to foreign resources.

CSChasapartnerroleintwoESFRIlistprojects,ELIXIRforbioinfor-

matics and CLARIN for linguistics. We are developing European infra-

structure policies in the e-InfraNet projects and have steered the

work to develop European data infrastructure through the PARADE

collaboration.

CSC gained a lot of international attention as a result of the

FinHPC project. The Tekes-funded high-performance computing

development project helped to optimize almost thirty software

codes and to create benchmark software for assessing supercom-

puters. The project, which ended on December 31st, 2008, raised

the performance of Finnish HP-computing and programming exper-

tise to the highest international level. Even before the project was

completed, project members were invited to join similar EU proj-

ects. As a result, CSC was invited to major EU projects, such as EUFO-

RIA and PRACE.

In May 2009, the European Space Agency ESA launched the

Planck satellite to investigate the composition and origin of the uni-

verse. Planck measures cosmic background radiation, microwave

radiation originating from the early universe. The data analysis con-

tains computationally demanding algorithms that will be run on

CSC’sLouhisupercomputer (CrayXT4/XT5),mainlywithDEISAre-

sources. Planck has been chosen as one of the DEISA Virtual Com-

munities, which are allocated supercomputer calculation time.

SUPPORTINg FINNISH RESEARCH

During the past year four Grand Challenge projects were completed.

Alex Bunker (University of Helsinki) used long-time molecular dy-

namics simulations to study protein Prolyl Oligopeptidase (POP).

POP is a very important protein that has a key role in many meta-

bolic and neurological functions. Luca Monticelli and Emppu Sa-

lonen (Helsinki University of Technology), and Ilpo Vattulainen

(Tampere University of Technology) used atomic-level molecular

dynamics to investigate how clusters of fullerene and gallic acid

disturb the function of cell membranes and the ionic channels in

them. As part of their project, Maarit Korpi, Petri Käpylä (University

of Helsinki) and Axel Brandenburg (Nordita) used computational

modeling to show how large-scale ordered magnetic fields can be

generated within the turbulent solar convection zone. Scientists

have tried to model the solar magnetic field generation for more

than two decades. Correspondingly, five new Grand Challenge proj-

ects were started during 2009.

The use of computing services has significantly increased due to

increased resources, but the most essential feature of CSC’s opera-

tions is the fact that we can offer all-inclusive, high-quality services

to Finnish researchers. The Funet network, data services, software,

and diversified specialist support together produce the most signifi-

cant positive impact in providing the operational prerequisites for

Finnish research. CSC is continuously looking for new means to im-

prove its services and to improve the quality and reliability of the

services. Although, when viewed as a whole, the 2009 statistics of

use are excellent, we also had problems concerning the usability of

our hardware environment. We had to fight both technical problems

and hacking attempts, which caused occasional down time periods,

mainly in our computing services. Although we managed to avoid

severe consequences, we need to pay more and more attention to

our ever more complex technical environment to increase its fault

tolerance. CSC has named 2010 the Year of Quality, and we will focus

intensively on the usability of our system environment.

CSC’soperationalcontrolhasbeenmanagedbytheCSCBoardof

Directors and the Ministry of Education. Communication with both

important groups was active and successful. We have been able to

bring forth the issues we find important and gained guidance on di-

recting our operations. At the beginning of 2009 our strategy work

wasreformed,withanimportantinputfromtheBoardofDirectors

and the Ministry.

During the past year CSC continued to grow both in human re-

sources and turnover. At the end of December 2009 we had 191 em-

ployees, i.e. 25 more than the figure of 2008. Thanks to a good com-

munity spirit and competent staff we were, once again, able to pro-

duce an excellent year. Employee motivation and wellbeing are

fundamentally important. We have invested in the health and well-

being of our staff, trying to encourage an interest in exercising by

providing physical condition tests and by supporting club activities.

Towards the end of 2009, for the first time in CSC’s history, a staff

representative was elected to the Management Board, which, I

believe, will improve both internal information flow and the possi-

bilities of the staff to influence our operations at all levels.

In conclusion, I would like extend warm thanks to our staff, cus-

tomers and collaboration partners for the successful year 2009. Suc-

cess requires input from all stakeholders, and you have provided

that. These results allow us to continue with the same enthusiasm

and zest to tackle the challenges of the present year.

Kimmo Koski

Managing Director

CSC–ITCenterforScienceLtd.

ToIMITUSjohTAjAn k ATSAUSMAnAgIng DIreCTor'S reVIew


TWO COUPLES © Janne Ignatius


SoCIeTAL IMPACT

THE STRATEgY OF PARADE COMPLETED

European collaboration has long been carried out on building re-

search infrastructures in fields such as high-performance comput-

ing, Grid networks, and data communication. The collaboration

should now be extended to improve the efficiency of data infra-

structure as well. Indeed, the management of databases and infor-

mation is one of the most significant development targets at the

moment. CSC is intensively involved in the development work of data

infrastructure.

Europe will need extensive collaboration in order to be able to

meet the increasing challenges of managing scientific information

(processed raw data, consisting of information, knowledge and

know-how). One of the major questions puzzling researchers is how

we can guarantee the preservation of data (raw data) for tens or

hundreds of years ahead.

In October, the Partnership for Accessing Data in Europe (PA-

RADE) consortium published its strategy plan (white paper), in which

it evaluates the challenges of data management and proposes solu-

tions relating to its improvement. The activities of the PARADE con-

sortium are based on the actual needs of users. We are not dealing

with merely scientific data storage but a complete service package

to increase the accessibility and usability of the data. Data Services

for Science and Culture is one of the fastest growing and most de-

manding service areas at CSC. Through international collaboration

we can improve inter-operability and quality of our systems. The de-

velopment of data infrastructure is essential for Finland also be-

cause Finland is considered to be an excellent country for data stor-

age due to its suitable climate and favorable bedrock. In the future,

Finland may be a major host country for different types of data

centers.

CSC jOINED THE ALLIANCE FOR PERMANENT ACCESS (APA)

In summer 2009, CSC became a member of the Alliance for Perma-

nent Access (APA). The aim of the Alliance is to ensure accessibility

and preservability of scientific information in Europe. Organizations

concerned with the long-term preservation of research materials

can become members in APA. The main goal of APA is to build a per-

manent infrastructure for the preservation of scientific information.

Long-term digital preservation of scientific information is a burn-

ing question. New research instruments, detecting equipment and

computers are continuously producing more and more data. In 2007

the amount of data produced exceeded the storage capacity, and

the trend is becoming stronger every year. Long-term preservation

is a many-sided question, and inter-organizational and cross-sec-

tional collaboration is needed to find answers.

The Alliance has worked for several years already, and it has built

relationships with, for example, political decision-makers, European

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research funders, and several information producers, distributors

and custodians.

The following leading European information producers are mem-

bers in the alliance:CERN, the EuropeanOrganization forNuclear

Research, the European Space Agency ESA, and several archives,

museums and libraries. In addition to CSC, the Federation of Finnish

Learned Societies is also a member of APA.

A PREPARATORY PROjECT ON REMOTE USE OF RECORDS INFORMATION TO IMPROVE qUALITY AND RELIAbILITY IN RESEARCH

The Ministry of Education is funding survey work carried out by CSC

and the Finnish Information Centre for Register Research (ReTki),

during which a detailed plan will be created for a system allowing

the remote use of the records maintained on various registers. CSC

and ReTki will organize a steering group for the project by inviting

representatives from different ministries, record keeper organiza-

tions, as well as universities and research institutes. The preparatory

project will be completed by the end of 2010.

Administrative and statistical records comprise a gigantic infor-

mation resource for research into various fields in Finland. This in-

formation is in active use both for academic research and research

serving practical decision-making.

In the remote use system the researcher can use data attained

fromseveral recordkeepersdirectly fromhis/herowncomputer.

Hence, researchers do not download the data onto their own com-

puter, for data handling is carried out on a special server that is part

of the system, and the necessary programs are also available on the

server. The records keeper provides a secured access, free of charge,

from the researcher’s own computer to the platform where it is pos-

sible to collect specific research material and combine materials col-

lected from different records, as well as inquiry and interview mate-

rials. Data analyses are also conducted on the platform, and statis-

tics programs are provided for this purpose. Original information

materials are retained by the record keeper organizations, protected

byfirewalls:researcherscanextractandanalyzeinformationonthe

platform, but they can export only the results of their analyses.

Integration of information systems and cross-organizational flow

of information are common trends also at the global scale. The inter-

national health care spheres have named this development trend as-

sociated with a strong customer-oriented approach as "eHealth”.

The aims in this type of development projects include application

integration and improved information management through infor-

mation technology, round-the-clock availability of information, re-

gardless of place, and high level of privacy protection and informa-

tion security.

CSC CONDUCTED A SURVEY ON THE RESEARCH DATA ENVIRONMENT

In May the Ministry of Education set up a national cross-functional

survey project to map and coordinate better utilization of electronic

data materials and resources generated with public funds. The sur-

vey was conducted by CSC and directed by a steering group chaired

by the Chancellor of the University of Helsinki, Ilkka Niiniluoto.

The summary report (2008) of the Finnish national-level road-

map on research infrastructures recommended that the usability of

national registers and availability of data materials be improved and

the costs for users be reduced, if necessary, by changing the appro-

priate legislation.

The broad-based steering group provided suggestions and rec-

ommendations for players in the field regarding activities needed to

improve the usability of research data. It also created a national plan

on how the availability and preservation of research data should be

developed taking into consideration solutions relating to e-Infra-

structures. The group also created a suggestion on national-level re-

sponsibility sharing, collaboration, and coordination between differ-

ent players. CSC was represented by Pirjo-Leena Forsström, Direc-

tor, Data Services for Science and Culture.

CSC COORDINATED RESEARCH E-INFRASTRUCTURE IN FINLAND

In March CSC organized a discussion forum with management rep-

resentatives from various universities and research institutes. The

theme of the conference was the effective use of IT in research and

the practical measures it requires.

At the conference it was generally agreed that Finland needs a

sustainable and competitive policy on e-Infrastructure. In practice,

this requires that the universities and research institutes commit to

developing their operations, collaborate in new ways and success-

fully utilize information and communications technology. During

the past year, CSC organized regional workshops and meetings, in

which the plans were developed further. During these meetings co-

operation and roles of the players within the national and interna-

tional e-Infrastructure were established. At the end of the year a dis-

cussion event was held for a wider audience. During the event, the

common vision of the participating organizations was articulated.

wEb PAgES OPENED FOR THE RESEARCH DATA ENVIRONMENT PROjECT

The cross-functional Research Data Environment survey project ini-

tiated by the Ministry of Education is moving ahead. CSC is respon-

sible for the project implementation and opened web pages where

background information and the objectives of the project are avail-

ableforpublicviewing.Thepagesarelocatedat:http://www.csc.fi/

sivut/e-infra/tietoaineistot.

The importance of accessibility and preservability of scientific in-

formation in electronic format has grown consequent to the devel-

opment of information technology and increasing demand for in-

formation. Such materials embrace, for example, statistical data or

data from registers, as well as materials collected specifically for a

study, including observation and measurement data. For many rea-

sons, accessibility and preservation of information can be a problem

in Finland, and this represents a significant hindrance to appropriate

utilization or reuse of the information.

The Research Data Environment project is conducting and coor-

dinating a survey on the status of electronic information and data

resources collected with public funds, creating proposals for devel-

opment to improve the accessibility and effective use of the infor-


mation. The aim is to make scientific information accessible for use

as widely as possible through effective systems, yet taking into ac-

count various conditions, such as information protection and eco-

nomic limitations.

CSC is responsible for the implementation of the survey relating

to the project. The survey work consisted of arranging, for example,

broad-based discussion, seminar and panel events, questionnaires,

interviews of key persons, and secondary data analyses. The survey

report was due to be completed during the first part of 2010.

gÈANT3: A NEw-gENERATION EUROPEAN RESEARCH AND EDUCATION NETwORkS

During the past few years the European Union has strongly support-

ed the building of e-Infrastructure. An essential part of it has been

theimplementationofaEuropean-widebackbonenetworkGÈANT2.

A new phase in the research network development has recently

been initiated. The GN3 project is placing more emphasis on the de-

velopment of new network services.

An important goal of the GN3 project is to extend the user base

of dedicated network connections into new disciplines, projects

and institutions. The GN3 project is liaising with life sciences, space

research (European Space Agency, ESA), seismology, climate re-

search, meteorology, fusion reactor research (ITER test reactor),

high-performance numerical computing (the PRACE project), and

other growing fields of research. The aim is to become a dependable

service component of the European e-Infrastructure for a wide

range of scientific disciplines. There are high expectations especially

from the 100 Gbps transfer connections and the emerging Ethernet

and optical fiber technologies, and it is hoped that these will serve

as cost-effective solutions for future transmission and switching

technologies.

CSC is concentrating on user authentication, collaboration on

campus support functions, and development of data security for

the services. We are trying to apply the experiences gained, for ex-

ample, through the Haka federation in international network com-

munities, so that for member organizations of the same federation

the user ID provided by the home organization will allow access to

international network services.

The recently completed, EU-funded GN2 project upgraded the

backbone using leased optical fibers and wavelength division multi-

plexing (WDM) technology. GÉANT2 now connects the European re-

search networks with fast fiber connections.

The 36 national research and education networks (NRENs) that

joined GÉANT2 provide services for 4000 campus networks with a

total of 40 million end users. GÉANT2 and several national networks

have adopted hybrid connection technology. This means that the

basic network traffic, including emails, web pages, files, and other

tcp/iptrafficishandledoverthenetworks’ownchannels,whileded-

icated light paths can be reserved for users and applications requir-

ing large data transmission capacity.

The Nordic research networks, including Funet, which is main-

tained by CSC, are connected to the GÈANT backbone network

through the Nordic NORDUnet network. The build-up of the pan-

European backbone network is important also for NORDUnet, be-

cause Nordic researchers will have a chance to participate in, and al-

so lead international research projects.

BeingconnectedtoGÈANTpavesthewaytoefficientcollabora-

tion and enhances massive data transfer. In Finland, this capability is

being utilized, for example, in the tasks relating to transmission of

measuring data produced by the Metsähovi Radio Observatory and

the Large Hadron Collider of CERN. Currently other fields of science,

with biosciences leading the way, are intensifying collaboration and

seeking new ways for conducting research over high-capacity net-

work connections.

Network technology innovations and progressive services for end-users represent the cornerstones for the future internet. National European research and education networks have initiated a shared GÈANT3 project, the objective of which is to create a third-generation network infrastructure. The European Commission has granted EUR 93 million for the project’s implementation. The financial investment by the EU is half of the project’s total budget, and the remainder is co-funded by the European National Research and Education Networks (NRENs). The project is scheduled to run to 2013, and the implementation will be carried out by the NRENs and DANTE (Delivery of Advanced Network Technology to Europe), which is developing and operating the European research network GÈANT.

CSC jOINED T&H SHOk LTD, THE STRATEgIC CENTRE OF ExCELLENCE FOR HEALTH AND wELL-bEINg

T&HSHOKLtdwasestablishedonMay27,2009tomanagetheop-

erations of the Strategic Centre of Excellence for Health and Well-

being(T&HSHOK).Thelimitedcompanywasfoundedby29organi-

zationsintheFinnishhealthandwell-beingsector–16enterprises

and13otherorganizations.ABoardofDirectorswasnominatedat

the founding meeting, and CSC’s representative on the Board is

Juha Haataja.

SHOK links the essential Finnish operators within industry as well

as research. CSC is extremely interested in collaboration possibilities

and strives to boost innovative activities by providing a powerful IT

infrastructure for, for example, analyses of research data and bio-

computing.

yhTeISkUnnALLInen VAIkUTTAVUUS

10 Gbps

Lit Fibre

2.5 Gbps

1 Gbps310 Mbps

155 Mbps

34/45 Mbps

Planned Link

“Lit Fibre” links provide multiple wavelengths currently at 10 Gbps.

*Connections between these countries are part of NORDUnet (the Nordic regional network)

United Kingdom UK

TurkeyTR

SlovakiaSK

SloveniaSI

Sweden*SE

SerbiaRS

RussiaRU

RomaniaRO

Norway*NO

NetherlandsNLLuxembourgLU

LithuaniaLT

ItalyIT

Iceland*IS

IsraelIL

IrelandIE

HungaryHU

CroatiaHR

GreeceGR

FranceFR

Finland*FI

SpainES

Czech Republic

Germany

Denmark*

EstoniaEE

DK

DE

CZAustria

Belgium

Bulgaria

Switzerland

Cyprus

AT

BE

CY

CH

BG

Backbone Topology November 2009. GÉANT is operated by DANTE on behalf of Europe’s NRENs.

GÉANT is co-funded by the European Commission within its 7th R&D Framework Programme.

Transforming the way users collaborate

This document has been produced with the financial assistance of the European Union. The contents of this document are the sole responsibility of DANTE and can under no circumstances be regarded as reflecting the position of the European Union.

the pan-European research and education network

MaltaMT

F.Y.R. MacedoniaMK

MontenegroME

LatviaLV

PortugalPT

PolandPL

SoCIeTAL IMPACT


ICE2SEA: CSC jOINED A SEA-LEVEL RESEARCH PROgRAM

Ice2sea is a collaborative research program involving partners from

13 countries, including CSC representing Finland. The Ice2sea pro-

gram focuses on investigating the sea level rise, caused by the melt-

ing of continental ice sheets and glaciers, and the consequences of

this sea level rise.

Even partial melting of continental ice sheets has significant af-

fects in Europe, as fifteen EU countries have substantial coastlines

that will be affected by global sea level rise. In many of these coastal

areas, future sea level rise will increase rates of coastal erosion, ac-

celerate the destruction of natural sea defenses, and increase the

risk of coastal flooding. Ice2sea aims to improve the research into

sea level predictions based on the most up-to-date climate and ice

sheet modeling. CSC’s multi-physical simulation software, Elmer

and its application software ElmerICE adapted to simulations of ice

sheets are used in the project.

The participants are from Belgium, Chile, Denmark, Finland,

France, Germany, Iceland, Italy, the Netherlands, Norway, Poland,

Switzerland, and the UK. Ice2sea is part of the European Union

Framework 7 Programme and receives funding from the European

Commission, and from the many national agencies funding the in-

stitutionalpartners.Theprogramwillrunforfouryears(2009–2013)

and is planned so that results will be available in time for the next

intergovernmental Panel on Climate Change assessment of climate

change and its impacts.

jANNE kANNER TO CHAIR TERENA

CSC’s Janne Kanner, Director of the Funet Network Services, was

appointed as President of TERENA, the Trans-European Research

and Education Networking Association for the following three year

period(2009–2011).JanneKannerhasalsobeenchairoftheNordic

academicnetworkNORDUnetA/Ssince2008.

TERENA is the Trans-European Research and Education Network-

ing Association connecting 37 European national research and edu-

cation networks. It is a unique association in which Europe’s research

and education networking organizations can meet, exchange infor-

mation and experience, and collaborate on a range of activities.

CSC’S PER ÖSTER ELECTED CHAIRMAN OF EgI COUNCIL

The EGI (European Grid Initiative) Council chose CSC’s Per Öster to

be its chairman on 24 September 2009, during the EGEE’09 confer-

enceinBarcelona,Spain.

This election constitutes another important step towards the

implementation of EGI, which aims to establish a sustainable grid

service for the European scientific community. EGI provides an ex-

cellent opportunity to make the latest and most advanced comput-

ing resources, applications, tools, and data available to European

researchers.

The EGI Council, which is made up of National Grid Initiatives

(NGIs) as well as other members represented in the EIROforum, will

govern the direction of the EGI collaboration on a long term basis,

and is therefore one of the key bodies in the EGI.

ÖsterhasbeenactivelyinvolvedintheEGIDesignStudy(EGI_DS)

project, in which he has been responsible for the EGI promotion and

links with other initiatives.

The headquarters of EGI (EGI.eu) is in Amsterdam, and it acts as

the coordinating body for the EGI organization. One of its main roles

is to facilitate the interaction and collaboration between the NGIs of

the participating countries. Together EGI.eu and the NGIs operate

and further develop the pan-European grid infrastructure, in order

to guarantee its long-term availability for performing research and

innovative work.

LETTER OF INTEREST SIgNED bETwEEN CSC AND RUSSIAN T-PLATFORMS

InJuneCSCandtheRussiancompany,T-Platformssignedaletterof

interest on shared use of scientific software developed by CSC and

the hardware solutions developed by T-Platforms.

CSC and T-Platforms have a common interest in solving their cus-

tomers’ problems relating to modeling and computing, and to do

SoCIeTAL IMPACT

Mikhail Kozhevnikov (on the left) and Kimmo Koski (on the right).

© L

eif

Laak

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© V

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Mie

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this together, the expertise and computer resources of both part-

ners are required.

Collaboration with European HPC projects, such as PRACE and

PROSPECT, is essential for T-Platforms. CSC provides support to

T-Platforms in its efforts to integrate Russia into the European

e-Infrastructure community.

The Letter of Interest was signed in Amsterdam in May by Kimmo

Koski, Managing Director of CSC and Mikhail Kozhevnikov, Vice-

President of T-Platforms.

T-Platforms is the leading Russia-based developer and provider

of complete turn-key solutions for high performance computing.

The company provides solutions for all sectors of the national econ-

omy, embracing government, industry, science, education, and tele-

communications. T-Platforms is the only Russia-based company to

have five in-house developed cluster systems rated in the global Top

500 list of the most powerful computers in the world.

FINNISH RESEARCHERS AND CSC HAVE A kEY ROLE IN PROCESSINg MEASUREMENT DATA FROM THE PLANCk SATELLITE

In May 2009, the European Space Agency ESA launched the Planck

satellite to investigate the composition and origin of the universe.

Planck measures cosmic background radiation, i.e. microwave radi-

ation originating from the early universe. The functionality of the

instruments has been tested using simulated data, which was pro-

duced utilizing the Monte Carlo simulation method on CSC's Louhi

supercomputer.

One of the uses planned for the measurement results is to pro-

duce frequency maps covering the entire universe at nine different

microwave frequencies, and component maps derived from them,

representingvarioussourcesofradiation:interstellardust,particles

radiating upon the impact of galactic magnetic fields, and cosmic

background radiation itself. The results will be completed in 2012.

The analysis of Planck observations has many phases, and in-

volves an international chain of cooperation, involving Finnish re-

searchers from the Department of Physics and the Department of

Astronomy at the University of Helsinki, from the Helsinki Institute

of Physics (HIP), the Metsähovi Radio Observatory of the Helsinki

University of Technology, and from the Tuorla Observatory of the

University of Turku. Finnish researchers have particular responsibil-

ity for the measurement of the 70-gigahertz frequency area, which

is part of the tasks of the Low Frequency Instrument (LFI). The mea-

suring devices have been manufactured in Finland, and the measur-

ing data is analyzed by physicists from the University of Helsinki.

A software application called Madam, developed at the University of

Helsinki, is used to analyze the LFI data. The LFI data is analyzed in an

LFI computing center (LFI DPC) based in Trieste, Italy.

The data analysis involves computationally demanding Monte

Carlo simulations which exceed the capacity of the LFI computing

center. These data analysis stages are carried out using CSC's Louhi

supercomputer(CrayXT4/XT5)withresourcesgrantedmainlyby

the Distributed European Infrastructure for Supercomputing Ap-

plications (DEISA). Planck has been chosen as one of the DEISA Vir-

tual Communities, which are allocated supercomputer calculation

time.

yhTeISkUnnALLInen VAIkUTTAVUUSSoCIeTAL IMPACT

The Planck satellite was launched on May 14, 2009, and its main task is to investigate the early universe. The first microwave observatory mission lasted two weeks, from August 13th to August 27th, yielding maps of a strip of the sky, one for each of Planck's nine frequencies. Each map is a ring, about 15° wide, stretching across the full sky. Preliminary analysis indicates that the quality of the data is excellent.

© E

SA


PRACE IMPLEMENTINg A PERSISTENT RESEARCH PLATFORM

In early 2009, CSC joined the STRATOS project that strives to create a

persistent hardware and service platform for research. Twelve of

the contract partners are PRACE partners and two are associate part-

ners. The mission of PRACE (Partnership for Advanced Computing

in Europe) is to create a persistent European HPC services infra-

structure.

STRATOS (PRACE advisory group for Strategic Technologies)

forms a unique collaboration of PRACE partners and industry either

directly or through consortia that include PRACE members. The ob-

jective of STRATOS is to foster the development of HPC technologies

in Europe. Its associate partners are the European industrial-aca-

demic association PROSPECT and Ter@tec.

Industrial and other innovative European HPC development proj-

ects engaged in development or evaluation of HPC technology can

become members of STRATOS for the duration of the projects. The

final cooperation agreement of the STRATOS partnership will be es-

tablished as soon as the PRACE research infrastructure has become

a European legal entity. During the initial period, STRATOS is admin-

istered in accordance with the STRATOS Memorandum of Under-

standing.

PRACE PROTOTYPE TESTINg STARTED

PRACE, the Partnership for Advanced Computing in Europe, invited

researchers from academia and industry to test applications on pro-

totypes of potential future HPC petascale systems. PRACE partners

have installed six systems of different architectures that are now

available for assessment. CSC is one of the host sites for the PRACE

prototypes.

One of the main goals of the PRACE project is investigating peta-

scale prototypes and carrying out research into scaling and opti-

mizing applications on petascaling machines. The applications were

carefully reviewed, giving priority to applications that are different

from those already being investigated by PRACE.

CSC ACqUIRED A NEw SUPERCOMPUTER FOR THE FINNISH METEOROLOgICAL INSTITUTE

The Finnish Meteorological Institute (FMI) is upgrading its high-per-

formance computing environment for weather forecasting and sci-

entific computing. CSC was responsible for the procurement of the

new supercomputer solution.

The new supercomputer is used for operational weather fore-

casting and supporting the related research functions. The capacity

of the equipment is 20-fold that of the previously used computer

system, and it is estimated that it will meet the needs of computa-

tional weather forecasting for roughly four years.

In addition to weather forecasts, the FMI will use the supercom-

puter for research on global climate change and, for example, calcu-

lating the dispersion of radioactive and other pollutants. The solu-

tion also provides improved possibilities for other FMI research proj-

ects needing computing capacity. The equipment was installed and

ready for use towards the end of 2009.

CSC served as a specialist in advancing the acquisition. CSC has a

profoundexperienceinthefield:forthreedecadesCSChashosted

the most powerful computers in Finland in its machine room facili-

ties. CSC’s machines are used by researchers at higher education in-

stitutions, the FMI, etc.

CSC is also reserving computing time for the FMI on its Louhi su-

percomputer (CrayXT4/XT5) for testing theCrayenvironment. In

accordance with the signed agreement, CSC will also supply special-

ist resources for theFMI for theperiod2009–2012tosupport the

programming and maintenance of the computing environment.

Technical consultation will be based on CSC’s currently existing soft-

ware and server environment. The new supercomputer of the FMI

comprises two server platforms. The new system configuration is

manufacturedbyCrayandthemodelisXT5m.Thetheoreticalpeak

performance of the system to be acquired for the FMI is more than

34,000 billion calculations per second (34.6 Tflops). Should addi-

tional capacity be needed, CSC will be able to provide it.

A supercomputer solves a weather model over a precisely defined geographical area, described as a three-dimensional grid of points. Each grid node serves as a computation point, where equations describing the development of atmospheric conditions are solved. The model produces information about parameters, such as temperature, atmospheric pressure, wind pressure and velocity, and humidity. Finally, the weather model is run on a supercomputer to produce a weather forecast. With higher computation power it is possible to produce forecasts of two days covering the whole of Europe with 7.5 km resolution instead of the current 16.5 km resolution. Forecasts are completed roughly twice as fast as before.

CSC’S STORAgE CAPACITY ExCEEDED ONE PETAbYTE

The disk capacity of CSC’s storage systems exceeded 1 petabyte in

April. The capacity growth has been strong, for at the turn of the

millennium the disk volume was less than 10 terabytes. Storing one

petabyte of data corresponds to about 1.5 million compact discs.

When storing huge amounts of data, the long-term manage-

ment and accessibility needs extra attention. In fact, a prerequisite

of EU projects related to scientific and cultural data is that all con-

tent should be easily accessible. Common practices and standards

should be followed in order to be able to share the data electroni-

cally.

SoCIeTAL IMPACT


COMMON RECOMMENDATION ON THE USE OF SMART CARDS wITH CERTIFICATES FOR UNIVERSITIES

During the spring, the Ministry of Education published guidelines and

best practices on deployment and administration of smart cards in

universities. The guidelines were formulated by a working group of

experts representing the universities and CSC. The working group

was of the opinion that strong authentication methods should be

taken into use with caution, comparing different alternatives.

A smart card with certificates is a smart card that contains certifi-

cates for personal identification verification for use in data networks.

The working group reviewed the implementation of the smart

cards with certifications and recommended that the important func-

tions in critical data systems be secured with a verification method

that is more reliable than using the username-password combina-

tion. The smart cards with certifications do not alone guarantee se-

curity in services, but in the best case they improve it. When new

security technologies are taken into use, care must be taken not to

create additional risks. New solutions must be more secure but also

easy to use and cost-effective.

One of the most important objectives set for the working group

was to define the services for which the smart card and the smart card

with certificates should be applied. In the final report these are divided

into three groups: the required services forwhich username-pass-

word identification should at least be replaced by a stronger method;

recommended services for which the use of stronger authentication

methods would be preferred; and additional services for which imple-

mentation should be considered on a case-by-case basis.

CSC NOw USINg THE FANC ECO-ENERgY LAbEL

CSC took into use the new eco-energy label of the Finnish Associa-

tion for Nature Conservation (FANC). The energy consumption of

CSC’s two server centers during the past year was 8.1 gigawatt

hours. Starting in 2009, both centers have used environmentally

friendly energy. The FANC eco-energy label is granted only to re-

newable energy meeting strict environmental criteria.

CSC’s decision means that the money used to pay the company's

electricity bills supports environmentally friendly electricity produc-

tion instead of the use of fossil fuels. Alternating weather conditions

have to be taken into account in machine room planning. Since

weather conditions may vary from the heat of summer to extreme

cold, the necessary technology must be installed to secure that the

ambient air temperature and humidity remain constant to meet the

machine room requirements.

BothCSC’sservercentershaveafreecoolingsystem.Thismeans

that the cooling effect of cold air or water outside is transferred from

one space to another in a controlled manner, which makes automat-

ic coolers redundant. This saves significant amounts of energy.

Eco-energy efficiency is measured by the Power Usage Effective-

ness (PUE) factor, which refers to the total power divided by the

power consumed by the servers. Hence, the minimum is 1, if all en-

ergy is used by the servers. Normally server centers operate be-

tween 1.8 and 3.0. Google has reported that it has a few centers with

a PUE factor 1.2 or below.

CSC’s newest machine room “Pohja” attained 1.48 during its first

year of operation. This means that per each 100 watts, 67.5 watts

was used by the server and 32.5 watts for cooling.

In the Green500 list, CSC’s (and Finland’s) biggest and most pow-

erfulcomputerCrayXT4/XT5 (Louhi) ranked128th.Green500 isa

list that provides biannual rankings of the most eco-efficient super-

computers in the world. The most eco-efficient supercomputer is

thePRACEprototypelocatedinattheFZJResearchCentreJülichin

Germany.

gREEN RENEwALS AT CSC

The theme of 2009 at CSC was the Year of the Environment, and se-

veral environmentally friendly initiatives were taken during the year.

To promote green perspectives, the GreenCSC committee was foun-

ded, with representatives from different employee groups. CSC’s

staff have welcomed all of the changes relating to protecting the

environment, even the ones that require personal efforts, with an

extremely positive attitude.

Waste sorting was improved by placing a dedicated waste cart for

energy waste on each office floor. At the same time, collecting mixed

waste from rooms was discontinued and now the employees them-

selves sort the waste they generate and take it to the waste collect-

ing sites on each floor. This significantly reduces the amount of un-

sorted waste and the number of plastic bags changed weekly for the

mixed waste containers in rooms. On the waste collecting site of

each office floor, in addition to the energy waste container there are

also carts for white and colored recycling paper as well as a data se-

curity receptacle for confidential documents. Containers for mixed

and compostable waste are located in the recess facilities on each

floor. There is also one centralized collecting site for batteries, card-

board, and data disks. In addition to these collecting sites within the

office facilities, CSC delivers other waste (computer scrap, fluores-

cent lamps, glass) to the waste containers located in the property

company’s waste facility.

During 2009, CSC focused on reducing paper consumption by

making two-sided printing the default in network printers, and by

changing the default settings so that the cover page containing the

owner ID was removed from the print command. Additionally, the

weekly newsletter for the staff is no longer printed; the only version

is the intranet publication.

During the Year of the Environment, water pressure was reduced

in order to save water. Information was disseminated to the staff on

eco-efficient procedures in the office facilities. In several acquisi-

tions environmental issues have been addressed as a significant fac-

tor affecting decision-making (e.g. invitations for tenders for office

cleaning services). CSC participated in the international Earth Hour

2009 event, wishing to express its concern about the environmental

state of the world.

yhTeISkUnnALLInen VAIkUTTAVUUSSoCIeTAL IMPACT


FINNISH ARCHIPELAGO © Harri Sylvander


The rapid expansion and reliable archiving of research data repre-

sent enormous challenges requiring a great deal of work in data

processing and analysis. A researcher submerged in the flood of in-

formation needs effective high-quality tools for managing the en-

tire life span of materials. CSC offers various possibilities to meet

the demanding needs of data processing. The offering includes

short- and long-term storage services, reliable backup and archiving

systems that guarantee data preservation and accessibility, 70 sci-

entific databases, and a broad-based spatial data content. The serv-

er environment also hosts the academic library systems Linnea (a

shared library system for Finnish universities), Armas (a shared da-

tabase for Finnish universities of applied sciences), Nelli (a national

information retrieval system for Finnish libraries) and Radio and

television archives.

NATIONAL DIgITAL LIbRARY

CSC is a key input provider in the planning of long-term preserva-

tion and web-based services.

The aim of the National Digital Library project, initiated in 2008,

is to improve the prerequisites for access to information, learning

and research and provide new opportunities for arts and creative ac-

tivities. Improving access to the materials ensures that information

on our culture and history is actively used. The public interface Web

service will be available to all in 2011, providing access to electronic

information resources and services of libraries, archives and muse-

ums. Even in its earliest stage, the Web service will comprise over

100,000 museum pieces and photographs, over one million pages

of old newspapers, over 20,000 scientific journals, over 300,000

e-books, hundreds of thousands of documents and reference and

availability of information on 30 million items in public and scien-

tific libraries.

DATA SerVICeS for SCIenCe AnD CULTUre




The project also aims to improve the productivity of the partici-

pating organizations. The joint solutions reduce the over-lapping

costs of digitization and management and distribution of electronic

materials, releasing resources for other tasks and consequently,

making the use of public funds more effective.

At the same time, the impact benefits gained from the creation

and maintenance of information resources will be multiplied as the

materials form a common, easy-to-use national entity. The aim of

digitization and improvement in the availability of electronic materi-

als is to attain the positive social impact created by the use and reuse

of digitized content.

The National Digital Library project works to develop technical

solutions for the long-term preservation of national heritage mate-

rial for the organizations responsible for storing cultural and histori-

cal data. CSC has prepared a preliminary project specifications docu-

ment, Requirements for long-term preservation, published in spring

2009. Additionally, in 2009 CSC participated in the work to design

the joint total architecture, to create the procurement documenta-

tion of the Web service, supplemented various definitions when re-

quested, and initiated a risk and cost evaluation relating to long-

term digital preservation.

The National Digital Library is one of the projects under the Na-

tional Information Society (Arjen tietoyhteiskunta) Strategy projects

set up to implement the Council of State’s decision of principle on

the objectives for a National Information Society Policy 2007−2011.

The total working body in this project initiated by the Ministry of

Educationconsistsof35organizations:ministries,nationalinstitu-

tions responsible for preservation of cultural heritage, scientific and

public libraries, archives, museums, and representatives of other

main interest groups.

TEST RUNS OF CERN’S PARTICLE COLLIDER STARTED

The LHC Large Hadron Collider of the European Organization for

Nuclear Research CERN will be used in particle physics experiments

to provide new information on the basic structure of matter.

Proton−proton collisions in new energy regions create several

new particles, and the detectors of the four major experiments, AL-

ICE, ATLAS, CMS, and LHCb will be taking digital images of the traces

left by the particles. In order to detect and identify a new particle or

phenomenon, the traces left by such collisions must be analyzed us-

ing an immense number of computers. CERN will disperse the raw

data from computations and pre-processing to computing centers

located in 11 different countries, and the national centers will dis-

tribute the data to other centers. CSC maintains Finland’s share of

CERN’s pan-Nordic Tier-1 computing center. The Tier-2 center is ad-

ministered by CSC together with Helsinki Institute of Physics and

theUniversityofJyväskylä.

The LHC was started up for the second time on November 23,

2009 and a number of tests were run until December 18, 2009. Dur-

ing this period, maximum colliding energies were approximately

2TeV, measured also in actual experiments (ALICE and CMS). ALICE (A

Large Ion Collider Experiment) is an experiment specifically designed

for the LHC. Measuring data is analyzed to investigate the behavior

and properties of quark-gluon plasma. The CMS experiment works

to identify the Higgs boson. The results can be applied to research

into the generation of particle matter in the early universe.

The re-start of the LHC has not affected the activities at CSC, as

yet. Slightly more than the normal volume of computing and data

storage resources was used for testing the system and ensuring that

the equipment and software work as they are supposed to.

DIgITAL ARCHIVINg OF RADIO AND TV PROgRAMS STARTED©

DIG

ITA

The LHC Large Hadron Collider will be used in particle physics experiments to provide new information on the basic structure of matter. The LHC is the biggest particle collider in the world, and the massive experiments to be performed on it will produce a total of more than 15 petabytes of data per year. It was initiated in 2009. CERN will disperse the raw data from computations and pre-processing to computing centers located in 11 different countries. The Nordic Data Grid Facility (NDGF) consists of the Nordic computing centers in Norway, Sweden, Finland, and Denmark. NDGF is one of the eleven “Tier-1” or main computing resources at which the scientific work relating to the LHC will be performed. CSC maintains Finland’s share of CERN’s pan-Nordic Tier-1 computing center.

The National Audiovisual Archive (KAVA) works to preserve the national film, television and radio culture. The activities are based on legislation, with the primary motive being to save and preserve the Finnish film heritage to future generations.

© C

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CSC and the National Audiovisual Archive (KAVA) have started the

digital archiving of television and radio programs broadcast in Fin-

land. The archiving will not only revolutionize Finnish media re-

search but will also preserve the radio and TV programs that repre-

sent our cultural tradition for our own and for future generations.

The Finnish radio and television archives (RTVA) started record-

ing operations in 2009 by recording programs broadcast over ten

Finnish television channels and six radio channels round the clock,

ten radio channels for six months at a time, and 18 TV channels and

73 radio channels as one-week samples. This totaled almost 200,000

hours of broadcast packages in high-quality capture format, i.e.

about 50 terabytes of radio and television recordings and metadata.

The first viewing point was opened at KAVA and the first researcher

was allowed access to the archive contents in December 2009. The

management system is still being finalized, official opening ceremo-

nies will be held in February 2010, and the possibilities for use will be

extended during 2010 one legal deposit library at a time. After com-

pletion of the RTVA system development phase, the system will be

finalized and the maintenance phase will be ready for use.

CSC OPENED A DATAbASE SERVICE

In March 2009 CSC opened a new database service that enables us-

ers to save the data they receive from supercomputer runs directly

into their own relational databases. Using databases for data stor-

age facilitates data processing and analysis performed with differ-

ent methods.

CSC provides the database platform and the connection between

the computing servers and the databases. The service also makes it

possible to store large amounts of data in the database. A customer

survey carried out in 2008 indicated a clear need for this type of

service.

The recently opened database service is part of the long-term

strategic development of CSC’s Data Services for Science and Cul-

ture service field. It is a significant addition to information manage-

ment in our computing environment.

PAITULI SPATIAL DATA SERVICE FOR RESEARCH AND TEACHINg AT HIgHER EDUCATION INSTITUTIONS

At the end of April 2009, CSC opened the PaITuli spatial data service

for use at Finnish higher education institutions. The service pro-

vides spatial data services free of charge to be employed by research

and teaching staff at higher education institutions.

The service is part of the geographic information (GI) spatial data

development activities funded by the Ministry of Education. With

PaITuli, Finnish higher education institutions gain access to the first

downloading service for national spatial data. The aim of the service

is to increase the knowledge and use of spatial data, and advance the

related research and teaching in Finnish higher education institu-

tions.

PaITuli spatial data service is a GI loading service intended for stu-

dents, researchers and staff members at higher education institu-

tions. The service offers a range of Finnish spatial data materials of

high-quality, from basic maps to bedrock and soil maps and daily

climate data. Spatial data produced by the Geological Survey of Fin-

land (GTK), the Finnish Meteorological Institute, the National Land

Survey of Finland, the National Board of Antiquities, and Finnish

Transport Agency. Later spatial data offering will be extended to

meet the spatial data needs of Finnish higher education institutions

on an even wider scale.

The PaITuli spatial data service utilizes Haka, the user authentica-

tion system that is jointly used by Finnish higher education institu-

tions and operated by CSC. The user can access the service by using

the user name and password assigned by their own home organi-

zation.

THE FINNISH NATIONAL gALLERY CHOSE CSC AS THEIR INFORMATION SYSTEM MAINTAINER

CSC and the Finnish National Gallery signed a 4-year contract on

system services. Based on this contract CSC provides the Finnish

National Gallery with an integrated virtualization and server plat-

form as well as disk system services.

The decision on collaboration between CSC and the Finnish Na-

tional Gallery was a natural one, because both parties work under

the control of the Ministry of Education. In addition, the Finnish

Natural Gallery is already a member of Funet, the data network for

Finnish higher education and research, operated by CSC. The Finn-

ish National Gallery joined CSC’s information system environment

through a superfast and secure Funet light path connection.

The video and media bank, digital collections, and the Muusa

classification, description and listing software of the Finnish Na-

tional Gallery will be placed on virtual servers in the new system.

Additionally, CSC provides the Finnish National Gallery with disk

space as well as machine room and back up services. The disk

space volume to be provided is 10 terabytes, and the system will

be configured so that it is easy to add disk space and computing

power when necessary.

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PAIRSDb PROTEIN SEqUENCE ALIgNMENT DATAbASE UPDATED

The PairsDB protein sequencing database, jointly maintained by

CSCandtheBioinformaticsunitattheHelsinkiUniversity,wasup-

dated in January. The database now contains pre-computed se-

quence alignments for 7.4 million protein sequences. The pre-com-

puted data on the similarities between proteins expedite research

carriedoutinthefieldofbiosciences.ThePairsDBdatabaseenables

quick retrieval of sequences similar to the one queried and on align-

ments between them. The query can easily be focused to an indi-

vidual organism or a taxonomy group. It is also possible to select

only results for sequences belonging to a certain organism or a

taxonomic group.

REVISED DIgITAL MORPHOLOgY ARCHIVES LAUNCHED

CSC and the Department of Finnish Language and Literature at the

University of Helsinki have jointly published the revised and ex-

panded Digital Morphology Archives (DMA). The DMA is a database

for language research, containing information about the morpholo-

gy of Finnish dialects. It is an online service, which has been in use

since 2004.

As a result of the revision process, the dialect data has more than

doubled:thedatanowconsistsof279,248dialectsentencesfrom

160 different municipalities. Part of the data is linked to PDF format

dialect cards prepared on the basis of the archived cards in the origi-

nal paper archives. This means that researchers may choose to

browse the entries by those who collected the original dialect sam-

ples. The digital archives contain a total of 25,853 dialect cards in

PDF format. The usability of the archives has also been improved.

The DMA is based on the printed Morphology Archives of the De-

partment of Finnish Language and Literature at the University of Hel-

sinki, containing around one million sentences of Finnish dialects’

morphologically encoded material. Among other uses, the data is

used as research material for morphological, syntactic and lexical

studies of Finnish dialects. It is also good comparison material for

those who research written language.

TheDMAispartofCSC’sLanguageBankofFinland.TheLanguage

Bankisalanguageresearchserviceconsistingofacomprehensive

set of written and spoken material, as well as software suitable for

studying them, in an efficient hardware environment. Research

unitssubmittheirdatatotheLanguageBankformaintenanceand

distribution to researchers around Finland.

The DMA can be used through CSC’s Scientist’s interface online

service. Using the archives requires an access permit for the Lan-

guageBank.

RESEARCH MATERIAL ON ENDANgERED LANgUAgES IN CSC’S LANgUAgE bANk OF FINLAND

ThelanguageselectioninCSC’sLanguageBankofFinlandhasbeen

supplemented with very rare cognate languages to Finnish. The

new corpora are small or medium in size but unique and in high de-

mand among researchers. The corpora are vital in preserving re-

search material of endangered languages.

The new multilingual corpora are based on the University of Hel-

sinki’s research collection of more than 50 languages (Multilingual

Research Collection of the University of Helsinki Language Corpus

Server, UHLCS). The collection features samples of many endan-

gered languages spoken in Northern and Central Eurasia as well as

texts of different types in Finnish, Swedish, English, Russian and

Swahili.

The corpora in the UHLCS collection were compiled in the course

of several different projects. A significant part of the corpora of Ura-

lic languages was created in 1996−1998 with funding from the Acad-

emy of Finland to an international Uralic language data bank initia-

tive. Corpora of small, endangered languages were, among others,

receivedfromthe Institute forBibleTranslation inHelsinki,Stock-

holm and Moscow. In 2000, Max Planck Institute for Social Anthro-

pology in Leipzig supported the public distribution of corpora of

Uralic, Turkic, Iranian, North East Caucasian, Tungusic, Mongolic and

Chukotko−Kamchatkan languages.


A sugar molecule on a protein surface.




ICICLES © Juha Haataja


CSC’s computers run the widest range of scientific software in Fin-

land. Our computing environment contains of more than 200 dif-

ferent ready-to-use programs. Licenses have been acquired for

software in chemistry, biosciences, physics, statistics, computation-

al fluid dynamics, structural analysis, and mathematics, to mention

just a few areas. CSC provides training on the software, method

support in various disciplines, develops scientific software, and pro-

vides access to the Grid computing resources. Our user services are

internationally competitive and easily available. CSC also coordi-

nates national software consortia on behalf of the Finnish higher

education institutions.

ELMER SOFTwARE AVAILAbLE FOR LINUx OPERATINg SYSTEM

During the past year, several clear improvements and changes

were implemented in the Elmer project. The changes improve

our global visibility and directly affect the usability and user ex-

perience of the program. The changes concern, for example,

software user support, which was centralized and transferred

onto a new server at the end of the year. In the updated system

users have an open-format Wiki site for sharing and searching for

information, and an active discussion forum for technical ques-

tions, feedback, and suggestions for development.

In 2009 Elmer was included on the Linux platform that contains

the most popular ready-to-use software in the world. Of these,

Ubuntu-Linux is especially notable, being undoubtedly one of the

most popular open source code programs. Ubuntu-Linux is com-

monly used at several Finnish universities, both by departments and

individual researchers whose work involves techno-scientific com-

puting and software development.

A wide range of Elmer training courses was arranged. Extensive

basic and advanced courses were arranged both during the spring

and autumn. Practically all of the courses were fully booked. In ad-

dition to general courses we also arranged a number of smaller-

scale specialist courses, as well as hands-on training for staff when

separately ordered. The course material and updated user guides

can be downloaded from the web site of the software project at

http://www.csc.fi/elmer.

NEw SOLUTION METHODS FOR INHERENTLY COUPLED PRObLEMS OF ACOUSTICS

When several strongly inter-connected physical phenomena have

to be simultaneously taken into account, problems can be very dif-

ficult to solve using the commonly used simulation programs. In

2009, the Elmer software package was updated to improve its ability

to handle the strongly inter-connected problems that are common

APPLICATIon SerVICeS

© E

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in acoustics. There are several applications for the developed meth-

ods. For example, the interaction between sound waves and me-

chanical structures can now be modeled more effectively and reli-

ably. The advances were attained as results of a long-term project

in which Nokia Research Center and CSC collaborated to develop

Elmer software.

ELMER CHOSEN AS AN APPLICATION PROgRAM FOR PRACE

In 2009, Elmer was chosen as one of the application programs in the

pan-European Partnership for Advanced Computing in Europe

(PRACE) project. The three-year project aims to create a uniform

cross-European system for techno-scientific parallel computing re-

garding applications as well as machine resources. Elmer was in-

cluded as the only multiphysical modeling software using the Finite

Element Method (FEM) for solving complex models and problems

requiring parallel computing. Thanks to PRACE, we were able to test

Elmer’s parallel computing techniques for jobs that sometimes re-

quired as many as ten thousand processors. The results were excel-

lent and they were reported in the final report of PRACE. Having

proven its reliability, PRACE will employ Elmer also in the future,

benefiting from its improved computing capacity.

SOMA2 MODELINg ENVIRONMENT wAS UPDATED

SOMA2, operated through a standard web browser, provides an easy

and intuitive way to use molecular modeling software in the Unix

computing environment. The SOMA2 environment offers a possibil-

ity to construct a computational workflow consisting of one or sev-

eral programs run one after another. The SOMA2 software package

was released under an open source code license (GNU General Pub-

lic License), and the source code package and documentation are

available at our SOMA web site athttp://www.csc.fi/soma.

SOMA2 is available for CSC customers through the Scientist’s inter-

face. In April 2009 the SOMA2 modeling environment programs (e.g.

CORINA,obprop,ROTATE,andX-Score)wereinstalledonthenewHip-

pu application server. Additionally, the SOMA2 environment contains

several programs installed on Murska, such as AutoDock, Gaussian,

GOLD, GPAW, and Turbomole.

InJune,anewsoftwareversionSOMA21.2Sodiumwaspublished.

It contains some new features, minor improvements and several bug

fixes. In addition, version 1.3 Magnesium was released in September.

This version provides better support for web browsers and having

several significant improvements for usability through the several

interactive functions that have been added.

During last autumn, SOMA2 was introduced at CSC’s courses

(Gaussian workshop, for example) and customer events. During 2009,

75 CSC users had visited the SOMA2 service in the Scientist’s interface.

CHIPSTER ENAbLES gENE ACTIVITY STUDIES ALSO AT THE PROTEIN LEVEL

Chipster is a user-friendly and comprehensive program developed

by CSC for studies of gene expression activity data produced on mi-

crochips. Chipster has brought a great number of new customers to

CSC, and Chipster training was provided at several campuses. This

open code software has attracted a lot of attention abroad, too. Pre-

sentations on Chipster were given at the main conferences in the

field, and many research centers in different parts of the world,

even as far away as New Zealand, have taken Chipster into use and

purchased training on Chipster from CSC.

During 2009 Chipster’s functional features were extended to al-

low gene activity studies not only at the RNA but also the protein

level. Other improvements included the added support for micro-

RNA (miRNA) analyses; miRNA have essential effects on gene ex-

pression regulation. A new analysis technology was also developed

for Chipster to enhance visualization of NGS (next-generation se-

quencing) data.

For proteomics analyses, tools were created for all phases of the

analysis, ranging from imputation of the missing values to biological

interpretation of the results using a “pathway” analysis.

ThetoolsweredesignedincollaborationwiththeEuropeanBio-

informatics Institute (EBI) and the Max Planck Institute. Chipster

searches the interactive partners and signaling pathways, as well as

the biological processes enriched by the protein lists directly from

the databases located in these institutions.

Chipster’s wide range of tools for microarray screening and sta-

tistical testing are utilized in the miRNA analysis. Once the significant

miRNA molecules have been determined, Chipster helps to retrieve

theirtargetgenesdirectlyfromthemiRBasedatabase.Thebiologi-

cal role of the target genes can be determined by analyzing how the

genes are enriched into gene ontology (GO) categories or on the

metabolic pathways of the KEGG database.

Interaction between a sound wave and mechanical structure can significantly affect sound propagation in small devices. The picture shows a detail calculated with Elmer, a momentary temperature change occurring when sound proceeds in a tube with varying cross-sectional surfaces.

Currently Chipster is being actively developed for the next generation sequencing (NGS) platforms to handle data produced by the totally new analysis technology.



SOMA2 provides an easy and intuitive way to use molecular modeling software in the Unix computing environ-ment.

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A LOOK © Janne Ignatius


The Information Management Services function develops and main-

tains centralized data systems for administration of science and ed-

ucation and the Ministry of Education. The term “data systems for

administration of science and education” refers to the data systems

that are in shared use by institutions of higher education and that

support research and teaching activities. The services comprise

centralized data management services, such as Haka user identifica-

tion system and the databases providing statistics for performance

monitoring in universities and universities of applied sciences (Ko-

taplus and AMKOTA). Our specialists provide consultation in infor-

mation technology projects and IT development issues. CSC’s spe-

cial expertise embraces project planning and arranging invitations

for tenders, electronic transactions, user management develop-

ment, and data security. The most extensive development project

in the Information Management Services is RAKETTI.

RAkETTI PROjECT REACHINg FULL SPEED

RAKETTI, a project entity shared by Finnish higher education institu-

tions and the Ministry of Education to support structural develop-

ment through information management, was initiated in its entirety

in 2009. At the beginning of the year, the project embraced three

subprojects, one for creating a common concepts model and data

warehouse service (XDW subproject), one for building a common

basic eAdministration system (OPI subproject), and one for support-

ing quality improvement work based on the overall architecture

principle (KOKOA subproject). During the year, these were supple-

mented with a project that supports research to develop informa-

tion management (TUTKI subproject). At the end of 2009, 84% of all

higher education institutions (92% of the universities and 76% of

the universities of applied sciences) participated in RAKETTI, either

providing guidance or specialist input in the working groups or

pilots of the project.

DATA wAREHOUSINg SERVICE TO SUPPORT kNOwLEDgE MANAgEMENT

The higher education sector’s common concepts model served as

the basis for data warehousing and reporting services that will pro-

vide data, on the one hand, for knowledge management at individ-

ual institutions and, on the other hand, for steering the entire Finn-

ishhighereducationinstitution(XDWsubproject).Attheendofthe

year the subproject had reached the software implementation

phase and the data warehouse was being linked to the systems of

three higher education institutions one phase at a time. Implemen-

tations provide exact experimental information on how well the

concepts model works and about the work amounts still needed

on building the data warehousing service. The data warehousing

InforMATIon MAnAgeMenT SerVICeS



service for higher education institutions is scheduled for launch

during the first quarter of 2010, and the reporting service to sup-

port higher education monitoring and steering at the end of 2010.

In the concepts model subproject, common concepts and ad-

ministrational procedures for the model were implemented for the

entire higher education sector. The concepts model contains the

reliable, uniform information that forms the core of the data ware-

house. The model was created by dozens of specialists from differ-

ent higher education institutions, the Ministry of Education, and

other interest groups. The complete model is composed of 359

concepts or words and 48 diagrams. The diagrams explain the rela-

tionships between the concepts. The concepts model can be used

at the higher education institutions also when other information

systems are being built, and it can be downloaded free of charge at

https://rakettiwiki.csc.fi/wiki/XDW/. The model will be kept up to

date and extended when necessary.

ExPERIMENTAL LEARNINg IN THE OHATV PILOT

OhaTV, a small-scale data warehousing pilot, was completed at the

beginning of 2009. Data on curricula and degrees were transferred

fromthedatasystemsoftheUniversityofJyväskylä,theUniversity

of Oulu, and Hanken School of Economics. The transferred data was

limited in quantity as well as quality to cover data to be reported by

the institutions to authorities. An important objective of the com-

mon concepts model is to remodel the higher education institu-

tions’ administrative data to make it standardized. Piloting was used

to ensure that the concepts model works and to gain experiences

on how the different eAdministration systems can best be linked to

the data warehouse. The experiences gained in this project were

published as a document that can be downloaded from the website

of the Oodi consortium at http://www.oodi.fi/sites/default/files/

OhaTvRaportti.pdf.

A data warehousing service based on a national concepts model helps in the preparation of various types of official report.

HIgHER EDUCATION INSTITUTIONS AgREED ON bUILDINg A COMMON bASIC eADMINISTRATION SYSTEM

The planning of the basic eAdministration system (RAKETTI-OPI)

was continued based on the surveys conducted by the institutions’

own specialists and ordered by the Ministry of Education, as well as

experiences attained from the ProAMK project carried out at univer-

sities of applied sciences, and the OhaTV data warehousing project.

The views of the academic administration players were mapped by

visiting the institutions, arranging sessions under various themes at

academic administration events, and initiating Nordic collaboration

to address the topic.

At the beginning of spring the RAKETTI-OPI subproject produced

a memorandum that describes the target status to serve as the basis

for the basic eAdministration system; the memorandum agenda

was accepted by the higher education institutions after a commen-

tary round. During the autumn, working groups consisting of repre-

sentatives from the higher education institutions used the memo-

randum when they created cooperation structures and definitions

for requirements of the basic eAdministration system.

The RAKETTI project, started in summer 2008, and its subprojects proceeded as planned through 2009. By the end of 2009, the first subprojects were ready to offer a data warehousing service based on a national concepts model to higher education institutions. RAKETTI is a joint project of the Ministry of Education and higher education institutions, and it is coordinated by CSC.

RAkETTI SUPPLEMENTED wITH TUTkI SUbPROjECT TO COVER IT SUPPORT FOR RESEARCH ADMINISTRATION

In summer 2009 the RAKETTI project was extended to cover the IT

support for research and research administration (TUTKI subproj-

ect). TUTKI is steered by managers representing research, develop-

ment and innovation activities in higher education institutions, to-

gether with other key organizations (Academy of Finland, among

others). The work was started at the very end of 2009; the subproj-

ect is expected to generate proposals aiming to increase visibility of

research, development and innovation activities carried out in high-

er education institutions and the means to lighten the administra-

tive work relating to them.

AspartoftheTUTKIproject,ataskforcecalledJUREwasinitiated

to implement services on publication records. The first phase of the

JUREtaskforceclarifiedwhatkindofservicesdifferentsectorsex-

pect relating to publication records and what basic information

aboutpublicationsshouldberegistered.TheJUREprojectgainedin

value and importance during 2009, especially due to the metrics on

the state and quality of research in Finland and the international as-

sessments that showed improvement needs in the assessment of

research quality and especially regarding the knowledge base used

intheassessments.TheJUREprojectisespeciallyfocusedonsafe-

guarding the quality and comparability of this knowledge base.


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wORk ON OVERALL ACADEMIC ARCHITECTURE STARTED

At the beginning of 2009, overall architecture projects were being

started in several higher education institutions. The KOKOA subproj-

ect of RAKETTI is building quality into academic work from the in-

formation management perspective. The aim is to make IT planning,

leadership, implementation, and follow-up an integrated part of the

overall academic strategy. The overall academic architecture is to

improve cost-effectiveness of data management and to produce

uniform descriptions of the core concepts, data, data hierarchies,

and central data resources concerning, for example, students, study

attainments, curricula, and administration. A well-organized main-

tenance model will also enable phenomena, such as changes in the

operating environment, to be taken into consideration. CSC had an

active role also in setting the guidelines for the manuscript project

of the overall architecture.

An overall architecture pilot was created comprising ten institu-

tions, and the building of a common overall architecture model was

initiated. The pilot project consists of the following universities

of applied sciences: Metropolia, Laurea, HAMK, Lahti, TAMK and

PIRAMK, Kemi-Tornio, Rovaniemi, and Seinäjoki, added with the Uni-

versity of Lapland.

CSC SET UP A SERVICES PLATFORM FOR THE OPH.FI wEb SERVICES

After the summer, CSC and theNational Board of Educationbuilt

the oph.fi service. The service consisted of device acquisitions, or-

ganization of the services platform, and web load testing of the

overall system.

CSC STARTED AS THE OPERATOR FOR THE gOVERNMENT’S VIRTU FEDERATION

BasedonthepositiveexperiencesfromtheHakafederationCSChas

provided consultation for the Government IT Management Unit

(ValtIT) in the “Identification and user rights management for gov-

ernment employees” project, which aims to set up a federation for

public administration. As a subcontractor for the Government IT

Shared Service Centre, in 2009 CSC started as the operator of the

Virtu federation.

THE kALMAR UNION ENAbLES ACCESS TO NORDIC HIgHER EDUCATION INSTITUTIONS wITH ONE USERNAME

CSC integrated the Haka user authentication system of Finnish high-

er education institutions to the corresponding Nordic systems. This

project stands unique in the world. CSC signed a contract with the

other Nordic partners to link Finland’s Haka user authentication sys-

tem to Danish WAYF, Norwegian Feide and Swedish SWAMID.

Web-based services requiring user identification have become so

common that the number of user names and passwords that users

need to memorize has become insurmountable. Hence, higher edu-

cation institutions have developed systems that allow access to ser-

vices outside the home university, such as e-Learning services, li-

braries, and administrative services, with only one username-pass-

word combination.

Research and teaching at Finnish higher education institutions is

inevitably international, but previous networks of trust that enable

cross-organizational user identification have covered only one

country.

The project is called the Kalmar Union, and provides secure ac-

cess for the researchers, teachers and students of Finnish universi-

ties to web-based services in other Nordic countries by using the

username and password issued by their home university. The col-

laboration project was funded by NordForsk, an organ of the Nordic

Council of Ministers with responsibility for research funding.

”The idea is that the user is accepted in as many services as possible in the home organization and even when roaming outside, with just one identity.” In his doctoral thesis, CSC’s Mikael Linden has studied identification and authentication in inter- and intra-organizational network services.

EDUUNI SERVICES PLATFORM PROVIDES IT SERVICES FOR THE MINISTRY OF EDUCATION ADMINISTRATIVE FIELD

Eduuni(eJob)isaserviceconceptandtechnicalplatformthatwas

developed for public administration services. The work was super-

vised by the Ministry of Education, and conducted in collaboration

with offices under its jurisdiction and CSC. CSC provides the Ministry

of Education with consulting and use-related services to develop

the eduuni services. The eduuni concept embraces working group

services and the SALAMA item management system, started at the

beginning of 2010. The concept also involves strong collaboration

on information management between public offices.

CSC SERVICES PLATFORM FOR THE UNIVERSITIES’ PERSONNEL AND FINANCE ADMINISTRATION

CSC invested a considerable amount of work in the planning and set-

ting up of the system implementation of the SAP-based system for

the service center of the universities’ personnel and finance admin-

istration. CSC is providing the services platform for the systems. Al-

though relatively massive, the project was completed as scheduled

and successfully taken to production.



FJELLS © Juha Fagerholm


CSC provides high-quality computing capacity to meet research and

product development needs for modeling and simulations. CSC’s

supercomputers execute highly efficient parallel programs. The

computing efficiency of supercomputers can be as much as thou-

sands of times that of a single processor. Typically, parallel comput-

ing reduces the computing time needed for solving a problem

which makes it possible to use more accurate models.

In addition to computing resources, CSC also provides its cus-

tomers with state-of-the-art expertise in computing science. CSC’s

specialists help researchers in selecting and developing methods,

and selecting appropriate program; they provide instructions on

how to use and parallelize the programs, how to scale them and up-

load them onto CSC’s machines.

HIPPU, CSC’S NEw APPLICATION SERVER

In JanuaryCSCacquired twonewHewlett-PackardProLiantDL785

G5 servers. Used together these form an application server and it

will be used mainly for running interactive serial jobs. Murska or

Louhi supercomputers are recommended for parallel jobs.

Bothserversincludeeightquad-coreprocessors.Thusthetotal

number of processor cores is 64. A special feature of the new appli-

cationserversistheirlargesharedmemorycapacities:onecontain-

ing 512 gigabytes and the other 256 gigabytes of memory.

Although the system consists of two separate servers, for

the user it appears to be a single server with the domain name,

hippu.csc.fi.

FINAL REPORT OF FINHPC PUbLISHED

The FinHPC project, aimed at improving the performance of super-

computer software and sponsored by Tekes, has published its final

report. The project, which ended on December 31st, 2008, raised

the performance of Finnish HP-computing and programming ex-

pertise to the highest international level. Thanks to FinHPC, the rec-

ognition of CSC and Finland, too, has risen to a new level, and the

project made CSC eligible to participate in grand European HPC

projects such as PRACE.

Almost 30 scientific programs were processed in the FinHPC

project. Most of them have been created to serve researchers’ own

needs. Since scientists usually lack in-depth knowledge of program-

ming, programs have not been able to utilize the full capacity offer-

ing of the new supercomputers. Hence, significant improvements

adding to the performance capacity were made to most of the pro-

grams during the FinHPC project.

FinHPC was a joint project between several universities and CSC.

The HPC-lab of Åbo Akademi University played a very significant

role in code optimization. In addition to optimization, the project

CoMPUTIng SerVICeS

CoMPUTIng SerVICeS


arranged training courses in parallel programming, code optimiza-

tion, and use of software development tools.

Participation in this project was also especially important for the

HPC-lab of Åbo Akademi University, because through the project the

group was able to raise its profile as the leading European center of

excellence in fusion plasma simulation. HPC-lab participates in the

EUFORIA project being responsible for code optimization and paral-

lelization of the simulation codes for 12 fusion reactors.

The tangible outcome of the FinHPC project was 27 improved

codes or code libraries. In addition, a benchmark set for load testing

was also created, and it was used at the acquisition phase of CSC’s

new supercomputer. The project staff organized training and par-

ticipated in international conferences and workshops. A total of 12

scientific articles and a few articles for the general public were pub-

lished during the project.

The project was initiated at the beginning of April 2005 and

completed at the end of 2008. The full report in English can be

downloadedinPDFformatat:http://www.csc.fi/english/csc/publi-

cations/guidebooks

MORE POwER TO PRACE PROTOTYPE

InJune,morepowerwasaddedtoLoviatar,oneofthePRACE(Part-

nership for Advanced Computing in Europe) project’s six proto-

types. Loviatar is an extension module to CSC’s supercomputer

Louhi. The processors of Loviatar were upgraded to new-generation

AMD Opteron Shanghai 2.7 GHz quad-core processors. The exten-

sion module contains 1,440 compute cores. The upgrade increased

the L3-level cache memory available to the processors from two to

six megabytes.

The extension module’s capacity is primarily reserved for the

PRACE project. CSC’s other users can employ the additional power if

and when free capacity is left over from PRACE users. An automatic

batch run system directs jobs to the processors that have capacity free.

Limited opportunities to try out Loviatar and the other PRACE

prototypes have been afforded to researchers from all parts of the

world, even those outside the project.

After the processor upgrade the theoretical maximum capacity

exceeded100Tflop/s,i.e.ahundredbillioncalculationspersecond.

gRAND CHALLENgES

Computational Grand Challenge projects are aimed at high-impact

scientific research that requires computational or data resources ex-

ceeding CSC's standard project quotas or level of services. CSC allo-

cates a support group for each GC project, and the GC calls are ar-

ranged twice a year. A call for proposals was arranged during the

latter part of 2009, applications were accepted both for computa-

tional and data-intensive projects. During the past year a total of

nine projects were ongoing, five being new projects and four were

completed.

A METHOD FOR VIRTUAL DRUg SCREENINg

Professor Olli Pentikäinen and his research group started a Grand

Challenge project to develop a virtual screening method for drug

molecules. Using a new approach, the aim of the C-LIVE project is to

screen a large number of proteins to find active drug candidate mol-

ecules that affect selected target proteins.

Many of the molecular mechanisms of the cell are based on di-

rect interactions between proteins. Therefore, from the medical

point of view, the interest is focused on small molecules called li-

gands that block or strengthen these interactions. However, the

structural interfaces between proteins are not usually considered to

be potential docking sites for drug molecules, because two things

impedefindingsuitabledrugmolecules:(1)the3-dimensionalcon-

struction of proteins, or conformation, may change substantially

when they interact with other proteins, and (2) proteins’ structural

interfaces are usually rather flat with only few cavities where ligands

could bind.

In the C-LIVE project, Pentikäinen’s group aims to develop a

method that could facilitate identification of molecules that are po-

tentiallyabletoaffectafewoftheprotein–proteininteractivesites

regarding signal transmission. On the other hand, the method’s reli-

ability will be studied using the traditional target proteins of drug

development.

The research group will use a total of two million processor hours

on CSC supercomputers.

CoMPUTIng SerVICeS

© M

ich

ael K

arls

son

/ Å

bo

Aka

dem

i


CoMPUTIng SerVICeS

LARgE-SCALE SIMULATION ON CYTOCHROME FUNCTION

Photosynthesis and respiration are core cellular processes which

provide energy in form of ATP for all cellular functions. ATP synthe-

sis requires a proton gradient across a cellular membrane, generat-

ed via electron and proton transporters organized in chains where

cytochrome complexes play a crucial role as they contribute to the

generation of an electrochemical potential across a cellular mem-

brane. Despite its crucial biological role and numerous experimental

studies, the mechanism of cytochrome action is far from under-

stood. Understanding the functions of cytochrome complexes is

central to all cellular processes, since without ATP synthesis there

are no cellular processes.

In their Grand Challenge project, Thomasz Róg, Ilpo Vattulainen,

Oana Cramariuc and Karol Kaszuba (Tampere University of Technol-

ogy) will conduct large-scale molecular mechanism and quantum

mechanism simulations for the full cytochrome bc1 complex in an ex-

plicit lipid and saline environment. The objective is to resolve the

mechanism(s) of cytochrome action. The Grand Challenge project will

provide information on the pathways of proton and electron transfer,

the dynamics of the main elements of the system, and the interac-

tions stabilizing essential moieties of the protein complex.

The whole system subject to simulation consists of 400,000 atoms

and to simulate its function during 200 nanoseconds consumes

3,500,000 processor hours.

IRRADIATION EFFECTS IN CARbON AND bORON NITRIDE NANOSTRUCTURES

Effects of irradiation on bulk materials are well known, but they are

not well understood in nanomaterials, including technologically im-

portant carbon and boron nitride nanostructures. With his research

group, Arkady Krasheninnikov will simulate the response of nano-

systems to irradiation, defect creation, and annihilation. First-prin-

ciples molecular dynamics simulations will be combined with elec-

tronic structure calculations using advanced density functional the-

ory methods. This kind of research is computationally expensive

and Krasheninnikov’s research group will use four million processor

hours.

Irradiation is a powerful tool for engineering various nanostruc-

tures; the lack of fundamental understanding of defect production

and annihilation limits the use of electron and ion irradiation for engi-

neering nanostructures with desired properties.

COMPUTATIONAL IMPUTATION OF THE gENOME-wIDE INFORMATION OF 30,000 FINNS

The research group of Samuli Ripatti (Institute for Molecular Medi-

cine Finland, FIMM) studies variation in the human genome using

large population cohorts. Their purpose is to find genes associated

for instance with cardiovascular diseases and cholesterol levels and

to develop statistical and computational methods to assist in the

search.

The research group is launching the FinSeq project (Imputation of

Finnish population cohorts for identification of common disease as-

sociated variants utilizing 1000 Genomes data) to augment the ge-

nome-wide samples of 30,000 Finns through computational meth-

ods. The project employs a new approach where Finnish genotype

data acquired through genome-wide association studies (GWAS) will

be imputed through statistical models and with the sequence data

generated in the 1000 Genomes project.

Using a larger cohort will give a greater probability of distinguish-

ing the real disease genes from false ones and to analyze more effi-

ciently the causal genetic variants underlying diseases. Due to the

large volume of material involved, the FinSeq project will take up a

substantial quantity of computing resources and several terabytes of

storage capacity.

bIOPOLYMER DYNAMICS IN NANOPIT gEOMETRIES

In their RePoDyn project (Realistic Polymer Dynamics in Confined

Nanopit Geometries), Santtu Ollila and Tapio Ala-Nissilä (Helsinki

University of Technology) are modeling biopolymer dynamics in

the nano and micrometer scale with full hydrodynamics. The biopo-

lymer models being used have elastic properties that are similar

to organic polymers, for example, DNA, RNA, and starch found in

living organisms.A still frame of a boron nitride sheet just after an electron collision. Atoms are still moving.

© K

rash

enin

nik

ov


CoMPUTIng SerVICeS

The aim of this study is to explain the experimentally observed

rich and subtle dynamics of biopolymers in the complex nanopit ge-

ometry.

The nanopit geometry consists of a strongly confining slit region

followed periodically by a pit in which the polymer chain can swell.

The dynamics depend on the contour length of the polymer, the

nanopit geometry, and the flow conditions. Understanding and con-

trol of the dynamics has direct implications, for example, in pharma-

ceuticals manufacturing processes and, more broadly, nanotechnol-

ogy fields that require manipulation and positioning of polymers in

the nanoscale. Experiments directly related to the modeling are

underway at Brown University (Providence, U.S.A.) in Prof.Derek

Stein's group.

THREE FINNISH RESEARCH PROjECTS gRANTED ACCESS TO DEISA RESOURCES

Europe’s HPC infrastructure DEISA has announced the latest re-

source allocations on Europe’s most powerful supercomputers. Fif-

ty scientific projects have been awarded supercomputing resources

totaling more than 60 million processor hours, through the DEISA

Extreme Computing Initiative (DECI).

These DEISA Extreme Computing projects will each have access

to resources at one or more of the 11 DEISA partner sites which oper-

ate fourteen of the Top 100 most powerful supercomputers in the

world, including the only two European computers in the Top 10.

Successful projects are chosen for their potential to achieve

ground-breaking scientific results through the use of supercomput-

ers, enabling them to run more detailed and accurate simulations of

scientific problems than was previously possible.

Alison Kennedy, Coordinator of DECI said, “DEISA is delighted to

be able to provide compute resources and applications enabling as-

sistance to researchers in so many innovative projects. This year, we

attracted 75 proposals from 21 European countries. This shows the

wide appeal and relevance of DECI across Europe.”

The following three projects from Finland were granted access

to DEISA resources:

ADAPTIVE ESTIMATION OF CLIMATE MODEL CLOSURE PARAMETERS

International climate policy is critically dependent on the future cli-

mate simulations. While the climate models are becoming increas-

ingly accurate, inherent uncertainties remain. One of these is the

fact that all models contain some free (closure) parameters related

to the modeling of sub-grid scale processes (such as clouds or tur-

bulence). Optimal closure parameter values are approximately

known but their uncertainties are not well understood. Generally, it

is very hard to determine the parameter values based on observa-

tions.

In the ADAEST project, led by Prof. Heikki Haario from Lappeen-

ranta University of Technology, a computational parameter estima-

tion method, Markov chain Monte Carlo (MCMC), is applied to esti-

mate the closure parameter values and their uncertainties in the

ECHAM5 atmospheric general circulation model. The research group

will apply modern adaptive MCMC sampling techniques, developed

by the group. The cost function to be minimized consists of the

squared differences between the dominant modes of the observed

and simulated climate variability. The MCMC analysis interprets this

costfunctionasaBayesianlikelihoodfunction.IntheMarkovchain,

a large number of climate simulations are performed, making the

approach of the ADAEST project computationally very demanding.

The adaptive sampling technique implies, however, large computa-

tional savings. Thanks to the DEISA resources, significant scientific

and computational advances can be obtained in the research of the

reliability of climate predictions. The institutions taking part into this

projectareLappeenrantaUniversityofTechnology:Departmentof

MathematicsandPhysics,HelsinkiUniversityofTechnology:Depart-

ment of Information and Computer Science, and Finnish Meteoro-

logical Institute.

SIMULATIONS bEYOND THE STANDARD MODEL THEORIES

The Standard Model of particle physics has been extremely success-

ful in describing all the results from particle physics experiments.

However, there are tantalizing hints for physics beyond the Stan-

dard Model from astrophysical observations and also from theoreti-

cal analysis. Thus, it is possible that LHC (Large Hadron Collider) will

find signs of this ’new physics’. Technicolor and other strongly inter-

acting models are among the most popular alternatives for the new

physics. These models rely on so-called strong coupling phenome-

na, making their study with analytical methods difficult and often

impossible. Only large-scale numerical simulations can yield reliable

quantitative results; however, so far only initial studies have been

made, and most of the relevant questions remain open.

The simulation set-up resembles the well-studied lattice QCD

(Quantum Chromodynamics), but with different gauge fields and

fermions in different representations. The research group led by

Kari Rummukainen has developed a very flexible simulation pro-

gram suitable for studying this class of problems. It can simulate any

gauge group and fermions with varying representations. In this proj-

ect the research group aims to study the physical particle spectrum

and the evolution of the coupling constant as a function of the en-

ergy in a selected set of candidate theories. The institutions taking

part into this project are University of Helsinki, Department of Phys-

ics,andUniversityofJyväskylä,Finland.

PLASMA SIMULATIONS wITH ELMFIRE

Understanding the plasma turbulence is of major importance for

success of ITER, which is in turn the most important step in the de-

velopment of fusion energy. The research group led by Jukka Heik-

kinen is working with a gyrokinetic plasma simulation code ELM-

FIRE. It has been developed to study the dynamics of turbulence

and its influence on plasma global behavior. ELMFIRE can be used,

and has already been used, to understand the physics underlying

the formation and development of plasma turbulence and its unde-

sirable effects on plasma confinement.

Of particular importance in the study of plasma confinement is the

transition between L and H states, referring to Low and High confine-


CoMPUTIng SerVICeS

mentstates.UnderstandingthewaytoinduceanL–Htransitionina

plasma would lead to an immediate increase of plasma confinement

applicable to different plasma devices. The DECI resources obtained

for this year have supported simulations where agreement of the

simulated plasma poloidal rotation and contemporary synthetic di-

agnostics with the experimentally measured Doppler reflectometric

signal was observed. Further understanding of pedestal transport

and its control has been acquired. The diagnostics of turbulent

structures has been improved by correlation studies. These calcula-

tions have been so far promising and are now continued with more

memory-efficient code version (extending the calculations into the

SOL region) for longer (and heavier) simulations to collisional time

scale. Institutions taking part to this project are VTT (Euratom-Tekes

association), Helsinki University of Technology (Euratom-Tekes asso-

ciation), Finland and Universidad Nacional de Educación a Distancia,

Spain.

© E

u Q

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e, D

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PLACID SEA © Janne Ignatius


CSC maintains and develops the Finnish research and education

network Funet, an extremely reliable high-capacity network. Funet

links higher education institutions and research institutes providing

them with national and international network connections. Funet

has approximately 350,000 users. It is one of the most advanced re-

search networks in the world. The Funet network services also in-

clude the Funet CERT network security services, video conferencing

and streaming services, and wireless network roaming. The pan-

Nordic NORDUnet network allows connection to international re-

search networks and access to international services.

ROAMINg IN THE FUNET NETwORk ExTENDED

CSC started to offer a national Funet network roaming service for

students and staff of Funet member organizations. Network roam-

ingisbasedonreciprocitybetweenorganizations:iforganizations

have signed a roaming contract, their users can use the public ac-

cess networks of all roaming member organizations. Hence, visiting

researchers and students are allowed fast and convenient network

access by using the identification codes supplied for their home or-

ganizations.

TheservicewasextendedintheTampereareainJune,whenLan-

gaton Tampere (Wireless Tampere), a widely dispersed network

roaming community in the Tampere area joined the Funet network

roaming service.

All Funet members can join Funet network roaming. In addition

to the Funet roaming service, the Funet network also hosts the in-

ternational eduroam network roaming, which is open only for re-

search and teaching organizations, and it involves higher technical

requirements to allow access to the wireless network. Eduroam us-

ers visiting another organization are allowed network access using

their own organization’s credentials. Hence, they have easy and safe

connections when roaming in different higher education institu-

tions around Finland and Europe. Eduroam works also in Australia.

Currently, 16 wireless networks within Funet and Sparknet, a net-

work roaming community from Turku have been connected to Fu-

net network roaming.

LIgHTPATH REACHED OULU

CSC is building a new generation backbone network, which is based

on leased dark fibers and the wavelength division multiplexing tech-

nology (WDM). It enables an almost unrestricted communication

capacity, because one fiber can carry multiple data streams of 10 or

40 Gbps by using different wavelengths.

The fiber network makes it possible to offer dedicated, point to

point “light path” connections, which can continue worldwide

through NORDUnet or European GÉANT2 networks. The fiber net-

work is used for internet connections of universities and research

organizations as well. The new network is already in use from Espoo

fUneT neTwork SerVICeS



to Turku and Tampere. The latest connection to Jyväskylä was

opened at the end of March. During the spring and summer the im-

plementation was continued in Vaasa and Kuopio. In December the

connectionwasopenedinOulu.Bysummer2010theconnections

will cover all university towns in Finland.

HIgHER EDUCATION INSTITUTES wANT CENTRALIzED SERVICES ON VIDEO COMMUNICATIONS

The use of video communications is expected to increase in Finn-

ish higher education institutions where shared, centralized servic-

es at the national level are needed. This is the message that

emerged following a survey by the Educational Centre for ICT at

the University of Helsinki published in January. The survey was

funded by CSC.

The survey data was collected by means of internet question-

naires directed at specialists and users of digital video services, as

well as through workshop meetings of specialists. Cooperation be-

tween the VideoFunet participants must be increased and their ac-

tivities have to be intensified, and network coordination central-

ized. Additionally, the survey showed that there is a need for cen-

tralized video communications services. The wish list includes a

network video service or an 'academic YouTube', a video confer-

encing bridge service, and monitoring the development of web

conferencing systems.

SCIENCE PROgRAMS 24 HOURS A DAY FROM FUNET ANTENNA

The fast connections of the Funet network enable the transmission

of high-quality television broadcasts. The programming of the Fu-

net Antenna service produced by CSC and Maxisat Ltd was expand-

ed in February to include the programs of an American round-the-

clock science channel.

A new feature of the service is Research Channel, which shows

programs about various academic subjects produced by American

universities and research institutes; the programs range from tech-

nology to the natural sciences and the humanities. MIT, Stanford,

Yale, Microsoft Research and the National Science Foundation are

among the organizations producing these programs.

The channel shows science programs around the clock and it can

be seen by 35 million viewers in different parts of the world as sat-

ellite transmissions, and on the cable TV networks of cities and

campuses.

CSC CHOSE jUNIPER ROUTERS

Cygate Finland and CSC signed a five-year contract on supplying

backbone routers for the Funet research network. The contract also

covers extensions to the backbone routers and the maintenance

and specialist services needed.

During the contract period important developments are expect-

ed to include a breakthrough with the IPv6 technology and an in-

creasing need for IP multicast technologies. Cygate provides CSC

with a faster, more efficient system with better scalability.

FUNET LINkED TO NEw TRANS-ATLANTIC POLAR NET-wORk CONNECTIONS

Funet attained a new high-speed international network connection,

when the Scandinavian NORDUnet, the Canadian CANARIE, and the

global GLORIAD opened their undersea optical fiber connection for

use between the Scandinavian countries and North America.

NORDUnet, CANARIE, Canada’s Advanced Research and Innova-

tion Network, and the GLORIAD (Global Ring Network for Advanced

Application Development) project funded by the US National Sci-

ence Foundation NSF, launched their high-speed network connec-

tion IceLink. This arctic region network, passing through Iceland and

Greenland, links the national research and education networks of

Canada, the USA, and the five Nordic countries.

IceLink further improves the data transfer capacity between the

networks that represent the forerunners in the field. Iceland gained

the fast network connection that was long over-due. CANARIE, on

the other hand, gained a cable connection to Europe directly from

Canada. Prior to IceLink, CANARIE’s only link to Europe was via a con-

nection originating in New York.

Most of the costs from the new undersea optical fiber connection

will be paid by NORDUnet. Other financiers are CANARIE and the

GLORIAD project.

NORDUnet is a joint collaboration by the five Nordic National Research and Education Networks in Denmark (Forskningsnettet), Iceland (RHnet), Norway (UNINETT), Sweden (SUNET), and Finland (Funet). It operates a world-class Nordic and international network and e-Infrastructure service for the Nordic research and educa-tional community. For additional information, please visit www.nordu.net.


December 2009

GÉANT and sister networks enabling user collaboration across the globe

GÉANT CoverageALICE2-RedCLARA NetworkEUMEDCONNECT2 NetworkTEIN3 NetworkBSI NetworkUbuntuNet Alliance

At the Heart of Global Research Networking

GÉANT is co-funded by the European Commission within its 7th R&D Framework Programme.This document has been produced with the financial assistance of the European Union. The contents of this document are the sole responsibility of DANTE and can under no circumstances be regarded as reflecting the position of the European Union.

GLORIAD is constructed from a fiber-optic ring of light encircling the northern hemisphere connecting universities and national laboratories with individual network circuits providing up to 10 Gbps. In its present topology it represents a true “ring of rings” around the earth, providing richer bandwidth and redundant network paths for improved reliability. For additional information, please visit www.gloriad.org.


CONNECTIONS 2010

NORDUnet

Hamburg

Copenhagen

Internet

Internet

Reykjavik(IceLink: Greenland, Canada, USA)

London

New York

Amsterdam GÉANT

PoznanGLORIAD

GLORIAD

TRANSMISSION CONNECTIONS

FIBER CONNECTIONS

NORDUNET

INTERNATIONAL CONNECTIONS

IP- and fiber network connection sites

Fiber network connection sites

Rovaniemi

Sodankylä

Kemi

Oulu

Kajaani

Kuopio Joensuu

Mikkeli

Lappeenranta

St. PetersburgKotka

Lahti

HelsinkiEspoo

Salo

Pori

Vaasa Seinäjoki

Kokkola

Hämeenlinna

Tampere

Jyväskylä

Stockholm RUNNet

KouvolaRauma

TurkuOslo

The superfast Funet data network links Finnish universities, universities of applied sciences, and public research institutes with each other as well as to international research networks and the commercial internet. The network is maintained and developed by CSC in cooperation with the Funet member community. Funet has approximately 350,000 users. The services provided through the Funet network are used by approximately 80 member organizations.


Aalto University •Arcada Polytechnic•Central Ostrobothnia University of •

Applied SciencesDiaconia University of Applied Sciences •Finnish Academy of Fine Arts•HAAGA-HELIA University of •

Applied SciencesHAMK University of Applied Sciences•Hanken School of Economics•Helsinki Metropolia University of •

Applied SciencesHUMAK University of Applied Sciences•Jyväskylä University of Applied Sciences•Kajaani University of Applied Sciences•Kemi-Tornio University of Applied Sciences•Kymenlaakso University of •

Applied SciencesLahti University of Applied Sciences•Lappeenranta University of Technology •Laurea University of Applied Sciences•Mikkeli University of Applied Science•National Defence University•North Karelia University of •

Applied SciencesNovia University of Applied Sciences•Oulu University of Applied Sciences•Rovaniemi University of Applied Sciences•Saimaa University of Applied Sciences •Satakunta University of Applied Sciences•Savonia University of Applied Sciences•Seinäjoki University of Applied Sciences•Sibelius Academy•TAMK University of Applied Sciences•Tampere University of Technology•The Theatre Academy•Turku University of Applied Sciences•University of Eastern Finland•University of Helsinki•University of Jyväskylä•University of Lapland•University of Oulu•University of Tampere•University of Turku•University of Vaasa•Vaasa University of Applied Sciences•Åbo Akademi University •

OTHER MEMBER ORGANIZATIONS

Aalto University Student Union•Academy of Finland•Bank of Finland•Certia – the Service Center of Universities •CSC – IT Center for Science Ltd.•Finland's Environmental Administration•Finnish Communications Regulatory •

Authority (FICORA)Finnish Forest Research Institute•Finnish Literature Society•Finnish Medicines Agency•Finnish Meteorological Institute•Finnish National Board of Education•Finnish National Gallery•Finnish Student Health Service•Foundation for Finnish Inventions•Geological Survey of Finland•Hospital District of Helsinki and •

Uusimaa Institute for Russia and Eastern •

EuropeKiinteistö Oy Opintanner•Kuopio University Hospital•Lappeenranta Student •

Housing FoundationMinistry of Education•National Audiovisual Archive•National Board of Antiquities•National Institute for Health •

and WelfareNational Repository Library•Otaverkko Ltd•Parliament of Finland•Pirkanmaa Hospital •

District

Radiation and Nuclear Safety Authority of • Finland (STUK)

Research Institute for the Languages of • Finland

Statistics Finland•Tampere Student Housing Foundation•Tekes – the Finnish Funding Agency for •

Technology and InnovationVTT Technical Research Centre •

of Finland

Funet member organizations in the beginning of 2010


FUNET OPTICAL FIbER CIRCUIT AND FICIx3 POINT TO OULU

In February the work was completed on an optical fiber circuit for

the Oulu region, built in collaboration by CSC and the Funet mem-

ber organizations in Oulu. The optical fiber circuit serves as the

transmission medium through which all members can build secured

connections between the participating campuses.

The optical fiber circuit also made it possible to create a back-

bonelinkfromFunettotheFICIX3IXPpointwhereFunetandother

Finnish operators exchange Internet traffic. The third IXP point in

Ouluwastakenintouseinautumn2008.TheprevioustwoFICIXIXPs

are both in the metropolitan area.

CSC CONNECTED RUSSIAN RESEARCH NETwORk TO NORDUNET wITH FIbER TECHNOLOgY

RUNNet, the Russian research network received an advanced fiber

optic connection to the West. It was connected to the NORDUnet us-

ing Dense Wavelength Division Multiplexing (DWDM) technology at

the end of 2009. Instead of the previous bandwidth of 2.5 Gbps, the

new connection enables multiple parallel 10 Gbps paths.

CSC was closely involved in the planning and implementation of

the connection. For example, the physical switch is situated at the

premises of CSC. The upgraded connection enables better opportu-

nities for collaboration in various research areas between Russia and

Finland, as well as with the other Nordic and European countries.

The new connection enables the transmission of huge amount of

data between Russian and European research institutes.

IPV6 IN THE FUNET NETwORk

The Funet network has provided readiness for the new IPv6 proto-

col since the early 2000s. Funet’s network equipment supports the

IPv6 connections and since 2001 about 20 Funet customer organi-

zations have received IPv6 addresses. The Funet network services

have gradually been modified for IPv6 readiness. Recently the IPv6-

related activities have focused especially on domain name services.

The Funet Network service area has actively worked to promote

the implementation of IPv6. In 2009, Teemu Kiviniemi completed

his master’s thesis ”Implementation of an IPv4 to IPv6 Multicast

Translator” presenting a protocol converter for multicasting. The

thesis work was conducted as collaboration between Helsinki Uni-

versity of Technology and CSC.

Byusingaprotocolconverter,multicastservicesoftheIPv4net-

work are accessible through the IPv6 protocol, and hence, for ex-

ample, the IPTV broadcasts supplied by Funet Antenna can be con-

verted for reception over the IPv6 network. The protocol converter

service based on the thesis will be adopted at Funet in 2010, abreast

with other IPv6 transition services. No modifications are needed in

the equipment sending or receiving multicast material, so using the

service is easy.

THE FUTURE INTERNET IS ALREADY HERE

CSC’s Funet Network Services participated in the ICT SHOK project,

supportedbyTekes– theFinnishFundingAgency forTechnology

and Innovation. As a result, a description of the Future Internet test-


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DoMeSTIC fUneT TrAffIC 2004–2009


InTernATIonAL fUneT TrAffIC 2001–2009

bed architecture was produced. Kaisa Haapala, Pekka Savola, and

Jari Miettinen from CSC contributed as authors of the Research

Report.

The Future Internet was tested over various network layers or ar-

chitectural levels. The testbed for the physical connectivity are light

paths implemented using Funet's dark fiber network based on Wave-

length Division Multiplexing (WDM). An end-user sees the connec-

tion as a local area network although the access points can be in dif-

ferent cities or even in different countries. Potential challenges are

associated with the final stage from the network edge to the end

user’s computer. Optical fiber infrastructure may not be available

and delivery times can be long. One solution to this problem is pos-

sibly a media converter and the use of copper instead of the optical

fiber.

Another alternative is to offer a wireless access to the testbed

with base stations connected to the customer access networks.

The network layer of the testbed was regular IP connectivity, sup-

porting both IPv4 and IPv6 protocols. Additionally, Internet peering,

outsourced research network services, and extended connectivity

utilizing OpenVPN to provide virtual research network connectivity

were tested.

As the third level of connectivity, the Future Internet project

tested the AAA (Authentication, Authorization, Accounting) con-

nection. The protocols tested included RADIUS, Shibboleth and

DIAMETER protocols. RADIUS is used for user authentication in

wireless networks like Eduroam and Funet WLAN roaming. Shibbo-

leth extends the connectivity to the user authentication, authori-

zation and accounting on the application level. DIAMETER enables

dynamic authentication, authorization, and accounting. As a prac-

tical example the project used the Haka federation, which makes it

possible to offer and use web services between Haka member

organizations.

THE FUNET CERTIFICATE SERVICE OPENED

In December CSC signed a contract that provides Funet member or-

ganizations with an opportunity to join a certificate service. The ser-

vice is included in the Funet fee.

Certificates are used for securing network connections to show

that the communicating parties can trust each other’s identities.

The Funet certificates are produced by Comodo CA Limited, one

of the world’s leading providers of certificates. Comodo provides

the member organizations of TERENA (Trans-European Research

and Education Networking Association) with an unlimited number

of certificates at a fixed price.

Initially the Funet certificate service concerns phone line connec-

tions only but, if necessary, the contract can be extended to cover

fournewcertificatetypes:

e-ScienceServerCertificate–forauthenticationofGridservers •

and services

PersonalCertificate–foridentificationofusersandforsecured •

exchange of e-mails.

e-SciencePersonalCertificate–foridentificationofGridusers •

Code-signingCertificates–forauthenticationofsoftware •

distributed over the Internet.

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Outbound

Inbound



ROCK PLANTS AND A FOG WALL © Joni Nevalainen


In 2009, 643 computing projects were ongoing in the CSC server

environment, with 1,561 users. During the year, 280 new projects

were opened embracing 22 different fields of science, and new user

names were registered for 1,006 new customers. At the year end,

the total number of registered customers was 3,617.

In addition to computation users, CSC’s clientele contains an in-

creasing number of customers who receive their services through

licenses that CSC administrates, either as local installations or from

servers maintained by a third party. These services include several

chemistry, geosciences and biosciences database services, and

structural analysis programs. At the end of 2009 the estimated total

number of these users was approximately 2,500.

MURSkA COMPUTINg CLUSTER wAS THE MOST POPULAR

Throughout the year, CSC’s computing servers were in active use

and the monthly number of logins on CSC servers averaged 171,000.

A new record was again set in October 2009: 310,061 logins per

month. The previous record, 142,364 logins per month was reached

in October 2008. Since May 2009, this value was exceeded almost

every month. For the first time, the total number of logins per year

exceeded two million. The most popular computing server was

Murska, which had 430 customers. The next most frequently used

servers were the new application server, Hippu (338 customers) and

supercomputer Louhi (328 customers).

THE HEAVIEST USE IN NANOSCIENCE AND PHYSICS

Looking at the figures by discipline, projects on nanoscience and

physics have used the most computing time, their share being 30

and 26 percent, respectively. The next heaviest users were biosci-

ences (15%), chemistry (13%), grid usage (9%), and astrophysics

(4%). This was the first time that nanoscience was the biggest user

discipline, and the first time that biosciences beat chemistry in total

usage and ranked third. Of the total, the combined usage of nano-

science, physics, biosciences, and chemistry projects was more

than 80 percent. Compared with other disciplines, astrophysics

showed the strongest growth.

As a computation customer, the University of Helsinki was the

biggest user organization with 27 % of the usage. The next biggest

were Helsinki University of Technology (18 %), the University of

Jyväskylä (14%), theGrandChallengeprojects (11%),DEISAcom-

puting (10 %), and the University of Oulu (9%). Other higher educa-

tion institutions used a total of 11 percent of the computing time.

During 2009, five major projects were granted the Grand Chal-

lenge (GC) status entitling to massive computing time. Of these, the

projects of Ilpo Vattulainen (Tampere University of Technology),

Alex Bunker (University of Helsinki), and Maarit Korpi (University of

Helsinki) were started in late autumn 2008, and the computing was

mostly carried out in early 2009. The new GC projects, elected from

the2008GCproposals,werestartedinMarch2009,i.e.theCBC-ONE

project of Tomasz Róg (Tampere University of Technology) and the

CUSToMerS AnD CoLLAborATIonS


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C-LIVE project of Olli Pentikäinen (University of Jyväskylä). These

projects were run mainly between April and December. In August CSC

arranged a call for 2009 GC proposals, and the results were an-

nounced in November. The Grand Challenge status was granted to the

FinSeq project of Samuli Ripatti(UniversityofHelsinki),theIECBN09

project of Arkady Kraskeninnikov (Helsinki University of Technolo-

gy), and the Repodyn project of Tapio Ala-Nissilä (Helsinki University

of Technology). These projects were initiated at the turn of November

–Decemberandarecontinuingduringthefirsthalfof2010.

The DEISA project has actively utilized CSC’s supercomputer en-

vironment in 12 computing projects, and the biggest of these were

the HPQCD, SoMQarck, and HPQDC2 projects of the EPCC, the

PHASEALL,RNAHIVandBICaPSprojectsofCINECA,andthePLANCK

project of Hannu Kurki-Suonio (University of Helsinki). The new

DEISA projects elected in the autumn 2009 call will start their jobs in

early 2010. The DEISA projects have represented roughly 10 percent

on the total computing usage at CSC and the computing has been

performed on Louhi. Correspondingly, Finnish DEISA projects have

received computing resources from the supercomputing environ-

ments of EPCC, IDRIS, CINECA, and LRZ.

CSC’S OPEN SOURCE gPAw THE MOST POPULAR APPLICATION SOFTwARE

CSC’s open source code GPAW of density functional theory was used

the most and for the first time, its usage figures were higher than

those for quantum chemistry. GPAW’s share of software usage was

as high as 39 percent. The next most popular software were NAMD

(22 %) for biosciences and Gromacs (19 %), Turbomole (4 %) and

Gaussian (2 %) for quantum chemistry. The total share of all quan-

tum chemistry programs was 27.7%. The total usage of application

programs being registered was 22 million processor hours, i.e. more

than a third of all processor usage. The usage on Louhi was more

than83percent.Basedonthenumbersofusers,themostpopular

programswereMatlab (mathematics, 238 users), EMBOSS (biosci-

ences (177), and www-Lemmie (linguistics (168).

THE ACADEMY OF FINLAND CENTRES OF ExCELLENCE USINg A THIRD OF COMPUTINg TIME

The customer projects run by the Academy of Finland Centres of

Excellence have been separately monitored since the beginning of

2005. In 2009, the Centres of Excellence used 32.1 percent of CSC’s

computing resources. Most of this usage (over 98%) represents the

computing carried out by the Centres of Excellence nominated for

the period 2006–2011. Usage by the Centres of Excellence has

shown a generally rising trend, with previous years’ figures 25.9%

(2005), 29.9% (2006), 38.5% (2007), and 29.5% (2008).

CSC’S HELPDESk REFORMED

CSC developed its customer services by changing the former CSC

Helpdesk into a multiple-function ServiceDesk. The ServiceDesk is

managed by a coordinator specifically appointed for this task, pro-

viding a single contact point for customers.

As part of the development of customer services, CSC imple-

mented a new Request Tracker issue tracking system for internal

operations with a service line for 12 different functions. During

2009, the ticket service handled 5700 service requests, most of

them addressed to the Haka service (1,888), the Funet NOC emer-

gency service (1,712), and Helpdesk (1,006).

This new tool allows unambiguous task allocation at CSC while

solutions to problems and email correspondence are stored in a da-

tabase. The new issue tracking system is making internal coordina-

tion of tasks easier at CSC, and the persons on call can monitor the

process, making sure that customers’ service requests meet the

quality requirements within the time frame agreed.

CUSTOMER COMMUNICATION

During the past year CSC published 116 newsletters and 108 cus-

tomer bulletins. The number of customer bulletins has continued to

increase, and was almost doubled from the previous year. Funet

and Information Management Services both posted their letters to

customers on their webpages. Later the other service areas will also

place their customer communication on their dedicated webpages.

The journal for CSC customers, CSCnews concentrated on impor-

tantprojects and research results: theuseofCSCsoftwareon re-

search into allergy and asthma, modeling of ice sheets and climate

change, massive data handling in astrophysics, designing new drug

molecules to help cancer research, determining the genetic back-

ground of diseases, cholesterol, modeling arthritis, nanotechnolo-

gy, improved simulation of molecules, coupled climate models,

code optimization, research infrastructures, saving biosciences da-

ta, green machine rooms, scientific research materials, the GÉANT2

network, ICT SHOK, and data management at higher education insti-

tutions.


Medicines from the naturecoMputationally

Fighting osteoarthritis

genetic background

oF diseases

CSC

JUNE 2 /2009

news

Top class optimization

Trawling the data ocean

CSC

DECEMBER 4 /2009

news

New materials made with NANOTECHNOLOGY

How FINLAND'S CLIMATE will change?

BAD CHOLESTEROL

CSC

SEPTEMBER 3 /2009

news


TRAININg COURSES AND EVENTS

The training services staff were busy throughout 2009. A total of 71

courses or events were organized, with 2,020 customers participat-

ingonthecourses/eventsheldonthetotalof130days.Mostofthe

courses were arranged in English to provide maximum benefits for

the increasingly international clientele.

The main emphasis in the 2009 course offering was on arranging

courses for customers. Special efforts were made in training espe-

cially in the field of computational biosciences and high-perfor-

mance computing. The most popular customer-focused courses

were the workshop on coarse-grained models and intensive courses

on programming language. CSC also trained its customers in proces-

sor architectures and their programming by organizing a CUDA

course and an application workshop arranged with PRACE project

funding. A new product in the course portfolio was a training pack-

age on high-performance computing consisting of 1 to 4 days of

training at a time. This training package will serve as part of the

HPC training courses within academic curricula.

ThemajoreventsweretheEMBRACE-ENFINWorkshop,theAAPA

(IT managers at universities of applied sciences) 10th Anniversary

Seminar,theFunetTechnicalDaysinOulu,EuroPVM/MPI2009con-

ference, and the Energy-efficient Machine Rooms 2009 seminar. Ad-

ditionally, training on CSC’s own DNA microarray expression data

analysis software Chipster was also provided at the Turku Centre for

Biotechnology,BiomedicuminHelsinki,andtheGermanCancerRe-

search Center (DKFZ) in Heidelberg.


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News 01s234e56177e89s

NEwS AND CUSTOMER bULLETINS 2003–2009

During the spring CSC organized a seminar called Energiatehokas konesali 2009 (Energy Efficient Machine Rooms 2009), which brought together 70 machine room specialists. The seminar is part of larger developments within the academic IT infrastructure in Finland defined by the Ministry of Education.

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No.ofcoursesandevents Coursedays

COURSES AND EVENTS 2002–2009

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A NEw STANDARD FOR MPI CREATED IN HELSINkI

CSC hosted the 16th European PVM/MPI Users' GroupMeeting in

SpektriBusinessPark inEspoo7–10September2009.Anewstan-

dard for MPI (Message Passing Interface) was ratified in the preced-

ing MPI Forum meeting in Helsinki.

”This was the 16th meeting about the research and development

of message-passing communication on parallel systems. Initially, the

MPI standard grew from a standard communication package which

was developed in the USA”, told Jack Dongarra from the University of

Tennessee,thegeneralchairoftheEuroPVM/MPIconference.

Anewstandard–namelyMPI2.2.–wasagreedandratifiedin

theMPI Forummeeting inHelsinki preceding the Euro PVM/MPI

conference.

“The MPI 2.2 version is an important step in modernizing the MPI

standard. The changes include updating language support, some scal-

ability issues are addressed, and numerous corrections and clarifica-

tion are also included. This paves the way to focus on a broader set of

new functionality that may be added to the standard, with nonblock-

ing collectives already being voted into the next version of the stan-

dard”, stated Richard Graham from Oak Ridge National Laboratory,

chair of the MPI forum and responsible of for the MPI standard.

“The work with the third version of the MPI standard is already

going on. When researchers started to work with the MPI standard

there were some 10 to 100 processors that had to work in parallel.

These days we are talking about millions of processors that process

information in parallel. Researchers are continuously refining and

getting new ideas on how to get the MPI standard even better”, Don-

garra continued.

TheEuropeanPVM/MPIUsers’Groupconferenceisaforumforthe

users and developers of MPI, and other message-passing program-

mingenvironments.TheEuroPVM/MPI2009meetingattractedover

60participantsfromtheUSA,Germany,Spain,France,Japan,Ireland,

Austria, Mexico, China and Finland.

Video material from the conference is available on http://www.

csc.fi/pvmmpi09.

UPDATED TRAININg ROOM SUPPORTS NEw STYLE TEACHINg IN COMPUTINg

The IT infrastructure in CSC’s training facilities was updated in sum-

mer 2009. The old workstations were replaced with powerful state-

of-the-art technology quad-core workstations with extremely pow-

erful, general-purpose display adapters (Nvidia Tesla C1060) suit-

able for scientific computing and visualization. Additionally, a num-

ber of improvements were made to support use of participants’

own portable computers.

CUSTOMER SURVEY 2009 FOR CUSTOMERS USINg COMPUTINg, SOFTwARE AND DATA STORAgE SERVICES

In October 2009 CSC arranged a customer survey focused on custom-

ers who use CSC’s computing, software and data storage services.

The target group comprised 530 customers chosen on the basis of

threecriteria:beingancomputationuser,havinganactiveuserpro-

file, i.e. frequent logins on CSC computers during 2009, or using CSC’s

national software licenses or information management services. The

objective was to measure how well CSC’s services meet the needs of

our customers. Additionally, the aim was to collect suggestions for

development from customers in order to improve our services. Re-

sponse was received from 263 customers (50%).

The questionnaire contained 34 questions on five different ser-

vicefields.Thesurveyedservicefieldswere:softwareanddatabase

services, computing services, data storage and archiving services,

customer guidance (personal guidance, journals, guidebooks, web-


CSC hosted the 16th European PVM/MPI User’s Group Meeting in September. A new standard for MPI (Message Passing Interface) – namely MPI 2.2 – was ratified at the preceding MPI Forum meeting in Helsinki. The Euro PVM/MPI 2009 meeting attracted over 60 participants from the USA, Germany, Spain, France, Japan, Ireland, Austria, Mexico, China and Finland.

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pages), and customer support services (applications for user rights

and computing resources).

The respondents rated all service fields mainly as good or excel-

lent, and they considered CSC’s services extremely important for

their research. Customers were particularly satisfied with the conti-

nuity of remote use, the selection of programs and number of li-

censes available, the suitability of the computing environment for

research, the quality of the software environment, the reliability of

storage services, personal guidance, and customer services. Some

researchers also commented that recently the usability of CSC’s

hardware environment has not been the best possible. Further-

more, our communication on computer downtime has not satisfied

all our customers. Special attention will be paid to these issues dur-

ing the Year of Quality 2010.

Numerous suggestions were received for development of CSC

services. Many customers expressed a desire to have additional pos-

sibilities for long-term preservation of files (e.g. home directories

or increased disk space for projects). A possibility for increased

customer-specificdisksizeinarchivingservices(2–3TB)wasalsoon

the wish list. More frequent software updates were wanted for

many programs (such as free Python programs). Some customers

would like to have a beginner’s instructional page on our website,

with various examples of use and additional instructions on data

storage. Our customers regard the website as the most important

source of information, and they find it essential that the pages such

as those containing news about the machines and instructions are

up-to-date.

gROwTH IN HAkA USER MANAgEMENT SERVICES

New contracts were signed with two universities (Hanken School of

Economics and the University of Lapland), seven universities of ap-

plied sciences (Metropolia, Laurea, and Kemi-Tornio, Rovaniemi, Ka-

jaani, Satakunta and Turku Universities of Applied Sciences), and Cer-

tia the Service Center of Universities. Additionally, eight companies

becamenewHakaservicepartners:BytheMark,PrioInfocenterAB,

Promentor Solutions Oy, IT-Salonen Oy, Entecore Ky, Logium Oy, Tieto

Oyj/PublicIndustry,andtheNationalAudiovisualArchive(KAVA).

TheHakaMemberAgreementhasbeensignedby19/20univer-

sitiesand25/26universitiesofappliedsciences.TheIdPserversof

18 universities and 21 universities of applied sciences have been

registered to Haka (coverage of the services 98. 7% and 78.9%, re-

spectively). In 2009, the number of Haka services users increased by

approximately 18%. If the Haka partnerships are included, the Haka

service agreement has been signed by a total of 58 organizations.

Arecordnumberofcustomerlogins(820,760logins/month)were

registered in November. The previous record was reached in No-

vember2008(616,255logins/month).ThetotalnumberofHakalo-

gins per year is as many as 5.45 million.

USER LOg FOR CHIPSTER AND PAITULI INCREASINg

The DNA microarray expression data analysis software Chipster, de-

veloped by CSC, increased its number of users. During the first year,

2008, the service was used by individual users and had 129 custom-

ers, and in 2009 the number of users was as high as 195. In 2009,

the service ran 25,400 jobs, while the corresponding figure in 2008

was 18,300. Training on Chipster was provided at CSC and also at

the Turku Centre for Biotechnology, Biomedicum in Helsinki, and

the German Cancer Research Center (DKFZ) in Heidelberg.

In April 2009, a new spatial data service called PaITuli was opened

for use through the Scientist’s interface. During the first year of op-

eration, this browser-based service was provided for 1,124 custom-

ers who downloaded a total of 10,200 pages. Actual data was down-

loaded from the service 5,240 times and the number of users on the

server was 756 customers.

The usage statistics on Chipster and PaITuli are presented in the

section “CSC in statistics”, on page 84.

THE NEw APPLICATION SERVER AND AUTOMATIC CLEANINg SOFTwARE INTO USE

The new application server Hippu was implemented to customer

useonJanuary21st.TheoldapplicationserverCoronawasremoved

from customer use on April 21st. The upgrade increased our com-

puting capacity for interactive application use by over a third.


HAkA LOgINS bY SERVICES 2009

FinELibNelliportal

21%

TUTMoodle

16%

JyväskyläUniv.of

AppliedSciences

OpDEa1F%

Univ.Jyväskylä

OpDEa11%

SavoniaMoodle

10%

Univ.Oulu

OpDEaI%

Univ.Helsinki

Moodle5%

Univ.Kuopio

Moodle2%

Univ.Turku

Moodle2%

Univ.Helsinki

Wiki2%

Other

10%



InJuneanautomaticcleaningscriptwasimplementedintothe

work directories ($WRKDIR) of Louhi and Hippu. The script removes

oldfilesfromthediskspace.OnLouhi(CrayXT4/XT5)allfilesolder

than 180 days are destroyed and on Hippu the corresponding time

limit is 30 days. Murska received a corresponding cleaning script in

September, with a 180 day time limit for cleaning. The storage place

for files requiring long-term preservation is the home directory, the

project disk, or the archiving server.

INTRUSION INTO CSC’S COMPUTINg ENVIRONMENT

An intrusion into CSC’s computing environment was discovered on

April 21st, and CSC had to close access from its customers onto the

computing servers. It took three days to check the integrity of the

environment and passwords, generate new passwords and send e-

mails to customers. The servers were back in customer use on April

23rd. The customers had to create new passwords and also their ssh

security keys, if one had been used. Similar intrusions were reported

in certain other international computing centers as well.

COLLAbORATION PROjECTS 2009

In 2009 CSC had a total of 18 projects funded by Tekes - the Finnish

Funding Agency for Technology and Innovation, the EU, and other

organizations. More information on the collaboration projects is

available athttp://www.csc.fi/english/collaboration/index_html.

• Development of Data Analysis Environment for Extensive

Astronomical Data (Tekes), more information at

http://www.eso.org/sampo/

• Tools for large scale computational fluid dynamics (Tekes)

• Successful business model in national and international research

infrastructures (Tekes)

• ICT SHOK Future Internet Programme (Tekes)

• DEISA2, Distributed European Infrastructure for Supercomputing

Applications and eDEISA, Extended Distributed European

Infrastructure for Supercomputing Applications (EU),

more information at http://www.deisa.org/

• EMBRACE,AEuropeanModelforBioinformaticsResearchand

Community Education (EU), more information at

http://www.embracegrid.info/

• GN3, Multi-Gigabit European Academic Network (EU),

CSC participates in the project as a NORDUnet member.

More information at http://www.geant2.net/

• EGEE III, Enabling Grids for E-sciencE-II ja E-III (EU),

more information at http://www.eu-egee.org/

• TheEGI_DS,EuropeanGridInitiativeDesignStudy(EU)project was started in September 2007 and was scheduled for completion

at the end of 2009. More information at http://web.eu-egi.org/

• EUFORIA, EU Fusion for ITER Applications (EU)

• PRACE, Partnership for Advanced Computing in Europe (EU),

more information at http://www.prace-project.eu/

• e-IRGSP2, e-Infrastructures Reflection Group Support Programme

2 (EU), more information at

http://www.e-irg.eu/http://knowledgebase.e-irg.eu/

• CLARIN, Common Language Resources and Technology

Infrastructure (EU), more information athttp://www.clarin.eu/

• ELIXIR,EuropeanLife-scienceInfrastructureforBiological Information (EU), more information at

http://www.elixir-europe.org/page.php

• HPC EUROPA2, Pan-European Research infrastructure on High

Performance Computing for 21st century Science (EU), more

information at http://www.hpc-europa.eu/

• Ice2sea- estimating the future contribution of continental ice to

sea-level rise (EU)

• Dynamical evolution of Schaffenbergbotnen blue ice area since

theLateGlacialMaximum(UniversityofLapland/Academyof

Finland)

• Nordic DataGrid Facility (NDGF), more information at

http://www.ndgf.org/and http://www.nordugrid.org/


Supporting research and innovation, now and in the future

to

From


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DEISADEISA DIGEST 2008

Benefits of supercomputing

DistributedEuropean

Infrastructure forSupercomputing

Applications

THE RINGLET (Aphantopus hyperantus) © Sirkku Paajanen


The head count at CSC is approaching two hundred. In accordance

with our values, we want to focus efforts to motivating our staff and

well-being at work. While this allows various possibilities for indivi-

dual career development paths and specialist learning within the

growing organization, at the same time, in order to maintain effecti-

veness, certain processes and internal services need to be made uni-

form and streamlined. We encourage on-the-job development, ta-

king into consideration the fact that people are different, and we

provide continued learning and health at work. Examples of our ac-

tivities in this direction include our extensive input to training our

staff, arrangements for study leaves, and the extensive health in-

surance plan for all personnel acquired in 2009.

Leadership is the most important factor in motivation at work.

For leadership, an important tool is the performance and goals dis-

cussions held twice a year. To facilitate these discussions, CSC pur-

chased and implemented a new on-line tool that makes documenta-

tion and saving of the discussion contents easy.

Since there was increasing demand for CSC services, we set a re-

cord in the number of recruited employees. Still, in certain fields of

expertise (such as experienced programming and database specia-

lists) it is very difficult to attract qualified specialists. More than in

previous years, CSC also focused on international recruiting. Twen-

ty-five new permanent employees started and seven permanent

ones resigned. CSC’s age structure is good and we even managed to

improve it slightly. In spite of this, to safeguard our future, it is im-

portant to pay attention to the transfer of expertise and information

flow between our employees.

The growing number of employees led to a need to rent more fa-

cilities. CSC has now rented an entire building of the Life Science Cen-

ter, and the renting options agreed in 2004 have now been used.

Numberofstaffon31.12.2009:191 (countingallpersons)and

the 2009 average was 182.

orgAnIzATIon

orgAnIzATIon

Permanent: 175 (92 %)

Fixed-term: 16 (8 %)

Age distribution:

<30:12%

30–39:44%

40–49:32%

≥50:12%Averageage:39

Sex distribution:

Men:77%

Women:23%

Education distribution:

Basicandvocational:23%

University of applied

sciences:10%

University:42%

Post-graduatedegrees:25%


orgAnIzATIon

1. Johanna Blomqvist was elected the staff representative in CSC's operative management group starting January 1, 2010.

2. CSC's hunting club arranges fishing and hunting events. On an ice-fishing trip arranged on CSC’s winter sports day, club chairman, Jari Miettinen’s day’s catch included this ruff.

3. CSC employees making snow sculptures in the form of Moomin figures.

STAFF REPRESENTATIVE TO CSC’S MANAgEMENT

In December 2009 a staff representative was elected to CSC’s mana-

gement organs for the first time. The aim of staff representation is

to improve internal information flow and openness, as well as to

improve the staff’s possibilities to have an impact on decision-ma-

king and development. The staff representative is responsible for

presenting the staff viewpoint at the management level. Johanna

Blomqvist is the first staff representative in CSC's operative mana-

gement group.

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orgAnIzATIon

Managing Director Kimmo Koski

Services Support and Innovations

Jari Järvinen

Customer Services

Juha Haataja

CommunicationsAri Turunen

financial Services

Kimmo Niittuaho

hr and office Services

Jari Rajala

general Administration

Juhani Käpyaho

Customer Processes and Solutions

Tommi Nyrönen

funet network Services

Janne Kanner

Information Management Services

Klaus Lindberg

Data Services for Science and Culture

Pirjo-Leena Forsström

Application ServicesPer Öster

Computing Services

Janne Ignatius

business Services Development

Pekka Palin

Management Support

Tiina Kupila-Rantala

Internal IT ManagementTero Tuononen


ADMInISTrATIon

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boArD of DIreCTorS

CSC bOARD OF DIRECTORS (jANUARY 1ST – DECEMbER 31ST)

Taina Pihlajaniemi, Professor, University of Oulu (chair)

Outi Krause, Vice Rector, Aalto University, School of Science

and Technology (vice chair)

Kari-Pekka Estola, Private Investor

Erja Heikkinen, Counsellor of Education, Ministry of Education

Kimmo Koskenniemi, Professor, University of Helsinki

Jussi Nuorteva, Director General, National Archives Service

of Finland

Jouko Paaso, Rector, Oulu University of Applied Sciences

No deputy members

CSC Board of Directors 2009. Back row from the left: Kari-Pekka Estola, Kimmo Koski, Kimmo Koskenniemi, Jussi Nuorteva, and Jouko Paaso. Front row from the left: Outi Krause, Taina Pihlaja- niemi, and Erja Heikkinen.

ADMInISTrATIon AnD goVernAnCeThe administration of CSC is based on the Finnish Limited Liability

Companies Act and the CSC Articles of Association. CSC has decided

to comply with, as appropriate, the Corporate Governance Recom-

mendations for listed companies issued by HEX Plc, the Central

Chamber of Commerce and the Confederation of Finnish Industries

(EK) thatcame intoeffecton July1,2004.CSC’sadministration is

also subject to the Ministry of Education’s guidance for manage-

ment policies.

CSC’s statutory administrative bodies consist of the General

MeetingofShareholders,theBoardofDirectorsandtheManaging

Director. The operative management of the company is under the

responsibility of the Managing Director together with the Manage-

ment Group.

gENERAL MEETINg OF SHAREHOLDERS

The Annual General Meeting (AGM) is the highest decision-making

organofCSC.TheAGMmustbeheldbytheendofJune,andthe

meetingisconvenedbytheBoardofDirectors.TheGeneralMeeting

of Shareholders addresses the items assigned to it according to the

Finnish Limited Liability Companies Act and the CSC Articles of As-

sociation.


Notice of a General Meeting must be given to shareholders in

writing, delivered in a verifiable way, no earlier than four weeks and

no later than eight days before the meeting.

bOARD OF DIRECTORS

CSC’s BoardofDirectors includes4–7 regularmembers. TheAGM

elects themembersof theBoardofDirectors. Incompliancewith

theCSCArticlesofAssociation,theBoardmembers’termsofoffice

expire at the end of the AGM following their election.

ABoardmeetingconstitutesaquorumwhenoverhalfofthereg-

ular members, one being the Chair or, if the Chair is prevented from

attending, the Vice Chair, are present.

TheAGMelectstheChairandtheViceChairfortheBoardofDirec-

tors.TheManagingDirectorisnotamemberoftheBoardbutheacts

as reporting official and secretary in the meetings. The AGM follows in

its operation the work agenda accepted on 5th of March 2009.

TheBoardofDirectorsheldfivemeetingsduring2009.CSChas

no committees.

TheBoardmembers’personalinformationwithresponsibilities

andoutside interests ispresentedonpages64–65oftheAnnual

Report.

DUTIES OF THE bOARD

In accordance with the Finnish Limited Liability Companies Act, the

BoardofDirectorsattendstotheadministrationanddueorganiza-

tionofoperations.TheBoardofDirectorsisalsoresponsibleforthe

appropriate arrangement of the control of the company accounts

and finances.

TheBoardofDirectorsshallpromotethe interestsofthecom-

panyandallshareholders.InperformingitsdutiestheBoardofDi-

rectors may

• ConvenetheGeneralMeeting

• Controlandmonitorthecurrentmanagement

• AppointanddismisstheManagingDirectorofthecompany

• ApprovetheManagingDirector’scontractandotherbenefits

• Approvepossibleincentivebonusesforthecompany,allocation

rationale for incentive bonuses, and an incentive bonus for the

Managing Director

• Monitortheworkingenvironmentanditsdevelopmentinthe

company

• Approvethecompany’sriskmanagementprinciplesand

conduct annual reviews of the essential risks related to the

company’s operations and the management of the risks

• Consolidatethecompany’slong-termstrategicandfinancial

objectives and continuously monitor their realization

• Assembleatleastonceayearwithoutthecurrentmanagement

being present

• Approvethebudget

• ApprovethefinancialstatementsandthereportoftheBoardof

Directors

• Confirmanagendaforitself,tobeupdatedannually

• Assess,atleastonceayear,theimplementationandvalidityof

the administration and control systems (corporate governance)

All members of the Board of Directors are obliged to hold all

companyinformationdisclosedtothemintheircapacityasaBoard

member as confidential.

MANAgINg DIRECTOR

The Board of Directors appoints the Managing Director for the

company. The Managing Director’s terms of office are defined in a

writtencontractapprovedbytheBoardofDirectors.TheManag-

ing Director attends to the day-to-day administration of the com-

pany in compliance with the instructions and orders given by the

BoardofDirectors.TheManagingDirectorhasnoadditionalfinan-

cial expectation on retirement other than the statutory pension

scheme.

DEPUTY MANAgINg DIRECTOR

TheBoardofDirectorsmayappointadeputytotheManagingDirec-

tor. The company does not have a Deputy Managing Director at the

end of the fiscal year 2009.

MANAgEMENT gROUP

The Management Group is chaired by the Managing Director. The

Management Group creates plans for the company’s strategic poli-

cies, annual operational plans including the budget, plans invest-

ment schemes and follows their implementation, allocates resourc-

es, decides on key activities and significant operational issues, and

monitors the implementation of the decisions made. During 2009

the Management Group assembled 18 times.

The Management Group members’ personal information with re-

sponsibilitiesandconfidentialpostsispresentedonpages62–64of

the Annual Report.

COMPENSATION

According to the decision made by the AGM 2009 the remuneration

paidtotheBoardChairisEUR600permonth,whiletheViceBoard

Chair receives EUR 400 per month and regular members EUR 300

permonth. Inaddition, theBoardChair,ViceChair,andmembers

receiveEUR200permeetingasremunerationforattendingaBoard

meeting. Auditors’ fees are paid as invoiced.

TheBoardofDirectorsdecidesonthemanagementcompensa-

tionpolicy.TheBoardofDirectorsdecidesontheincentivebonus

apart from salary to be paid for the Managing Director, members of

theBoard,andotherstaff;thebonusisdeterminedonthebasisof

the company mission, vision, core values, and realization of the stra-

tegic goals. The company has not issued option loans or offered

stock options.

ADMInISTrATIon


MAnAgeMenT groUP

STRATEgIC MANAgEMENT gROUP (SMg)

Kimmo Koski, Managing Director (chair)

Juha Haataja, Customer Services

Jari Järvinen, Services Support and Innovations

Tiina Kupila-Rantala, Management Support (secretary)

Juhani Käpyaho, General Administration

Leif Laaksonen, EU Collaboration

Kimmo Niittuaho, Financial Services

Jari Rajala, HR and Office Services

Tero Tuononen, Internal Information Management

Ari Turunen, Communications

OPERATIVE MANAgEMENT gROUP (OMg)

Juha Haataja, Customer Services Director (chair)

Pirjo-Leena Forsström, Data Services for Science and Culture

Janne Ignatius, Computing Services

Jari Järvinen, Services Support and Innovations

Janne Kanner, Funet Network Services

Klaus Lindberg, Information Management Services

Tommi Nyrönen, Customer Processes and Solutions (secretary)

Pekka Palin,BusinessServicesDevelopment

Ari Turunen, Communications

Per Öster, Application Services

1. Kimmo Koski2. Jari Rajala, Tero Tuononen, Juhani Käpyaho, and Kimmo Niittuaho3. Juha Haataja and Jari Järvinen4. Ari Turunen, Leif Laaksonen, and Tiina Kupila-Rantala5. Klaus Lindberg, Janne Ignatius, and Janne Kanner6. Per Öster and Pekka Palin7. Tommi Nyrönen and Pirjo-Leena Forsström

ADMInISTrATIon

INTERNAL CONTROL, RISk MANAgEMENT, AND INTERNAL AUDITINg

TheBoardofDirectorsattendstotheadministrationanddueorga-

nization of operations. The Managing Director, together with the

Management Group, is responsible for the reliability and legality of

accounting, financial affairs, and routine operations.

Management control and monitoring and the related approval

processes are defined in CSC’s policy guidance on management and

governance.

The financial development of the company is followed on a

monthly basis through a company-wide financial accounting control

system. The system covers the income statement, balance sheet,

cash flow, forecast for the current fiscal period, as well as other sig-

nificant business transactions. Internal calculation controls are ap-

plied to monitor how the company’s annual operational plan is deliv-

ered. A unit-specific financial reporting system is applied at CSC. It is

used, for example, to monitor how the profit centers deliver their

annual operational plans.

There is no separate organization for internal auditing; responsi-

bility is divided according to the business function structure. The fi-

nancial management function conducts internal audits in coopera-

tion with the other managers and the auditor. The requirements set

for internal audits are taken into consideration in the audits of ac-

counts performed by the auditor.

The Chief Financial Officer is responsible for the cash manage-

ment and investments following the specific instructions set by the

BoardofDirectors.

TheauditormeetswiththeBoardofDirectorsatleastonceayear

andreportsonthestatusofsignificantfinancialitemstotheBoard.

Additionally, the auditor and the company management meet at

least twice a year. The auditor meets the financial management at

least four times per year.

CSC has observed changes that have occurred in the operating

environment and identified risks relating to operations and fund-

ing. Due to the nature of the services produced, CSC is especially

vulnerable to operational risks relating to data security. The prin-

ciples of operational risk management at CSC are defined in the

Data Security Policy. Realized incidents are reported to CSC’s man-

agement.

Security in CSC’s operations and services has been improved by

initiating business continuance and disaster recovery planning in ac-

cordance with good management practices and risk management

guidance proposed by the authorities. Special requirements are en-

joined with CSC’s special role as part of the national critical infra-

structure to secure critical activities in case of disorders and emer-

gencies. CSC’s practices and security management system have

been assessed in relation to public standards.

CSC’s insurance coverage was checked during 2009 and revised

to correspond to the present situation.

AUDIT OF THE ACCOUNTS

The company has one regular auditor, which is an authorized public

accountancy firm. The auditor’s term of office expires at the end of

the AGM following the auditor’s election.

The auditor reviews financial statements, accounting, and

governance.

For the fiscal period 2009 the AGM elected Moore Stephens Re-

winet Oy Ab, Authorized Public Accountants as the auditor, with

Jari Paloniemi, APA as the principal auditor.


ADMInISTrATIon

4 5

6 7

1 2 3


STRATEgIC MANAgEMENT gROUP

KIMMO KOSKI (born 1964)

D.Sc. (Tech.) •

Managing Director, CSC •

Employment history summary:

CSC,ManagingDirector,2004– •

Nokia Technology Platform Engineering Environment, •

Strategy and Roadmaps Manager, 2004

NokiaResearchCenter,ITManager,2000–2003 •

CERN,Switzerland,ScientificAssociate,1996–1997 •

CSC,positionsasManagerandSpecialist,1989–2000 •

Board member since:

SecretaryoftheCSCBoardofDirectorsfromAugust2,2004− •

Summary of concurrent confidential posts:

ERA Expert Group for Research Infrastructures, 2009− •

Member of the PRACE Management Group, 2008−2009 •

JuHANI KäpyAHO (born 1952)

Ph.Lic. (Applied Mathematics) •

Vice Managing Director, CSC •


CSC, administrative tasks relating to management and •

organization,1992–

CSC, various specialist positions in information technology, •

1981–1992

NokiaOyj,1974,1975,1980–1981 •

ComputingCentre,UniversityofHelsinki,1975–1980 •

JuHA HAATAJA (born 1965)

Lic. Sc. (Tech.) •

Director, Customer Services, CSC •


CSC,DirectorofCustomerServices,2007– •

CSC,DirectorofScientificServices,2005–2007 •

CSC, Development Manager, 1997-2004 •

CSC, Application Specialist, 1990-1997 •

Helsinki University of Technology, Application Specialist, •

1988–1990


UrsaAstronomicalAssociation,Boardmemberandvicechair •

SalWeOy(HealthSHOK),Boardmember •

JARI JäRvINEN (born 1966)

Ph.D., Adjunct Professor •

Director, Services Development, CSC •


CSC,Director,ServicesDevelopment,2007– •

CSCS, Swiss National Supercomputing Centre, •

ChiefScientificAdvisor,2005–2006

CSC,ScientificDirector,2000–2004 •


ADMInISTrATIon


Helsinki University of Technology, Department of Physics, •

AdjunctProfessor,2000–

TIINA KupIlA-RANTAlA (born 1963)

Ph.D.,MasterofBusinessAdministration •

Development Manager, Management support, CSC •


CSC,DevelopmentManager,2002– •

Nokia Networks, Project Manager, 2001 •

CSC,SystemExpert,1996–2001 •

University of Helsinki, Department of Physics, Assistant, •

ScholarshipResearcher(JennyandAnttiWihuriFoundation,

MagnusEhrnroothFoundation),1992–1996

NokiaTelecommunications,SystemAnalyst,1990–1991 •

Conservatoire National des Arts et Métiers, Laboratoire •

d’Informatique, Paris, France, Researcher, 1989


ChrysopoeiaOy,Boardmember •

lEIF lAAKSONEN (born 1954)

D.Sc. (Tech.), Åbo Akademi University •

Director, Collaboration, CSC •


CSC,Director,Collaboration,2007– •

CSC,DevelopmentDirector,2005–2007 •


Max Planck Institute for Astrophysics, Garching, Germany, •

Visiting Researcher, 1993, 1994, 1995, and 1996

AcademyofFinland,Researcher,1989–1992 •

Academy of Finland, Senior Research Fellow, •

1988–1989

University of Oxford, Research Assistant, 1984 •


e-InfrastructureReflectionGroup(e-IRG),Chair,2007–2008 •

and2009–2010

Developing World-Class Research Infrastructures in the European •

Research Area, a specialist group of the European Commission,

Finland’s representative, 2007

MoE working group Training and Research Strategy in Information •

Society:Informationsocietystructures,MoERepresentative,

2004–2005

European e-Infrastructure Reflection Group (eIRG), Ministry of •

EducationRepresentative,2004–

TheEUandTheCouncilofBalticSeaStates(CBSS)workinggroup •

NortherneDimensionActionPlan(NeDAP)ActionLine1:Internet

and Internet Applications Research and Development,

RepresentativeoftheMoE,2004–2006

JARI RAJAlA (born 1971)

M.A. (Education) •

HR Manager, CSC •

MAnAgeMenT groUP AnD boArD of DIreCTorS PerSonAL InforMATIon wITh reSPonSIbILITIeS AnD oUTSIDe InTereSTS (CorPorATe goVernAnCe)



CSC,HRManager,2007– •

CSC,AdministrativeDirector,2004–2007 •


KIMMO NIITTuAHO (born 1966)

M.Sc. (Econ.) •

Financial Manager, CSC •


CSC,FinancialManager,2003– •

PirelliOy,Controller,2001–2003 •

LMEricssonOy,BusinessController,2000–2001 •

AKBServices,Controller,1995–2000 •

TERO TuONONEN (born 1971)

M.Sc. (Computer science) •

IT Manager (Internal information management), CSC •


CSC,ITManager,2009– •

CSC,Developmentmanager,2006–2008 •

NokiaOyj,ITManager,1996–2006 •

ARI TuRuNEN (born 1966)

Lic. Soc. Sc. •

Head of Communications, CSC •


CSC,HeadofCommunications,2007– •

Finnish Forest Research Institute, Head of Communications, •

2004-2007

CSC,HeadofCommunicationsandPROfficer,1997–2004 •

UniversityofHelsinki,UniversityofJyväskylä,Researcher, •

1996–1997

YLE,theFinnishBroadcastingCompany,TVnewsreporter, •

1994–1995

YLE,theFinnishBroadcastingCompany,radionewsreporter, •

1990–1994


Interpedia,Boardmember,2009– •

PRACETechnicalBoard,member,2008– •

DIRECTORS OF CSC SERVICE AREAS

pIRJO-lEENA FORSSTRöM (born 1959)

Ph.D. •

Director, Data Services for Science and Culture, CSC •


CSC, Director, Data Services for Science and Culture, 2007− •

CSC, positions as Manager and Specialist, 1987-2007 •

University of Helsinki, Research Assistant, Assistant, Amanuensis, •

1981–1987

Academy Research Fellow (Academy of Finland, Vaisala), •

2005–2007


The National Digital Library, member of the long-term •

preservation division

The Nordic Ministerial Council for Information Technology, •

member

Electronic data for research project, steering group member •

Electronic data for research project, scientific panel member •

A preparatory project on remote use of records information, •

steering group member

JANNE IGNATIuS (born 1965)


Director, Computing Services, CSC •


CSC, Director, Computing Services, 2007− •

CSC, Development Manager, 2002−2007 •

CSC, Specialist in Computational Physics, 2001−2002 •

AcademyofFinland(UniversityofHelsinki),JuniorResearcher •

and Responsible Leader of Project, 1998−2000

NORDITA (Nordic Institute for Theoretical Physics), Copenhagen, •

Denmark, Postdoc Researcher, 1997−1998

Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany, •

Postdoc Researcher, 1994−1996

University of Helsinki, Departments of Physics (Dept. and Division •

of Theoretical Physics, Accelerator Laboratory, Research Institute

of Theoretical Physics, Department of Physics, Dept. of High

EnergyPhysics);SeniorResearcher,Researcher,JuniorResearcher,

Research Assistant, Intern, Teaching Assistant, 1987−1994, 1996,

2000


PRACEManagementBoard,member,2009− •

DEISA Executive Committee, member, 2008− •

Canon Professional Network, 2008− •

University of Helsinki, Adjunct Professor (Theoretical Physics), •

2001−

JANNE KANNER (born 1973)

M.Sc. •

Director, Funet Services, CSC •


CSC,Director,FunetServices,2007– •

CSC,TechnologyDirector,2004–2007 •


CSC,Specialist,1999–2002 •

UniversityofJyväskylä,1998–1999 •

VapoOy(part-time),1992–1998 •


TERENA (The Trans-European Research and Education Networking •

Association),ChairoftheBoard,2009–2011

NORDUnetA/S,Boardmember(2004−)andChair(2008−2010) •

OtaverkkoOy,Boardmember,2009– •

KlAuS lINdBERG (born 1958)

M.Sc. (Tech.) •

Director, Information Management Services, CSC •


CSC,positionsasDirector,2002– •

CSC, positions as Manager and Specialist, 1989-2002 •

Helsinki University of Technology, Research Assistant, 1984-1989 •


RAKETTI steering group nominated by the MoE, member •

Member of the SADe project ”Oppijan palvelukokonaisuus” cluster •

OpIT working group nominated by the MoE, member •

ADMInISTrATIon


pER öSTER (born 1959)

Ph.D. •

Director, Application Services, CSC •


CSC,Director,ApplicationServices,2007– •

KTH Royal Institute of Technology, Stockholm, Sweden, •

Parallelldatorcentrum (PDC), Associate Director, 2001−2007


Parallelldatorcentrum (PDC), Associate Director, Research and

Customer Relations, 1996−2001


Parallelldatorcentrum (PDC), Project Manager, Industrial

Applications,1994–1996

VolvoDataAB,Gothenburg,Sweden,Consultant,Applied •

Mathematics,1992–1994

VolvoDataAB,Gothenburg,Sweden,SystemAnalystand •

ProductManager,TechnicalComputing,1990–1992

Chalmers University of Technology and University of •

Gothenburg,PhDgrantandPhDresearchposition,1984–1990


Member of the EU e-Infrastructures project EGEE-II Project •

ManagementBoard(representativeoftheNorthernFederation,

i.e.Belgium,Denmark,Finland,Netherlands,Norway,and

Sweden), 2006−2008

EU FP7 e-Infrastructures project European Grid Initiative Design •

Study(EGI_DS)ManagementBoard(representativeofCSC),

member, 2008−2009

EU FP7 e-Infrastructures project EGEE-III Project Management •

Board,Chair,2008(May−Nov)

Member of the EU FP7 e-Infrastructures project EGEE-III Project •

ManagementBoard(representativeoftheNorthernFederation,

i.e. Finland, Norway, and Sweden), member, 2008−2010

European Grid Initiative (EGI) Council, chairman, 2009− •

EGI.euFoundationExecutiveBoard,chairman,2010− •

Finnish Graduate School in Computational Sciences (FICS) •

Strategic Committee, member, 2010−

MEMbERS OF THE bOARD OF DIRECTORS

TAINA pIHlAJANIEMI (born 1957)

Chair

M.D., Ph.D. •

ProfessorofMedicalBiochemistry,UniversityofOulu •


BiocenterFinland,Director2006−2007andViceDirector •

2008−2009

Institute of Molecular Medicine for Finland (FIMM), Senior •

Assistant Project Leader 2008−

BiocenterOulu,ScientificDirector •

UniversityofOulu,MedicalBiochemistryandMolecularBiology, •

Chair

UniversityofOulu,ProfessorofMedicalBiochemistry •

Rutgers Medical School, University of Medicine and Dentistry •

NewJersey,USA,PostdocResearcher1982−1985

Board member since: 1998


European Strategy Forum on Research Infrastructures (ESFRI), •

WorkingGrouponResearchInfrastructurefortheBiologicaland

Medical Sciences, member

ESFRI Finnish Coordination Group, member •

BioforumOulu,AdvisoryBoard,member •

KARI-pEKKA ESTOlA (born 1956)

D.Sc. (Tech.), Tampere University of Technology •

Private investor •


Nokia Research Center (NRC), Vice President and Head of •

Technology Exploration, 1998−2007

NRC, Electronics Laboratory, 1993−1997 •

VTT, Professor, Head of Electronics Laboratory, 1992−1993 •

VTT, Research Professor in Signal Processing, 1990−1992 •



EurekaAdvisoryBoard,Chair,2006− •

VTTTechnicalResearchCentreofFinland,Boardmember,2001− •

MidInvestFundOy,Boardmember,2000− •

ERJA HEIKKINEN (born 1964)


Counsellor of Education, Ministry of Education •


Ministry of Education, Counsellor of Education, 2005− •

Tekes, Technology Specialist, 2001−2005 •

University of Helsinki, Adjunct Professor, 2001− •

CSC–ITCenterforScienceLtd.,BiosciencesSpecialist,1997−2001 •

AcademyofFinland,JuniorResearchFellowattheUniversityof •

Tübingen(Germany)andtheUniversityofCaliforniaatDavis

(USA), 1992−1995

BiocenterOulu,Coordinator,1995−1997 •


KIMMO KOSKENNIEMI (born 1945)

Ph.D. •

Professor of Language Technology, University of Helsinki •


University of Helsinki, Department of Modern Languages, •

Professor, 1991−

Academy of Finland, Researcher and Senior Researcher, •

1981−1990

University of Helsinki, Computing Centre, Mathematician, several •

positions including Division Manager, 1967−1980


OuTI KRAuSE (born 1948)

Vice Chair

D.Sc. (Tech.) •

Vice Dean •

Professor, Head of the Laboratory of Industrial Chemistry, •

Aalto University, School of Science and Technology

ADMInISTrATIon



Aalto University, change organization’s Team Leader •

Helsinki University of Technology, Vice Rector •

HelsinkiUniversityofTechnology,DepartmentofBiotechnology •

and Chemical Technology

Neste Oy, Research Fellow •

Neste Oy, Research and Development Unit, Program Manager •

Neste Oy, Catalysis Research, Department Manager •

Neste Oy, Catalysis Research, Group Manager •

Neste Oy, Oil Research, Researcher •

Eindhoven University of Technology, the Netherlands, •

Researcher

Helsinki University of Technology, Department of Chemistry, •

Industrial Chemistry, Senior Assistant



Helsinki Institute of Information Technology (HIIT), •

ChairoftheBoard

TechnologicalFoundation,Boardmember •

LahtiScienceandBusinessParkLtd,Boardmember •

Micronova,Boardmember •

EuropeanResearchInstituteofCatalysis(ERIC),Boardmember •

JuSSI NuORTEvA (born 1954)

D.Theol., Phil.Lic., Adjunct Professor •

Director General, National Archivist •


NationalArchivesServiceofFinland,DirectorGeneral,2003– •

UniversityofHelsinki,AdjunctProfessor,1998– •

FinnishLiteratureSociety,SecretaryGeneral,2000–2003 •

Academy of Finland, Secretary General of the Research Council •

forCultureandSociety,1998–2000

Board member since: 2007 (Deputy member), 2008 (member)


UniversityofTurku,Boardmember •

NationalBoardofHeraldry,Chair •

General Directorate of the Civil Service Departments and •

Institutes, Executive secretary

UniversityofHelsinki,ScientificAdvisoryBoardattheCentrefor •

European Studies, Chair

JOuKO pAASO (born 1956)

Ph.D.(Tech.),eMBA •

Rector, Oulu University of Applied Sciences (OAMK) •

Docent, University of Vaasa •


Oulu University of Applied Sciences (OAMK), Rector, 2009− •

Vaasa University of Applied Sciences (VAMK), Rector, 2004−2009 •

PehrBraheSoftwareLaboratory,HeadofLaboratory,2001−2004 •

University of Oulu, Raahe Unit (OAMK University of Applied •

Sciences is also within the Raahe unit), Unit Director,

Acting Professor, 1994−2004

Fraunhofer-InstitutfürGraphischeDatenverarbeitung, •

Darmstadt, Germany, Visiting Researcher, 1993−1994

RaaheSchoolofEngineeringandBusiness,Information •

Technology, Senior Lecturer in Information Technology,

1990−1993

VTT Electronics Laboratory, Oulu, CAE Division, Researcher, •

1982−1990

LM Ericsson, Software Design Division, Software Designer, •

1981−1982



Arenery,Boardmember •

RAKETTI information management project, Steering group •

member

Virtual University of Applied Sciences, Chair of Management Group •

Arene ry’s Education Programme project, Steering group member •

The Association of Entrepreneurs of Northern Ostrobothnia, •

Education Committee member

Taitaja2010Oulu–AdvisoryCommittee,member •

POEMFoundation,Boardmember •

NordeaBank,Oulu,Controller •

Oulu Innovation Alliance (OIA), Management Group member •

ADMInISTrATIon


bALAnCe SheeT


bALAnCe SheeT

boArD of DIreCTorS’ rePorT jAnUAry 1 – DeCeMber 31, 2009

CSC – IT CENTER FOR SCIENCE LTD. FISCAL YEAR 2009

CSC provides and develops information technology services for re-

search, teaching, and administrative functions. The clientele com-

prises higher education institutions, research institutes, and com-

panies. CSC is part of the national research system. CSC implements

the information strategy of the Ministry of Education by providing

those IT services for science that it is most practical to handle cen-

trally. The most important tasks of CSC consist of providing special-

ist, software and information services for science and information

technology, national and international data communications con-

nections, as well as offering computing resources for high-perfor-

mance computing and large-scale data storage. In accordance with

the CSC Articles of Association, CSC performs its services to aca-

demic communities on a non-profit basis.

Financially the fiscal period exceeded expectations. The turnover

increased significantly, exceeding the forecast and showing growth

of approximately 11.4%. CSC’s operations were cost-efficient, as in

previous years. The operational costs over the period remained well

under control and were below forecast, although the proportional

cost level increased from the level of previous years. The operating

profit of the fiscal year slightly exceeded the forecast. The objectives

set for the fiscal period were met better than planned.

The turnover in 2009 was EUR 21,878,322.71 (19,633,670.10).

The operating profit after financial items was EUR 54,520.54

(282,577.28) and the net profit for the fiscal period amounted to EUR

39,222.33 (206,154.58).

The company’s research and development costs in 2009 were

approximately 9.6% (6.8%) of the turnover.

kEY FINANCIAL INDICATORS DURINg THE FISCAL YEAR

For a company not seeking to make a profit, CSC’s financial result,

solvency and liquidity were good.

key indicators 2009 2008 2007 2006

Operating profit (%) 0.12 % 0.49 % 0.19 % -0.32 %

Return on equity 3.09 % 18.00 % 13.91 % 6.82 %

Return on invested capital 4.56 % 24.85 % 19.59 % 9.50 %

quick ratio 2.5 1.9 2.2 2.8

Equity ratio 24.6 % 22.78 % 27.56 % 24.53 %

RISkS AND UNCERTAINTIES

CSC’s new, more accurate Risk Management Plan was implemented

in 2009. Risks and the probability of occurrence as well as activities

to prevent them have been evaluated from several different per-

spectives. In the 104Risk Management Plan risks have been classi-

fied as strategic, operative, and damage risks. The work on risk man-

agement is part of the annual operational planning process, and

risks are assessed on a regular basis.

Security in CSC’s operations and services has been improved by

providing policies on good operational practices and carrying out

data security audits to evaluate whether the services produced by

CSC correspond to the requirements set by public administration.

Special requirements are enjoined with CSC’s special role as part of

the national critical infrastructure to secure critical activities in case

of disorders and emergencies.

Staff security has been improved by implementing a security as-

sessment procedure concerning the maintenance staff. Preventive

data security has been performed by inspecting data systems vul-

nerability. In addition, security requirements will be integrated as

part of contracts and agreements signed with suppliers, partners

and customers.

MAIN EVENTS DURINg THE FISCAL PERIOD

CSC has consolidated its role as a service organization providing sci-

ence with IT support and resources and as impartial coordinator of

information management projects for public administration and

higher education institutions. Demand for CSC services has readily

increased particularly in challenges relating to preservation of sci-

entific data and cultural heritage and joint information management

projects of higher education institutions. CSC supports sustainable

and competitive research infrastructure also by providing rapid data

communications connections, broad-based multi-disciplinary spe-

cialist services, and national high-performance computing capacity.

In 2009 CSC continued the upgrading project of the Finnish re-

search and education network, Funet, covering the whole of Fin-

land. The new optical-fiber backbone network enables an almost un-

restricted communication capacity, because one fiber can carry mul-

tiple data streams of 10 or 40 Gbps by using different wavelengths.

The fiber network makes it possible to offer dedicated, point to

point “light path” connections. CSC integrated the Haka user authen-

tication system of Finnish higher education institutions to the cor-

responding Nordic systems. In December CSC also signed a contract

that provides Funet member organizations with an opportunity to

join a certificate service offered by TERENA (Trans-European Re-

search and Education Networking Association). The Director of Fu-

net, Janne Kanner was appointed to chair TERENA.

Regarding the number of employees, CSC’s Information Manage-

ment Services became the greatest service area in 2009. A major

part of the work was focused on the RAKETTI project, which aims to

achieve national-level improvements in the quality, inter-operabili-

ty, and availability of the information and IT solutions needed in the

guidance, impact monitoring, and internal management of higher

education institutions. This project is coordinated by CSC, and it was

supplemented with the TUTKI subproject to address research and

research administration in higher education institutions and the

bALAnCe SheeT


JUREsubprojecttoimplementpublicationregisterservices.CSCal-

so prepared the implementation of the Virtu identity federation for

the Government IT Shared Service Centre, and the maturity of the

service was audited against the instructions for use on Government

information security levels (Valtion Tietoturvatasot -käsikirja). The

service reduces the number of user IDs in the shared public informa-

tion systems and is being implemented at the beginning of 2010.

The Finnish National Gallery signed a four-year contract with CSC on

system services; based on the contract CSC will supply an integrated

virtualization and server platform as well as disk system services.

In 2009 CSC storage capacity exceeded one petabyte. At the be-

ginning of 2009, the RTVA project started to archive ten TV channels

and six radio channels in the archiving system at CSC on a continu-

ous basis. Additionally, periodic samples are saved from other chan-

nels, and the total annual volume of packed material will be 200,000

hours. Furthermore, CSC renewed its long-term contract with the

National Library and the higher education institutions’ library con-

sortia on their saving index databases. In spring 2009, the Ministry of

Education set up a national cross-functional survey project to map

and coordinate better utilization of electronic data materials and re-

sources generated with public funds. The survey was carried out by

CSC, funded by the Ministry of Education. Additionally, CSC strongly

advanced the development work of the National Digital Library par-

ticularly by participating in the work on the surveys on long-term

preservation.

CSC’s computing environment was upgraded by acquiring and

installing a new cluster server. CSC also acquired a new supercom-

puter for the Finnish Meteorological Institute and assisted in the

transfer of the weather forecasting model to the new platform. CSC

arranged two Grand Challenge calls for computing projects that re-

quire considerable computing resources. Five Grand Challenge proj-

ects were completed during the year.

CSC participates in international collaboration networks to

strengthen Finland’s competitive edge. In 2009 CSC participated in

14 European and Nordic e-Infrastructure projects. Leif Laaksonen

continued as the chairman of the intergovernmental e-Infrastruc-

tures Reflection Group (e-IRG) and the EGI (European Grid Initiative)

Council chose CSC’s Per Öster to be its chairman. In summer 2009,

CSC became a member of the Alliance for Permanent Access (APA).

The aim of APA is to ensure accessibility and preservability of scien-

tific information in Europe.

YEAR 2010

In 2010 CSC will start to implement the strategy planned for

2010−2012. The aim is to consolidate CSC’s position as a national in-

frastructure providing efficient and reliable services to the entire

research system. CSC will actively participate in the work to develop

European e-Infrastructures, and the expertise gained from this work

will be used to improve the competitiveness of Finnish research.

CSC will widen its funding policies by providing attractive services

and infrastructures for national and international top-level research-

ers. CSC will also promote solutions that comply with the principles

of sustainable development, such as Green IT and innovative com-

putational solutions.

CSC’s business activities are expected to continue the positive

growth also in 2010. The growth expectation for turnover and costs

is approximately 14.9%. The growth is based largely on external

funding and new funding sources. CSC has succeeded well in mak-

ing collaboration agreements and project work funded through ex-

ternal sources. However, the continuing recession and scarcity of

funding are imposing challenges that will be met by controlling op-

erative costs and accurate planning.

The central theme for 2010 is quality of the operations. CSC will

implement the European Foundation of Quality Management (EFQM)

model to be used in the development of internal, customer and ser-

vice processes and results assessment. Furthermore, the review of

organizational structures to be carried out during the summer of

2010 is another effort to improve effectiveness.

In 2010, CSC will support the strengthening of national e-Infra-

structure in several fields. The three-year Funet optical fiber network

projectwillbecompletedupgradingFunetto10/40gigabit/slevel.

TheXDWdatawarehousewillbe implementedwithintheRAKETTI

project coordinated by CSC, and CSC will continue to coordinate the

subprojects concerning the administration of teaching and research,

and the total architecture. In cooperation with national memory or-

ganizations, Data Services for Science and Culture will develop solu-

tions relating to long-term storage of data, particularly in the Nation-

al Digital Library project. CSC will also continue the development of

the Finnish Grid Infrastructure, FGI to be linked to the European Grid

network. Preparations relating to the acquisition of a new-genera-

tion supercomputer will be initiated, and CSC will actively look into

possibilities for founding an eco-efficient national-level machine fa-

cility outside the metropolitan area.

CSC will promote the competitiveness of the Finnish research

and innovation system through intensive international networking

and collaboration. In 2010 CSC will participate in more than ten Nor-

dic and EU collaboration projects, in which the aim is to build Euro-

peanresearchinfrastructure.Byparticipatingactivelyininternation-

al Grid and infrastructure projects CSC ensures that Finnish research-

ers will have access to world-class scientific instruments and IT

resources.

ORgANIzATION AND STAFF

The total number of staff on December 31, 2009 was 191. The aver-

age number of employees was 182 and the average age was 39.

The head count at CSC is approaching two hundred. In accor-

dance with CSC values, we focus our efforts to motivating our staff

and well-being at work. While this allows various possibilities for in-

dividual career development paths and specialist learning within the

growing organization, at the same time, in order to maintain effec-

tiveness, certain processes and internal services will be made uni-

form and streamlined. CSC encourages on-the-job development,

taking into consideration the fact that people are different, and we

provide continued learning and health at work. Examples of our ac-

tivities in this direction include our extensive input to training our

staff, arrangements for study leave, and the extensive health insur-

ance plan for all personnel acquired in 2009.

Leadership is the most important factor in motivation at work.

For leadership, an important tool is the performance and goals dis-

cussions held twice a year. To facilitate these discussions, CSC pur-

chased and implemented new on-line software that makes docu-

mentation and saving of the discussion contents easy.

bALAnCe SheeT


Since there was increasing demand for CSC services, we set a re-

cord in the number of recruited employees. Still, in certain fields of

expertise it is very difficult to attract qualified specialists (e.g. expe-

rienced programming and database specialists). More than in previ-

ous years, CSC also focused on international recruiting. Twenty-five

new permanent employees started and seven permanent ones re-

signed. CSC’s age structure is good and we even managed to im-

prove it slightly. In spite of this, to safeguard our future, it is impor-

tant to pay attention to the transfer of expertise and information

flow between our employees.

Numberofstaffon31.12.2009:191 (countingallpersons)and

the 2009 average was 182.

key indicators 2009 2008 2007 2006

Number of staff 191 166 152 147Permanent 175 150 131 126Fixed-term 16 16 21 21

Men 77 % 78 % 79 % 78 %women 23 % 22 % 21 % 22 %

Age distribution< 30 12 % 16 % 10 % 13 %30-39 44 % 36 % 41 % 43 %40-49 32 % 36 % 37 % 32 %> 50 12 % 12 % 12 % 12 %Average age 39 39 40 39

educationbasic and vocational 23 %University of applied sciences 10 %University 42 %Post-graduate degrees 25 %

ENVIRONMENT

At the beginning of 2009 CSC's machine facilities turned to the use

of environmentally friendly energy, and the Finnish Association for

Nature Conservation (FANC) granted CSC the right to use the FANC

eco-energy label. In 2009, the server centers used 8.3 GWh of ener-

gy generating 8.300 kg of carbon dioxide emissions and 5.9 kg of

particle emissions. The facilities’ eco-efficiency in international

comparison is extremely good. Eco-energy efficiency is measured

by the Power Usage Effectiveness (PUE) factor, which refers to the

total power divided by the power consumed by the servers, and for

CSC server centers these factors were 1.4 and 1.8.

The 2009 theme at CSC was the “Year of the Environment”. The

aim was to promote sustainable development in daily work. Collect-

ing mixed waste from rooms was discontinued and employees were

instructed to sort waste as carefully as possible and take it to the

waste collecting sites on each floor. To reduce the amount of mixed

waste, dedicated waste containers for energy waste were added to

the waste collecting sites on each floor. To reduce paper consump-

tion two-sided printing was adopted and the printing of cover pages

with print-outs was disabled. The water pressure was reduced in the

office floors to save water.

The GreenCSC committee, with representatives from different

employee groups, worked in a systematic manner to promote CSC's

environmentally friendly approach. During 2009 the committee cre-

ated a draft for CSC environmental policy, and added the staff’s

awareness on environmental issues by, for example, arranging a dis-

cussion session and an event on the theme of nature.

In addition to recycling of colored and white paper, there are

dedicated waste containers in the CSC facilities for confidential pa-

per material, disks, tapes and transparencies to be destroyed, as

well as for recycling cardboard. Additionally, there is a biowaste con-

tainer on each floor. CSC uses the waste containers in the waste facil-

ityoftheLifeScienceCenter(LSC)forthefollowingwaste:biowaste,

energy waste, glass, batteries, fluorescent lamps, and metal scrap.

CSC’s environmental load consists mostly of electronic office

equipment, machine room facilities, and HPC equipment, and is due

to the production and scrapping of the equipment and to the ener-

gy consumed by them. Obsolete office equipment and small devices

are forwarded to appropriate recycling points dedicated for elec-

tronic waste. HPC devices are dismantled in cooperation with the

supplier and they are usually returned to the supplier.

Thecontroloftheofficelightingandheating/air-conditioningat

CSC is based on energy-saving, room-specific infrared motion de-

tectors. The lighting and temperature controllers are activated when

a person moves in the room. At other times the room automatically

enters the energy-saving state, i.e. the lights go off and the heating

returns to the basic level.

THE bOARD OF DIRECTORS’ PROPOSAL FOR THE DISTRI-bUTION OF THE FISCAL PROFIT

TheBoardofDirectorsproposesthattheprofitofthefiscalperiod

2009, EUR 39,222.33, be carried forward to retained earnings from

the previous fiscal periods and that no dividends be paid.

bALAnCe SheeT


INCOME STATEMENT

Jan. 1 − dec. 31, 2009 Jan. 1 − dec. 31, 2008Euros

Turnover 21 878 322,71 19 633 670,10 Staff costs 10 899 915,22 9 657 785,91Depreciation 100 866,80 109 155,21Other operating expenses 10 850 960,87 9 770 679,83 Operating profit/loss 26 579,82 96 049,15 Financial income and expenses 27 940,72 186 528,13 profit before extraordinary items 54 520,54 282 577,28 profit before appropriations 54 520,54 282 577,28and taxes Taxes -15 298,21 -76 422,70 Net profit/loss for the period 39 222,33 206 154,58

bALANCE SHEET

Assets dec. 31, 2009 dec. 31, 2008Euros Fixed assets Intangible assets 9 239,92 12 319,96 Tangible assets 291 754,43 316 996,33Investments 22 522,82 12 522,82 323 517,17 341 839,11Current assets Short-term receivables 2 245 065,59 1 840 575,96Cash and bank balance 7 451 506,13 6 335 199,06 9 696 571,72 8 175 775,02 10 020 088,89 8 517 614,13 liabilities dec. 31, 2009 dec. 31, 2008Euros Capital and reserves Share capital 200 000,00 200 000,00Reserve fund 136 375,86 136 375,86Retained earnings from previous periods 911 688,68 705 534,10Netloss/profitfortheperiod 39222,33 206154,58Total capital and reserves 1 287 286,87 1 248 064,54 liabilities 8 732 802,02 7 269 549,59Current liabilities 8 732 802,02 7 269 549,59 10 020 088,89 8 517 614,13

bALAnCe SheeT


FUNDS

2009 2008Euros

Cash flow from operating activities Cash generated from operations 23 915 775,76 20 286 043,18 Expenses from operations -22 730 046,04 -17 797 130,32Net cash flow before financing and taxes 1 185 729,72 2 488 912,86

Interests and expenses paid on financing costs of operations -3 747,38 -2 950,23 Cash flow generated from interests of operations 31 688,10 189 478,36 Taxes paid -14 818,51 -75 463,30Cash flow from operating activities 1 198 851,93 2 599 977,69

Cash flow from investing activities Investing in tangible and intangible assets -82 544,86 -126 921,36Cash flow from investing activities -82 544,86 -126 921,36

Change in liquid funds 1 116 307,07 2 473 056,33Liquid funds at start of period 6 335 199,06 3 862 142,73liquid funds at end of period 7 451 506,13 6 335 199,06

bALAnCe SheeT


bALAnCe SheeT

NOTES TO THE FINANCIAL STATEMENTS DECEMbER 31, 2009

Financial reporting principles Comparability The financial statements 2009 and 2008 are comparable. Fixed assets and planned depreciations Fixed assets have been capitalized for unreserved acquisitions. Planned depreciations are calculated based on the foreseeable time of use for the fixed assed items. The following planned depreciations are presented in the financial statement December 31, 2009. Machinery and furniture 25% of the net expenditure. pensions The company’s pension scheme is insured with an insurance company. The Managing Director’s pension scheme is no different from that of the other staff. Tax write-offs Tax receivables are calculated as interim differences between taxation and the financial statement using the tax rate confirmed for the subsequent fiscal years on the date of the financial statement. The balance sheet contains the calculated tax receivables in the amount of estimated foreseeable receivables.


Notes to the income statement Euroa Turnover 2009 2008Domestic turnover 21 878 322,71 19 633 670,10 Notes to staff 2009 2008

Total number of employees during the fiscal period ending Dec. 31 191 166Average number of employees 182 163 Staff costs 2009 2008Salaries 8 923 931,82 7 932 315,43Pension costs 1 478 483,40 1 310 043,49Other statutory staff expenses 497 500,00 415 426,99Total 10 899 915,22 9 657 785,91 Salaries and remunerations to the management 2009 2008BoardofDirectorsandManagingDirector 210790,59 177242,13

Remunerations to the Accountant 2009 2008Auditing of the accounts 4 300,00 4 300,00Other statements 3 000,00 4 750,00 7 300,00 9 050,00 Other operating expenses 2009 2008 Telecommunications, equipment and software costs 6 202 491,55 5 647 613,09Other expenses 4 648 469,32 4 123 066,74 10 850 960,87 9 770 679,83 Financial income and expenses 2009 2008 Income from interests and financing from others 31 688,10 189 478,36Expenses from interests and financing to others -3 747,38 -2 950,23Total financial income and expenses 27 940,72 186 528,13 Breakdown of taxes 2009 2008 Income taxes from actual operations -14 818,51 -75 463,30Taxes from previous years Change of calculated tax receivables -479,70 -959,40Total -15 298,21 -76 422,70

bALAnCe SheeT


bALAnCe SheeT

Notes to the balance sheetFixed assets Intangible assets Tangible assets

Intangible rights Machinery and furniture TotalPurchasecostJan.1,2009 16487,58 1118932,53 1135420,11Additions 72 544,86 72 544,86Purchase cost Dec. 31, 2009 16 487,58 1 191 477,39 1 207 964,97 AccrueddepreciationsJan.1,2009 4167,62 801936,20 806103,82Depreciations during the period 3 080,04 97 786,76 100 866,80Accrued depreciations Dec. 31, 2009 7 247,66 899 722,96 906 970,62 BookvalueDec.31,2008 316996,33 329316,29BookvalueDec.31,2009 9239,92 291754,43 300994,35 Ownerships in other companies 2009 2008Shares owned by the company Otaverkko Oy ownership % per ownership % per number of shares number of sharesPurchasecostJan.1,2009 2522,82 5.3/75 5.3/75PurchasecostDec.31,2009 2522,82 5.3/75 5.3/75BookvalueDec.31,2009 2522,82 5.3/75 5.3/75

TivitOy/ICTSHOK ownership % per ownership % per number of shares number of sharesPurchasecostJan.1,2009 10000,00 0,9/100 0,9/100Purchasecost,Dec.31,2009 10000,00 0,9/100 0,9/100Bookvalue,Dec.31,2009 10000,00 0,9/100 0,9/100

TivitOy/ICTSHOK ownership % per ownership % per number of shares number of sharesPurchasecostJan.1,2009 0,9/100PurchasecostDec.31,2009 10000,00 0,9/100BookvalueDec.31,2009 10000,00 0,9/100

Short-term receivables 2009 2008 Sales receivables 439 066,23 371 804,38Receivables carried forward 1 776 398,89 1 438 691,41Calculated tax receivables 29 600,47 30 080,17Total 2 245 065,59 1 840 575,96


Capital and reserves 2009 2008 SharecapitalJan.1,2009 200000,00 200000,00Change 0,00 0,00Share capital Dec. 31, 2009 200 000,00 200 000,00

ReservefundJan.1,2009 136375,86 136375,86Change 0,00 0,00Reserve fund Dec. 31, 2009 136 375,86 136 375,86

ProfitfrompreviousperiodsJan.1,2009 911688,68 705534,10Profit from previous periods Dec. 31, 2009 911 688,68 705 534,10

Netprofit/lossfortheperiod 39222,33 206154,58

Total capital and reserves 1 287 286,87 1 248 064,54

distributable assets dec. 31, 2009 2009 2008Profit from previous periods 911 688,68 705 534,10Profit from the fiscal period 39 222,33 206 154,58Total 950 911,01 911 688,68

distribution of capital funds by share types 2009 2008 number of shares number of sharesThe shares are entitled to one vote per share 10 000 10 000

Current liabilities 2009 2008

Advances received 4 787 232,36 3 039 479,50Accounts payable 786 066,61 1 778 695,74Other current liabilities 970 936,12 477 444,01Adjusting entries for liabilities 2 188 566,93 1 973 930,34 8 732 802,02 7 269 549,59 Key figures 2009 2008 2007 2006- Operating profit (%) 0,12 % 0,49 % 0,19 % -0,32 %- Return on equity 3,09 % 18,00 % 13,91 % 6,82 %- Return on invested capital 4,56 % 24,85 % 19,59 % 9,50 %- Quick ratio 2,5 1,9 2,2 2,8- Equity ratio 24,60 % 22,78 % 27,56 % 24,53 %

bALAnCe SheeT


bALAnCe SheeT

CSC – IT CENTER FOR SCIENCE LTD. SIgNINg OF THE bOARD OF DIRECTORS' REPORT AND THE FINANCIAL STATEMENTS

In Espoo, March 18, 2010 Taina Pihlajaniemi Kari-Pekka Estola Erja Heikkinen

KimmoKoskenniemi OutiKrause JussiNuorteva

JoukoPaaso KimmoKoski Managing Director

Auditor’s Report to the Financial Statements As a result of the conducted audit of the accounts the Auditor’s Report was submitted today.

In Espoo, March 31, 2010 MOORESTEPHENSREWINETOYAB

JariPaloniemi

APA

A LIST OF THE LEDgERS DURINg THE FISCAL PERIOD jANUARY 1, 2009 – DECEMbER 31, 2009

Cash book

Journal

General ledger

Accounts receivable ledger

Accounts payable ledger

Invoice ledger

Purchase invoice ledger

Postdated receipts

Salary summary

Salary payment receipts

Payment receipts

VAT payment receipts


bALAnCe SheeT

AUDIT rePorT

TO THE ANNUAL gENERAL MEETINg OF CSC – IT CENTER FOR SCIENCE LTD.

We have audited the accounting records, the financial statements,

theReportoftheBoardofDirectors,andtheadministrationofCSC

–ITCenterforScienceLtd.forthefinancialperiodJanuary1–De-

cember 31, 2009. The financial statements include income state-

ment, balance sheet, funds statement, and notes to the financial

statements.

RESPONSIbILITY OF THE bOARD OF DIRECTORS AND THE MANAgINg DIRECTOR

TheBoardofDirectorsand theManagingDirectorare responsible

for the preparation of the financial statements and the report of the

BoardofDirectors,aswellasforthefairpresentationoftheminac-

cordance with laws and regulations governing the preparation of fi-

nancialstatementsandthereportoftheBoardofDirectorsinFin-

land.TheBoardofDirectors is responsible for theappropriatear-

rangement of the control of the company’s accounts and finances,

and the Managing Director shall see to it that the accounts of the

company are in compliance with the law and that its financial affairs

have been arranged in a reliable manner.

AUDITOR’S RESPONSIbILITY

Our responsibility is to perform an audit in accordance with good

auditing practice in Finland, and to express an opinion on the finan-

cial statementsand the reportof theBoardofDirectorsbasedon

our audit. Good auditing practice requires that we comply with ethi-

cal requirements and plan and perform the audit to obtain reason-

able assurance whether the financial statements and the report of

the Board of Directors are free from material misstatement and

whetherthemembersoftheBoardofDirectorsandtheManaging

Director have complied with the Limited Liability Companies Act.

An audit involves performing procedures to obtain audit evi-

dence about the amounts and disclosures in the financial statements

andthereportof theBoardofDirectors.Theproceduresselected

depend on the auditor’s judgment, including the assessment of the

risks of material misstatement of the financial statements and of the

reportoftheBoardofDirectors,whetherduetofraudorerror. In

order to design audit procedures that are appropriate in the circum-

stances the auditor may also consider internal control relevant to

the entity’s preparation and fair presentation of the financial state-

ments and the report of the Board ofDirectors. An audit also in-

cludes evaluating the appropriateness of accounting policies used

and the reasonableness of accounting estimates made by manage-

ment, as well as evaluating the overall presentation of the financial

statementsandthereportoftheBoardofDirectors.

The audit was performed in accordance with good auditing prac-

tice in Finland. We believe that the audit evidence we have obtained is

sufficient and appropriate to provide a basis for our audit opinion.

OPINION OF THE FINANCIAL STATEMENTS AND THE REPORT OF THE bOARD OF DIRECTORS

Inouropinion,thefinancialstatementsandthereportoftheBoard

of Directors give a true and fair view of the financial performance

and financial position of the company in accordance with the laws

and regulations governing the preparation of the financial state-

mentsandthereportoftheBoardofDirectorsinFinland.Theinfor-

mationinthereportoftheBoardofDirectorsisconsistentwiththe

information in the financial statements.

OPINION bASED ON THE DECISION MADE bY THE ANNUAL gENERAL MEETINg

The Board of Directors’ proposal for the distribution of the fiscal

profit is in compliance with the rules of the Finnish Limited Liability

CompaniesAct.WesupportthattheMembersoftheBoardofDirec-

tors and the Managing Director should be discharged from liability

for the financial period audited.

Espoo March 31, 2010

Moore Stephens Rewinet Oy Ab

JariPaloniemi,APA


CSC In STATISTICS

orgAnIzATIon ProjeCTS USerS

University of Helsinki 187 563Helsinki University of Technology 109 273CSC (DEISA) 49 130University of jyväskylä 30 88University of Oulu 28 65University of Turku 41 58CSC (Projects) 24 51University of kuopio 20 47Tampere University of Technology 26 40CSC (PRACE) 18 34Industry 17 32CSC (EgEE) 4 29University of Tampere 14 28CSC (grand Challenge) 8 19Åbo Akademi 11 17Lappeenranta University of Technology 13 16University of joensuu 10 15Helsinki School of Economics 10 12CSC (M-grid) 2 11CSC (HPC-Europa2) 9 9Finnish Meterological Institute 1 5Tampere University of Applied Sciences 5 5Lahti University of Applied Sciences 1 5University of Lapland 2 4Metropolia University of Applied Sciences 2 2Rovaniemi University of Applied Sciences 1 2kemi-Tornio University of Applied Sciences 1 1Total 643 1561

DISCIPLIne ProjeCTS USerS

biosciences 170 345Physics 89 263Chemistry 53 168grid usage 46 130Nanoscience 41 120Language research 35 116Earth sciences 17 78Computer science 14 61Computational fluid dynamics 30 50Engineering 27 35Mathematics 23 32Industry 17 32Astrophysics 15 25Structural analysis 21 23Computational drug design 4 18Environmental sciences 8 15Electromagnetics 10 13general usage 4 13Social sciences 4 8Economics 6 6Statistics 5 6Medical sciences 3 3Materials sciences 1 1Total 643

USerS of CoMPUTIng SerVerS by orgAnIzATIon 2009

USerS of CoMPUTIng reSoUrCeS by DISCIPLIne 2009

Muut 94 180

36 %

17 % 8 %

6 %

4 %

4 %

3 %

3 %

3 %

2 %

2 %

12 %

Tietokoneresurssien käyttäjät organisaatioittain 2009

Helsingin yliopisto

Teknillinen korkeakoulu

CSC (DEISA)

Jyväskylän yliopisto

Oulun yliopisto

Turun yliopisto

CSC (Projektit)

Kuopion yliopisto

Tampereen teknillinen yliopisto

CSC (PRACE)

Teollisuus

Muut

University of Helsinki

Helsinki University of Technology

CSC (DEISA)

University of jyväskylä

University of Oulu

University of Turku

CSC (Projects)

University of kuopio

Tampere University of Technology

CSC (PRACE)

Industry

Other

36 %

17 %

6 %

8 %

4 %

3 %

3 %

3 %

4 %

2 %2 %

1561

biosciences

Physics

Chemistry

grid usage

Nanoscience

Language research

Earth sciences

Computer science

Computational fluid dynamics

Engineering

Other

22%

17%

11%8%

8%

7%

5%

4%

3%

2%

13%

!"#$%&%'#(#)*())"#'+&,-.,/,$+0#1#23%".2"'+4556++

*i,-eteet

Fysiikka

Kemia

7ri9:k;y<=

>an,-e9e

Kielentutkimus

7e,-eteet

Tiet,Cenk;si<ely-e9e

Virtauslaskenta

Tekniikka

Muut

17 %

8 %

4 %

5 %

3 %

13 %22 %

2 %

7 %

8 %11 %

12 %


CSC In STATISTICS

USAge of ProCeSSor TIMe by orgAnIzATIon 2009

USAge of ProCeSSor TIMe by DISCIPLIne 2009

orgAnIzATIon ProCeSSor TIMe*

University of Helsinki 16 802 637Helsinki University of Technology 11 475 343University of jyväskylä 8 806 822CSC (grand Challenge) 7 113 352CSC (DEISA) 6 340 074University of Oulu 5 456 391Lappeenranta University of Technology 1 904 227University of Turku 1 198 618Tampere University of Technology 1 131 996CSC (HPC-Europa2) 825 772CSC (Projects) 764 645CSC (PRACE) 295 690University of kuopio 273 852Metropolia University of Applied Sciences 140 084University of Tampere 90 242Finnish Meterological Institute 44 092Åbo Akademi 34 074Industry 25 651CSC (EgEE) 4 192University of joensuu 3 085Helsinki School of Economics 2 213Rovaniemi University of Applied Sciences 224CSC (M-grid) 195Tampere University of Applied Sciences 53University of Lapland 23Lahti University of Applied Sciences 1kemi-Tornio University of Applied Sciences 1Total 62 733 549* Cray XT4/5 cpu hours

DISCIPLIne ProCeSSor TIMe*

Nanoscience 19 027 991Physics 16 292 067biosciences 9 187 191Chemistry 8 096 565grid usage 5 588 276Astrophysics 2 855 412Computational drug design 732 393Computational fluid dynamics 422 705Earth sciences 260 400Engineering 154 399Mathematics 36 872Industry 20 618Environmental sciences 17 607Structural analysis 15 721Computer science 13 966general usage 4 146Economics 2 764Electromagnetics 2 678Language research 923Statistics 460Medical sciences 393Social sciences 1Materials sciences 1Total 62 733 549* Cray xT4/5 cpu hours

University of Helsinki

Helsinki University of Technology

University of jyväskylä

CSC (grand Challenge)

CSC (DEISA)

University of Oulu

Lappeenranta Univ. Tech.

University of Turku

Tampere University of Technology

CSC (HPC-Europa2)

Other

Muut 1 678 317

27%

18%

14%

11%

10%

9%

3%

2%2%

1% 3%

!"#$%&%'#(#)*())"#'+&,-./+%(01'")112%".1"'+3445++

Helsinginyliopisto

Teknillinenkorkeakoulu

Jyväskylänyliopisto

CSC(GrandChallenge)

CSC(DEISA)

Oulunyliopisto

Lappeenrannanteknillinen

yliopisto

Turunyliopisto

Tampereenteknillinen

yliopisto

CSC(HPC‐Europa2)

27 %

18 %11 %

14 %

9 %

3 %

10 %

2 %2 %

3 %1 %

Muut 530 949

30%

26%

15%

13%

9%

4%1%

1%1%

!"#$%&%'#(#)*())"#'+&,-./+0#1#23%".2"'+4556++

+an./e1e

Fysiikka

7i./eteet

Kemia

;ri1=k>y?@

A>B//e1e

C>>keainesuunni?elu

Virtauslaskenta

Muut

Nanoscience

Physics

biosciences

Chemistry

grid usage

Astrophysics

Computational drug design


Other

15 %

13 %

9 %

1 %

30 %

4 %

26 %

1 %1 %


CSC In STATISTICS

ToP-TwenTy ACADeMIC CoMPUTIng ProjeCTS ACCorDIng To ProCeSSor TIMe USeD 2009

orgAnIzATIon ProjeCTS LeADer ProjeCT nAMe DISCIPLIne

University of Oulu kari Laasonen Ab initio molecular dynamic methods Chemistry

CSC grand Challenge Tomasz Rog/ TUT Large-scale dynamics of the cytochrome bc1 complex biosciences

University of Helsinki Flyura Djurabekova Radiation damage in particle accelerator materials Physics

DEISA (CSC) jeremy Nowell DECI projects HPqCD, SoMquark and HPqCD2 grid usage

University of Helsinki Petri käpylä Differential rotation and dynamos in convective stellar envelopes Astrophysics

University of jyväskylä Hannu Häkkinen Electronic, magnetic, optical and chemical properties of nanoparticles Nanoscience

University of jyväskylä Olli Pentikäinen Computational study on structures biosciences

University of Helsinki Arkady krasheninnikov Modification of carbon nanotubes Nanoscience

Tampere University of Technology Ilpo Vattulainen Physics of biological systems Nanoscience

University of Helsinki Tapio Ala-Nissilä Research of stochastically disturbed systems Physics

University of jyväskylä karoliina Honkala Nano catalysis on metal surfaces Nanoscience

DEISA (CSC) giovanni Erbacci DECI projects bICaPS, PHASEALL and RNAHIV grid usage

CSC grand Challenge Olli Pentikäinen C-LIVE project of University of jyväskylä biosciences

Lappeenranta University of Tech. Matti Alatalo Multi scale modeling of surfaces and surface reactions Nanoscience

University of Oulu Perttu Lantto Theoretical computation of NMR parameters in realistic physical states Chemistry

Helsinki University of Technology Rainer Salomaa Numeric modeling of plasma and fusion physics Physics

Helsinki University of Technology Risto Nieminen qUEST Physics

Helsinki University of Technology Risto Nieminen Carbon nanotubes Nanoscience

University of Helsinki kari Rummukainen Relativistic theories of simulation in lattice Physics

Helsinki University of Technology Martti Puska Using and developing electron structure programs Physics

ProjeCT CLASS* ProjeCTS %

< 500 cpuh (small usage) 425 66,1500-20 000 cpuh (medium size usage) 101 15,7>20 000 cpuh (major usage) 117 18,2Total 643 100

ProCeSSor TIMe* %

66 044 0,11576 310 0,9262 091 195 98,9762 733 549 100 *converted to Cray XT4/XT5 cpu hours.

ProjeCTS ACCorDIng To USeD CoMPUTIng reSoUrCeS 2009

66,1%

15,7%

18,2%

!askenta(r*+ek,en+akautu/inenk*k*lu*kkiin2334

(vertailusuureenalaskentayksiköt)

*lle500ly(0ie2k4y567

500‐20000ly(keskisuuri

k4y567

yli20000ly(suurk4y567

18,2 %

15,7 %

66,1 %

< 500 cpuh (small usage)

500-20 000 cpuh (medium size usage)

>20 000 cpuh (major usage)


CSC In STATISTICS

SofTwAre ProCeSSor TIMe* DISCIPLIne

gPAw 8 554 408 Density Functional TheoryNAMD 6 480 661 biosciencesgromacs 4 162 646 quantum ChemistryTurbomole 1 011 026 quantum Chemistrygaussian 484 166 quantum ChemistryCPMD 455 448 Density Functional TheoryADF 165 707 quantum ChemistrybLAST 149 679 biosciencesElmer 139 713 Engineering (FEM)Molpro 130 750 quantum ChemistryOther 308 256 Total 22 042 460

*cpu hours Louhi's share of software usage is 83.0%.

DISCIPLIne ProjeCTS

biosciences 64Language research 39grid usage 32Physics 27Engineering 19Chemistry 17Structural analysis 14Computational fluid dynamics 11Computer science 10Mathematics 8Nanoscience 8Other 31Total 280

APPLICATIon SofTwAre USAge ACCorDIng To ProCeSSor TIMe 2009 (Louhi, Murska, Hippu and Corona servers)

new ProjeCTS by DISCIPLIne 2009

39%

29%

19%

4%

2%

2%1% 1%

1% 1%

1%

!"#$%%&'"()$%*+',"-./01234"'$''"4+5)562*&-55627889222

GPAW

NAMD

Gromacs

Turbomole

Gaussian

CPMD

ADF

BLAST

Elmer

Molpro

Muut

gPAw

NAMD

gromacs

Turbomole

gaussian

CPMD

ADF

bLAST

Elmer

Molpro

Other

39 %

29 %

19 %

4 %2 %

2 %1 %

1 %

1 %1 % 1 %

biosciences

Language research

grid usage

Physics

Engineering

Chemistry

Structural analysis


Computer science

Mathematics

Nanoscience

Other

64

39

32

27

19

17

14

11

10

8

8

31

!"#$%&'()*$+,%&,$#$-.)/0-/1&2334&

+i-.eteet

Kielentutkimus

8ri:;k<y>?

Fysiikka

Tekniikka

Kemia

Rakenneanalyysi

Virtauslaskenta

Tiet-Eenk<si>ely.e:e

Matema.ikka

Gan-.e:e

Muut

64

39

3227

19

17

14

11

10

8

31

8


CSC In STATISTICS

AVAILAbILITy of CSC'S CoMPUTIng AnD APPLICATIon SerVerS In 2009

0

10

20

30

40

50

60

70

80

90

100

Tammi Helmi Maalis Huh78 Touko Kesä Heinä Elo Syys Loka Marras Joulu

%#$%&'()$*$+,'+-.-'(&/0)'1/,00%,23(($4556

Corona Hippu Louhi Murska

821.G23.4.2009kaikillapalHelimillaoli56tunninpituinen7etoturHakäyJökatko.KaikkienasiakastunnustensalasanatHaihLeMin.

(poistuikäytöstä21.4.) (aHaMinasiakkaille21.1.)

jan Feb Mar Apr May jun jul Aug Sep Oct Nov Dec

* between 21st and 23rd of April there was 56 hours usage break due to security reasons. All customer passwords were changed.

%100

908070605040302010

0

Corona Hippu Louhi Murska(phased out on 21.4.) (opened to customers on 21.1.≈)

LogInS AnD bATCh jobS

AT CSC'S SerVerS 2005–2009

0

50 000

100 000

150 000

200 000

250 000

300 000

350 000

Tammi Helmi Maalis Huhti Touko Kesä Heinä Elo Syys Loka Marras Joulu

Lkm

Sisäänkirjautumiset ja eräajot CSC:n palvelinympäristössä 2005–2009

2005 2006 2007 2008 2009

310 061

Count

350 000

300 000

250 000

200 000

150 000

100 000

50 000

0

310 061


2005 2006 2007 2008 2009

(Including maintenance and other service breaks)


CSC In STATISTICS

foreIgn USer ACCoUnTS AT

CSC'S CoMPUTIng enVIronMenT 2009

(770 users from 63 countries)

CoUnTry USerS

germany 149France 73Italy 72United kingdom 59The Netherlands 44China 41Spain 38Russia 33Poland 30India 28Other (53 countries) 203Total 770

19%

10%

9%

8%

6%5%5%

4%

4%

4%

26%

CSC:npalvelinympäristönulkomaalaiset

käy6ä7ätunnukset899:;<<9käy6ä7ää=>maasta?

Saksa

Ranska

Italia

En6lan7

Alankomaat

Kiina

Espanja

Venäjä

Puola

In7a

Muutmaat(53kpl)

26 %

4 %

4 %

4 %

5 %

5 % 6 %

8 %

9 %

10 %

19 %

ProCeSSor TIMe USAge of The ACADeMy of fInLAnD'S

CenTreS of exCeLLenCe on CSC'S SerVerS 2006–2009

CoE period 2002–2007 CoE period 2008–2013 CoE period 2006–2011 Othet academic processor time usage

0

10 000 000

20 000 000

30 000 000

40 000 000

50 000 000

60 000 000

70 000 000

2006 2007 2008 2009

Nor

mal

isoi

tua

pros

esso

ritun

tia

Suomen Akatemian huippuyksikköjen prosessoriajan käyttö CSC:n palvelimilla 2006–2009

SA kausi 2002–2007 SA kausi 2006–2011

SA kausi 2008–2013 Muu akateeminen laskentakäyttö

SA-käyttöosuus

29.9 %

38.5%

29.5 %

32.1 % 70 000 000

60 000 000

50 000 000

40 000 000

30 000 000

20 000 000

10 000 000

0

Norm

alize

d pr

oces

sor h

ours

CoE share 29.9 %

2006 2007 2008 2009

38.5 % 29.5 % 32.1 %

germany

France

Italy

United kingdom

The Netherlands

China

Spain

Russia

Poland

India

Other (53 countries)


CSC In STATISTICS

nUMber of jobS AT ChIPSTer SerVICe 2008–2009

0

500

1000

1500

2000

2500

3000

3500

4000

4500

5000

Tammi Helmi Maalis Hu23 Touko Kesä Heinä Elo Syys Loka Marras Joulu

Töidenlkm Chipster‐palvelussaajetuttyöt2008–2009

2008 2009

A2iBsCerDBalEeluaEaFinasiakkaillemaaliskuussa2008G4526


Count

5 000

4 000

4 500

3 500

3 000

2 500

2 000

1 500

1 000

500

0

4 526

2008 2009

Chipster was opened to customers in March 2008.

USAge of PAITULI geogrAPhIC InforMATIon SerVICe 2009

0

500

1000

1500

2000

2500

Hu() Touko Kesä Heinä Elo Syys Loka Marras Joulu

Lkm %&'()*+,-&+kk&./01-&*2/*)3k4567899:

Sivulataukset Aineistolataukset

1162

@aATuliBCalveluavaDinasiakkaille(u()kuussa2009F1980

Count

2 500

2 000

1 500

1 000

500

0

Hits per pages Material downloads

Apr May jun jul Aug Sep Oct Nov Dec

1 980PaITuli web service was opened to customers in April 2009.

1 162


CSC In STATISTICS

enD-USerS of The hAk A feDerATIon 2005–2009

0

50 000

100 000

150 000

200 000

250 000

300 000

350 000

hu

hti/0

5

ke

sä

/05

elo

/05

loka

/05

jou

lu/0

5

he

lmi/0

6

hu

hti/0

6

ke

sä

/06

elo

/06

loka

/06

jou

lu/0

6

he

lmi/0

7

hu

hti/0

7

ke

sä

/07

elo

/07

loka

/07

jou

lu/0

7

he

lmi/0

8

hu

hti/0

8

ke

sä

/08

elo

/08

loka

/08

jou

lu/0

8

he

lmi/0

9

hu

hti/0

9

ke

sä

/09

elo

/09

loka

/09

jou

lu/0

9

Lkm

Haka-luottamusverkoston loppukäyttäjät 2005–2009

Sopimuskattavuus Palvelun loppukäyttäjät (IdP-palvelin liitetty Hakaan)

Count

350 000

300 000

250 000

200 000

150 000

100 000

50 000

0

Agreement coverage End-users (IdP-server connected Haka)

04/2

005

06/2

005

08/2

005

10/2

005

12/2

005

02/2

006

04/2

006

06/2

006

08/2

006

10/2

006

12/2

006

02/2

007

04/2

007

06/2

007

08/2

007

10/2

007

12/2

007

02/2

008

04/2

008

06/2

008

08/2

008

10/2

008

12/2

008

02/2

009

04/2

009

06/2

009

08/2

009

10/2

009

12/2

0 09

LogInS To hAk A SerVICeS 2006–2009USAge of PAITULI geogrAPhIC InforMATIon SerVICe 2009

Marras 143 968 312 149 616 255 820 760

Joulu 97 440 221 972 442 185 534 277

Yhteensä 497 342 1 994 698 3 818 229 5 451 752

820 760

0

100 000

200 000

300 000

400 000

500 000

600 000

700 000

800 000

900 000

Tammi Helmi Maalis Huhti Touko Kesä Heinä Elo Syys Loka Marras Joulu

Lkm Kirjautumiset Haka-palveluihin 2006–2009

2006 2007 2008 2009 Count

900 000

800 000

700 000

600 000

500 000

400 000

300 000

200 000

100 000

0 jan Feb Mar Apr May jun jul Aug Sep Oct Nov Dec

2006 2007 2008 2009

820 760


RESEARCH RESULTS ObTAINED wITH CSC RESOURCES



SoLAr MAgneTIC fIeLD generATIon VerIfIeD by MoDeLIng

As part of their Grand Challenge project, Maarit Korpi, Petri

Käpylä (University of Helsinki) and Axel Brandenburg (Nordita)

have used computational modeling to show how large-scale or-

dered magnetic fields can be generated within the turbulent

solar convection zone.

Scientists have tried to model the solar magnetic field generation for

morethantwodecades.Basedontheoreticalevidenceithasbeenknown

that a large-scale hydromagnetic dynamo involving convective turbulence

and large-scale shear due to solar differential rotation should be able to

generate magnetic fields, and now the research group was able to verify

this phenomenon computationally. In addition, the researchers also

showed the saturation level of the large-scale magnetic field to be indepen-

dent, within given error limits, of the Reynolds number.

Producing large-scale magnetic fields in local direct numerical simula-

tions has proven to be surprisingly challenging, even when the minimum

requirements for the classical dynamo theory, stratification and differen-

tial rotation, have been included. The idea behind the Dynamo08 project

was to include dynamic shear, which is known to be a significant factor in

the solar dynamo process, in addition to the previously mentioned pa-

rameters.

The project of Maarit Korpi et al. exploited more than 2000 processors

and some 1,660,000 processor hours of CSC’s computing resources. n

The y-component of a magnetic field in a simulation that exhibits a large-scale dynamo. The grid size in this simulation is 5123 and the computing took about six weeks with 512 cores.

© P

etri

Käp

ylä

by/beq2,5

0,0

-2,5

t=1500.0

DISSerTATIon on The reLIAbILITy of MeThoDS USeD In MoDeLIng of SheLL STrUCTUreS

In his doctoral dissertation, Antti Niemi analyzed the reliability of

computational methods used in the modeling of thin shell struc-

tures, and proposed improvements to the simplest and most fa-

vored models. Niemi performed his thesis studies at Helsinki Univer-

sity of Technology using CSC’s software and computing services.

Relative to their weight, shell structures are strong, so they are

commonly used in, for example, aviation and space technology.

These structures are usually studied by computational shell model-

ing, which allows calculation of strains caused by external loads on

the shells, using the finite element method.

Most commercially available programs commonly favor simple

bilinear elements for structural analysis of shells. However, finding

an appropriate formulation for such elements has turned out to be a

challenging task due to various numerical locking phenomena that

are characteristic to shell problems when modeled by finite ele-

ments of low order. Although the numerical methods have been un-

der constant development, most experts in this field still regard the

accuracy of current models to be insufficient.

This thesis a new type of formulation which is based on a thor-

ough mathematical analysis of the locking phenomenon. Numerical

experimentsusingtheABAQUSandADINAcodesshowthatunder

certain circumstances the accuracy of the new element is superior to

the currently used elements. Additionally, mathematical error analy-

sis supports the new formulation, unlike most of its commercial

competitors. n

Lowest eigenmode of the cylindrical shell at R/t = 100, 1000, 10000 and 100000: uniform 7×N meshes of MITC4S elements with N = 19, 32, 58 and 104.

© A

ntt

i Nie

mi



Perttu Lantto and his NMR research

group have used CSC’s supercom-

puter Louhi for calculating NMR

shielding tensors forxenon (Xe)andother

heavy nuclei. In this Xe-NMR study, they

showed chemical shift of, for example, xe-

non, to occur in various nanosystems, such

as carbon nanotubes and clathrates. Clath-

rates are molecular complexes consisting

typically of a cage formed from one type of

molecule containing a second type of atom

ormolecule(inthiscase,Xe).

TheXeatomworksasasensitivechemi-

cal sensor for the construction being stud-

ied:theNMRspectrumparametersprovide

information on the chemical environment

oftheXe”spyatom”anditselectronstruc-

ture. Computation is used to solve the mes-

sage of the signal, i.e. what kind of environ-

mental effects are involved and the real

properties of the environment.

The overall purpose of the study is to ex-

plain experimental, and partly still not inter-

preted NMR phenomena. The aim is to cre-

ate an atomic-level simulation, in which the

effects of electron correlation, relativistic

theory, thermal motion, and environment

are taken into account. In addition to raising

interest as a computational topic in general

and developing the theory of NMR parame-

ters, the research helps experimental NMR

research used for determining and develop-

ing material properties.

In ordinary quantum chemistry calcula-

tions coarse-grained methods are sufficient

to describe the electrons on the shells close

to the nucleus, since the target of interest

is, for example, atom-atom interactions.

These, as many other chemical properties

of molecules, are mainly determined by in-

teractions between valence electrons far

away from the nucleus.

As the nucleus becomes heavier, the

speeds of the electrons close to the nucle-

us become very great, and relativistic the-

ory is needed to describe them sufficiently.

For valence electrons these relativistic ef-

fects become visible only with quite heavy

elements.

In contrast, NMR spectrum parameters

depend on interactions between the nucleus

and its electron shielding, where not only

good valence electron description but also

the electron system immediately next to the

nucleus play key roles. Therefore, the entire

electron system spectrum must be mea-

sured well. Since inner-shells electrons move

quite rapidly close to relatively light nuclei,

the group has observed relativistic effects of

NMR spectrum parameters for molecules

that contain only the first and second order

elements, e.g. carbon and sulfur.

The Breit-Pauli perturbation theory

(BPPT)modeldevelopedby thegroupcan

be used for calculating relativistic phenom-

ena due to NMR nuclear shielding parame-

ters due to heavy or near-heavy nuclei.

When supplemented with Hartree-Fock (HF)

and density functional theory (DFT), it is

currently the only theory for problems of

correlated wave function theories (MP2, CC,

etc.), which makes it possible to perform ac-

curate benchmark modeling of both large

systems and small molecules. n

xenon USeD AS A SPy broUghT new InforMATIon on MATerIALS’ ProPerTIeS

© J

yrki

HH

okk

anen



In their Grand Challenge (GC) project called “Y-Nano-

Kills” Luca Monticelli and Emppu Salonen (Helsinki

University of Technology), and Ilpo Vattulainen (Tam-

pere University of Technology) used atomic-level molec-

ular dynamics to investigate how clusters of fullerene

and gallic acid disturb the function of cell membranes

and the ionic channels in them.

In their earlier studies they observed that cells are not

significantly affected when exposed separately to either

fullerenes or gallic acid. However, when fullerenes and

gallic acid are present in the cell culture at the same time,

they interact to form structures that cause cell death

within a few tens of minutes. The objective of the Grand

Challenge project was to find out why this happens. n

whAT MAkeS nAnoPArTICLeS AbLe To CAUSe CeLL DeATh?

© L

uca

Mo

nti

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, Hel

sin

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f Te

chn

olo

gy

The two pictures show fullerene being linked to the cell membrane and an ion channel traversing the membrane. Simulations provide a means for studying the micro-scale mechanisms that enable fullerene and gallic acid to affect cell membrane properties and the functionality of proteins present in cell membranes. These include changes in the internal pressure and elasticity of the cell membrane, which can, in turn, affect the structures and dynamics of some membrane proteins, and thus their functionality. Additionally, simulations make it possible to investigate the complex dynamic phenomena that occur in the cell membrane, such as the properties relating to diffusion of proteins and lipids within the “interactive commu-nity”, under the circumstances of a pure water phase or the cell membrane being exposed to carbon nanoparticles and gallic acid.

© L

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Researchers at the Nanoscience Cen-

ter(NSC)oftheUniversityofJyväs-

kylä, together with researchers from

theUniversityofBirmingham,haveshown

that scanning tunneling microscopy (STM)

measurements of nanoscale phenomena

can be affected by the measurement de-

vice.

The research group at the University of

Birminghamexperimentallyobservedmono-

layer-thick islands of potassium atoms on

graphite substrate. Using STM imaging they

discovered that the edges of the potassium

islands shone brightly.

Using ab initio density functional calcu-

lations and SMT simulations, the NSC re-

searchers at the University of Jyväskylä

showed that the results are affected by po-

tential difference between the measuring

probe and the target and that the bright

edges are caused by the potential field of

the device itself.

Hence, measuring in the quantum world

may change the measuring object, and this

should be taken into account in future STM

imaging.

“The dependence on potential in STM

imaging is also an important finding for the-

orists, because the potential field is com-

monly ignored in STM simulations”, says

Jukka Akola(UniversityofJyväskylä,Nano-

science Center and Tampere University of

Technology, Department of Physics). n

brIghT eDgeS of PoTASSIUM ISLAnDS on grAPhITe Are CAUSeD by The MeASUreMenT DeVICe



C limate modeling combined with investi-

gation of fossils enables researchers to

investigate how environmental change

has affected the evolution of mammal commu-

nities.

Researchers at the University of Helsinki

have shown how climate factors explain the

long-term development of mammal commu-

nities in pre-historic Eurasia. Using an exten-

sive database of fossil mammalian fossils they

were able to follow the rise and fall of the geo-

graphic distribution of mammal communities

over a much longer time scale than before.

When this data is coupled with climate model-

ing, researchers can conclude which atmo-

spheric processes are associated with the

changes in distributions. This is one of the first

studies in which climate modeling and tradi-

tional paleontological materials are seamlessly

combined in one study. The results of the

study help to relate changes in the longitudi-

nal climate development to the evolution, ex-

tinction, and community structure of mam-

mals.

The study, published in the Proceedings of

the National Academy of Sciences (USA) jour-

nal, explains how pre-historic mammal com-

munities developed into a regionally uniform

fauna and which factors directed the behavior

of the fauna. The research was conducted

jointly by paleontologists and a climate mod-

eler and it utilized the NOW (Neogene of the

Old World) database that contains information

on mammalian fossils, maintained by the Uni-

versityofHelsinki.Bycombining information

about features of the mammals with climate

modeling, researchers could monitor the gen-

eration, distribution and disappearance of

mammal communities chronologically and

geographically, and also explain the climatic

mechanisms involved.

According to the climate model, some 7−11

million years ago, the atmospheric pressure in

the eastern Mediterranean area was higher

than today, and westerly winds from the Atlan-

tic brought rains to Central Europe and caused

drier conditions to the Mediterranean zone.

Hence, approximately ten million years ago

the eastern Mediterranean area developed in-

toabiome–aregionwithitsowndistinctive

flora and fauna called the Pikermian paleo-

biome, after the fossil discovery site at Pikerm,

Greece. Mammal communities were spread

widely over all of Eurasia, comprising odd-toed

ungulates, various antilope species, giraffes,

rhinos, and distant relatives of today’s ele-

phants. The community of these animals

spread from east to west, starting 14 million

years ago and climaxing about eight million

years ago.

Seasonal changes between summer and

winter as well as the mosaic of forests and

fields consisting of leathery-leaved, evergreen

trees and bushes were typical of these envi-

ronments. The savanna vegetation, as we

know it today, had not yet emerged, and wide

areas of grassland were only just starting to

develop. The results of climate modeling show

that the high pressure zone prevailing in the

eastern Mediterranean area and moist west

winds directed to Central Europe made this

type of grassland biome possible.

Approximately five million years ago chang-

es in the atmospheric cycles brought drier air

to Central Europe and precipitation to the

Mediterranean. The climate change caused in-

creasing variation and more mosaic-like condi-

tions. The widely spread and consistent Pik-

ermian mammal community fell apart. The re-

sults of the research show how mammals

reacted to climate changes over long periods

and on a continental scale. The results also

help to understand how climate processes im-

pact on evolution, extinction, and community

structure.

The research was based on more than

twenty years of international collaboration,

initiated by the authors, Professor Raymond

L. Bernor (Howard University, USA) and Profes-

sor Mikael Fortelius. The most recent phase in

the research was made possible as collabora-

tion by Jussi Eronen and climate modeler

Arne Micheels (Senckenberg Museum of Nat-

ural History and Research Institute, Germany),

and the expertise, storage, and computing re-

sources provided by the CoMS (Coupled Model

Systems) project and CSC. The study was fund-

ed mainly by the Academy of Finland.

CSC received funding from Tekes – the

Finnish Funding Agency for Technology and

Innovation for building the infrastructural sup-

port, for coupled model systems development

together with universities, and for shared re-

search institute work within the CoMS project.

n

Pre-hISTorIC CLIMATe ConTroLLeD The DeVeLoPMenT of MAMMAL CoMMUnITIeS



MATheMATICAL MoDeLIng of wAVe ProPAgATIon

Problems of physics and chemistry often

require mathematical modeling of

acoustic, elastic or electromagnetic

wave propagation. For several decades, numer-

ical modeling of these phenomena has been a

challenging target of research. Over this time, a

large number of modeling methods have been

developed. However, the currently available

traditional numerical methods (finite element-,

finite difference-, ray-tracing methods) pro-

duce inaccurate results for the problems being

calculated.

Increases in computation capacity over re-

cent years together with the extensive develop-

ment in numerical methods have paved the

way for precision modeling of wave propaga-

tion. Methods for this include discontinuous

Galerkin (DG) and ultra-weak varional formula-

tion (UWVF).

The above-mentioned calculation methods

(DG and UWVF) have been successfully applied

to several problems of physics and engineering.

For example, DG was used for solving a time-

domain acoustic propagation problem, where

sound was produced from a loudspeaker and

wave propagation in a conical object was ob-

served (see Figures 1 and 2). The propagation

results could also be measured in a laboratory,

which made it possible to compare the results

from numerical simulations with the measured

results. This provided important information

on how well the applied numerical method and

the used model describe the real situation. An

example of modeling propagation at the fre-

quency level is a problem of electromagnetics,

which was solved using the UWVF approach. In

this case the magnetic field propagation from

an aircraft hull was investigated (see Figure 3).

The calculations of both problems men-

tioned here were solved using CSC’s Cray su-

percomputer (louhi.csc.fi).

In2007CSC–ITCenterforScience,Ltd.an-

nounced a call for applications on computation-

al research and development projects. The suc-

cessful applicants were entitled to use CSC’s

mostpowerfulsupercomputerCrayXT4intheir

research.

In addition to CSC, Cray and the micropro-

cessor manufacturer AMD also participated in

the arrangements of the grant program. The

grantrecipientswereabletousetheCrayXT4

supercomputer in their research. Additionally,

they were allowed to utilize CSC’s specialist

services in the implementation of the powerful

computation methods. n

W ithin the past 20 years, advances in

computational power and meth-

odology have made computer

simulations an integral part of studies of

biomolecular systems. Simulations on all-atom

level are routinely used to study, e.g., micro-

scopic details of lipid aggregates and proteins.

However, many phenomena are still outside

the reach of all-atom simulations, and coarser

models are needed.

Detailed information from all-atom models

can provide input data for parameterizing

coarse-grained models. Techniques for such

parameterization are called systematic coarse-

graining methods, and can be based, e.g., on

matching forces or structural information be-

tween the two resolutions.

Teemu Murtola’s (Helsinki University of

Technology) dissertation employs inverse

Monte Carlo (IMC) for constructing coarse-

grained models for a lipid membrane contain-

ing dipalmitoylphosphatidylcholine (DPPC)

and cholesterol. Three 2D models are con-

structed at different levels of resolution, in

each case matching the radial distribution

functions (RDFs) of the coarse-grained model

to those from atom-scale simulations.

The main results are the presence of cho-

lesterol-rich and cholesterol-poor domains at

intermediate cholesterol concentrations and

the presence of strong tail density fluctuations

at low cholesterol concentrations. The former

agrees with the experimental studies of the

system, while the latter was confirmed through

atom-scale simulations. Accurate quantitative

studies were restricted by transferability prob-

lems in all the coarse-grained models; hence,

the focus is on comparing the different mod-

els and critical discussion of the RDF inversion

as a basis for coarse-graining. The IMC method

is also improved by increasing its tolerance to

statistical noise, as well as through inclusion of

a virial pressure constraint and generalization

to models where particles have internal de-

grees of freedom. Teemu Murtola used the

M-grid computing resources. n

DISSerTATIon on CoArSe-grAIneD MeThoDS

2. Computational surface mesh for objects under study.

1. Wave propagation from a conical object using DG method.

3. Magnetic field propagation from an aircraft hull.



The diversity of life is based on very ef-

ficient energy production machinery,

which has evolved during the last 3.5

billion years. This molecular machinery, also

known as the respiratory chain, is located in

the mitochondria of the eukaryotic cell. The

respiratory chain is powered by an enzyme

called cytochrome c oxidase (CcO), which uti-

lizes very efficiently nearly all of the oxygen

taken up by the organism. CcO reduces oxy-

gen to water, and employs the energy released

in the reaction to transfer hydrogen ions (pro-

tons) over the mitochondrial inner membrane.

As in a battery, this produces a voltage over

the mitochondrial membrane, which can be

utilized further to drive energy-requiring pro-

cesses, such as the synthesis of the energy

molecule of the cell, ATP.

In his doctoral thesis Ville Kaila from the

University of Helsinki studied the catalytic

mechanism of CcO, using computational re-

sources and software provided by CSC − IT Cen-

ter for Science. The computational models used

in the research were based on experimental

structural information, and results from many

biochemical and biophysical studies on the en-

zyme. Kaila studied the dynamics, energetics,

and structure of CcO in its catalytic cycles in dif-

ferent intermediate states, by employing both

classical molecular dynamics simulations and

quantum chemical calculations.

The general functional principle of CcO has

been known for over 30 years, and the atomic

structure of the enzyme was discovered more

than ten years ago. However, the proton-

pumping mechanism of CcO is still unknown.

This mechanism refers to a molecular scale

functional explanation of how the energy re-

leased by oxygen reduction is employed for

transferring protons over the mitochondrial

inner membrane (i.e. proton-pumping). This

mechanism is of central importance in bio-

chemistry and bioenergetics because CcO is

the basis for aerobic life. CcO dysfunction has

been shown to be associated with many dis-

eases, e.g. Parkinson’s and muscle degrada-

tion diseases. In addition, oxygen radical for-

mation, which is indirectly controlled by CcO,

might cause tissue damage arising as a result

of heart infarct, and degradation caused by

ageing. The functional principle of CcO is also

interesting for the energy industry, because

the enzyme works as a fuel cell, although more

efficiently. In the future the functional princi-

ple of CcO might be used as a model for devel-

oping bioinspired fuel cells.

The most important result of the thesis is

a new model for the pumping mechanism.

This model helps to explain how CcO sepa-

rates the pumped protons from the chemical

protons, which are used in the reduction of

oxygen to water. This principle is known as

the gating mechanism, which is one of the

central questions in solving the functional

principle of CcO. In addition, as a result of this

work, a particular amino acid (Glu-242) close

to the enzyme’s active center was found to

work as a valve for preventing protons from

leaking backwards in proton-pumping. Thus,

this amino acid works like a molecular engine

shaft. A mechanism was also suggested by

which CcO activates and switches between its

two proton-conducting channels. Further-

more, a new method was developed for mod-

eling complex metal centers in enzymes, by

efficient classical simulations, and quantum

chemically derived parameters. Parameters

derived for the metal centers of CcO were

used in the other studies of the thesis. n

DISSerTATIon on enzyMe MoDeLIng

© V

ille

Kai

la

The active center of the enzyme.

Kari Rummukaisen’s research group used grid

simulations in their Grand Challenge project to

test one of the technicolor models that can be

used to supplement and extend the Standard Model of

particle physics.

As a result of their massive supercomputing, the lat-

tice phase diagram and the excitation spectrum of SU(2)

gauge field theory has been determined. This is a neces-

sary step to resolve the strongly connected dynamics of

the theory, which is, in turn, an important test of the va-

lidity of technicolor theory.

The research group used 500,000 processor hours at

the FZJResearchCentre Jülich inGermany. This study

was part of the “Experimental cycle change” agreement

betweenCSCandJülich. Inaccordancewiththeagree-

mentCSCandJülichexchangecomputingtime.n

reSeArCh TeSTIng The VALIDITy of TeChnICoLor TheorIeS

© F

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Breast cancer is the most common can-

cer in women in the western countries.

Approximately two-thirds of breast

cancer tumors are hormone dependent, re-

quiring estrogens to grow. One approach in

treating hormone dependent breast tumors is

to block the local estrogen production by in-

hibiting enzymes. Inhibitors are relatively

small compounds that bond with enzymes

rather than with hormone precursors, thus

preventing the hormones from being made. In

Sampo Karkola’s dissertation (University of

Helsinki) aromatase enzyme was modeled.

CSC’s supercomputing resources and chemis-

try software and databases were utilized in the

dissertation.

Estrogens are formed in the human body

via a multistep route starting from cholesterol.

The final steps in the biosynthesis include the

CYP450 aromatase enzyme, converting the

male hormones androgens (preferred sub-

strate androstenedione ASD) into estrogens

(estrone E1), and the 17beta-HSD1 enzyme,

converting the biologically less active E1 into

the active hormone 17beta-hydroxyestradiol

E2. E2 is bound to the nuclear estrogen recep-

tors causing a cascade of biochemical reac-

tions leading to cell proliferation in normal tis-

sue, and to tumor growth in cancer tissue.

Computer-assisted molecular modeling is

an invaluable tool in modern drug design, en-

abling research into structures and phenome-

na that cannot be experimentally studied or in

situations where experiments would be ex-

pensive and time-consuming. Molecular mod-

eling has applications in predicting the activi-

ties of theoretical inhibitors and in finding pos-

sible active inhibitors from a compound

database. Experimental methods have been

insufficient to clarify the structure of aro-

matase, but inhibitor binding at atomic level

can also be studied with molecular modeling

based on a related enzyme conformation. To

clarify the interactions between the aro-

matase enzyme and its substrate and inhibi-

tors, a homology model was generated based

on a mammalian CYP450 enzyme, rabbit pro-

gesterone 21-hydroxylase CYP2C5, which is

the only experimentally isolated mammalian

CYP450 enzyme involved with steroid metab-

olism. The model was carefully validated using

molecular dynamics simulations (MDS) with

and without the natural substrate ASD. n

DISSerTATIon: MoDeLIng gIVeS new InforMATIon for PreVenTIng The breAST CAnCer

© S

amp

o K

arko

la

The overview of the aromatase model.

In her doctoral dissertation defended at the

University of Oulu, Ludmila Vigo studied

the reactions involved in the formation of

metal complexes. During her studies, she used

CSC’s Conquest, a search program for retriev-

ing information from the Cambridge Struc-

tural Database.

Oxygen, sulfur, selenium, and tellurium be-

long to the group 16 of the periodic table of

elements, also known as chalcogens (ore form-

ers). Organic chalcogen compounds, such as

chalcogenoethers and chalcogenolates, react

with metals to form metal complexes. Going

from hard to soft down the group from oxy-

gen to tellurium the properties of the chalco-

gen donors change as do those of the metal

complexes. Abundant information is available

on oxygen and sulfur complexes, but especial-

ly on tellurium studies are notably fewer.

Metal-chalcogen complexes can be used as

catalysts in organic syntheses, and they are

also useful starting materials for the prepara-

tion of semiconductor materials. A common

way to synthesize chalcogen compounds in-

volves the use of an inert atmosphere since

they are moisture and oxygen sensitive. The

use of gas protection makes the work involved

with the reaction slower and more complicat-

ed. The compounds prepared in this study are

not sensitive to moisture or atmospheric oxy-

gen. Additionally, several phases of the syn-

theses can be performed without the use of

inert atmosphere. Hence, the complexes are

easy to prepare and store even in large

amounts. The complexes may provide a pos-

sibility for low-temperature preparation of

new catalytic and electronic materials.

In the course of the study several factors

were found to affect the reaction progress

and reaction products. Three different tel-

luroethers and five metals were investigated.

In the case of palladium and platinum, the

reactions were also performed using thioether

and selenoether ligands, and the results were

compared with the corresponding tellurium

reactions. Additionally, preparations of metal

complexes containing sulfur and tellurium li-

gands were also studied.

The doctoral thesis work involved a total

of 23 new chalcogen-metal complexes. Reac-

tions were monitored using NMR spectrosco-

py, and both the intermediates and the prod-

ucts were structurally characterized using

X-ray diffraction techniques. Some dinuclear

metal complexes exhibited interesting struc-

tural properties: the coordination spheres of

the two metal centers were different. The cat-

alytic properties of these metal complexes will

be investigated further. The results obtained

in this research have provided much new fun-

damental information on the chemistry of

chalcogen-containing metal complexes. n

DISSerTATIon: PrePArATIon AnD STrUCTUrAL ChArACTerIzATIon of ChALCogenoeTher



The group of researchers from Helsinki

University of Technology, Sampsa Rii-

konen, Arkady Krasheninnikov and

Risto Nieminen, and Adam Foster from Tam-

pere University of Technology, are studying

boron nitride nanotube synthesis by calculat-

ing the energy cost to form bonds between

individual boron and nitrogen atoms on a

metal surface. The structure of boron nitride

nanotubes is very similar to the more well-

known carbon nanotubes, but some of their

physical properties are much more attractive

than their carbon cousins.

The structure of boron nitride nanotubes

and sheets are analogous to carbon nanotubes

and graphene: instead of a single atom spe-

cies, boron nitride sheet consists of alternat-

ing boron and nitrogen atoms and instead of

carbon-carbon bonds, boron nitride sheet fea-

tures the more ionic boron-nitrogen bonds.

This results in a band gap that is independent

of the boron nitride tube chirality and is always

approx. 5.5 eV, allowing to produce semicon-

ducting nanotubes only. This is very different

to the case of carbon nanotubes, where the

conducting/semiconducting nature of the

tubes depends strongly on their chirality.

The mechanical properties of boron ni-

tride nanotubes are very similar to carbon

nanotubes, so it is extremely strong and light

material.

Boronnitrideisalsoknowntobeveryresis-

tant to oxidation, making it an ideal candidate

for shielding and coating applications. Iron

nanoparticles encapsulated into boron nitride

nanotubes have been produced very recently;

by boron nitride shielding, the oxidation of the

nanoparticle can be avoided and the magne-

tism of the nanoparticle does not suffer.

Unfortunately, the production of boron ni-

tride nanotubes has proven to be very diffi-

cult. The same chemical vapor deposition

techniques, using catalyst metals such as iron

or nickel to produce carbon nanotubes do not

seem to work in the case of boron nitride nan-

otubes. The best synthesis method currently

available was developed by Tang et al. and it

has been speculated that the magnesium pres-

ent in their synthesis method plays the role of

the catalyst.

The researchers observed that on a flat iron

surface,B2 formationwilldominateover the

BN production and the synthesis is spoiled.

However, in a realistic iron nanoparticle, steps

are always present and according to the re-

search group’s calculations, in these step edge

regions, boron nitride molecule becomes the

most stable end-product. This is good news

from the point of boron nitride nanotube syn-

thesis. It seems that catalyst morphologies

with high number of steps and very narrow

terraces might improve the boron nitride nan-

otube yield when transition metal catalysts are

used. n

A new ProMISIng nAnoMATerIAL froM boron AnD nITrIDe

© A

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The Marine Technology

unit at the Department of

Applied Mechanics at the

Helsinki University of Technolo-

gy has studied wave loads which

cause springing vibration of

ships. The research has been car-

riedoutin2005–2009underthe

supervision of professor Jerzy

Matusiak in a project funded by

TekesandSTXEurope.Theinves-

tigation and utilizing of related

numeric modeling continues in a dissertation

work carried out by Satu Hänninen at the

graduate school of Computational fluid dy-

namics.

The research focuses on wave loads which

are weak in relation to the size of the ship and

which cause long-term, small vibration (spring-

ing) of the hull of large ships. For shipbuilding,

studying the springing vibration is an important

topic because in the long term, vibration of this

kind results in fatigue of the hull, and also

causes momentary disturbances in traveling

comfort. The phenomenon is particularly relat-

ed to large ships, because the size of the ship

has an impact on the characteristics of the hull.

The numeric modeling of wave loads that

result in springing is challenging. This is par-

tially due to the fact that their physics is not

entirely understood. Model experiments con-

ducted by the Marine Technology unit of the

Helsinki University of Technology have indicat-

ed that wave breaking in the bow area of the

ship is a significant factor for the springing

excitation. Traditional methods used for the

seakeeping cannot take into ac-

count the impact of wave breaking.

By using the computing re-

sources allocated by CSC, it has

been investigated whether the Na-

vier-Stokes solver could be used for

the evaluation of springing loads.

The Navier-Stokes solver connect-

ed with an interface capturing

method is also able to model

breaking wave loads. Before this,

the method has not been applied

to springing excitation, which means that the

on-going study started off by investigating

the numeric accuracy of the solution provid-

ed by the method. The computation results

have been compared with the results of the

model experiments. The comparison has in-

dicated that the computing method provides

reasonable results. The advantage of the

computing is that it is possible to analyze the

physics of the phenomenon in detail by using

a high resolution. n

wAVe LoADS CAUSe SPrIngIng VIbrATIon of ShIPS

© S

atu

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en



InCreASIng hyDroeLeCTrIC Power by IMProVIng The ACCUrACy of InfLow foreCASTIng

Successful flow regulation in lake-riv-

er systems depends on the accuracy

of inflow forecasting of the regulat-

ed lakes. However, little attention has been

paid to methods of increasing hydroelec-

tric power production by improving the ac-

curacy of inflow forecasts. Instead, discus-

sions on increasing Finnish hydropower

production have focused on building new

man-made reservoirs and hydropower

plants and on renewing machineries in old

plants.

One of the aims in Jarkko Koskela’s

doctoral thesis work was to evaluate the

dependence between the accuracy of in-

flow forecasts used in making discharge

and runoff plans and success in regulation

and hydroelectric power production. Addi-

tionally, Koskela also evaluated the poten-

tial for increasing hydroelectric power pro-

duction in Finland by improving the accu-

racy of inflow forecasts. Koskela also

developed a new type of a forecast model

for long-term discharge forecasts. The ac-

curacy of the new forecast model was test-

ed in case studies in Lake Päijänne, Lake Py-

häjärvi at Säkylä, and in two small catch-

ment areas just upstream of Lake Päijänne.

The results show that the new forecast

method based on pattern recognition is

useful in real-time inflow forecasting at

sites like Päijänne where the catchment ar-

ea is large and lead-times are long. The

forecasts made with the new model in the

small catchment areas and in Lake Pyhäjär-

vi are fairly good, but forecasting long-

term inflows during autumn turned out to

be difficult irrespective of the model used.

CSC’s computing resources were utilized in

Koskela’s research work carried out at Hel-

sinki University of Technology.

The impact of forecast accuracy on suc-

cessful regulation was investigated both in

Lake Pyhäjärvi at Säkylä and in the Kymijoki

lake-river system. The results show that

when long-term forecasts were used in the

regulation planning of lake-river systems,

the length of the period of the forecast has

a significant impact on the forecast’s suc-

cess. The suitable length for the forecast

will depend on both the characteristics of

the lake-river system and the forecast ac-

curacy. If the live capacity of the system

under consideration is high, forecasts for

several months should be utilized in plan-

ning without the need to pay too much at-

tention to forecast accuracy. On the other

hand, lake-river systems with a small live

capacity benefit more if shorter but more

accurate forecasts are used.

Koskela’s case studies show that if fore-

cast accuracy is increased, it can lead to a

realistic, maximum increase of 0.52% in hy-

droelectric power production. At the same

time, problems caused by floods and

droughts would significantly decrease. At

the scale of Finland as a whole, an increase

of one percent represents an increase of

130 GWh in annual electricity production.

In other words, if the accuracy of forecasts

can be improved, it would provide sub-

stantial potential for increasing hydroelec-

tric power. n

© P

oh

jola

n V

oim

a



Interactions between chiral compounds are studied by high lev-

el computational calculations in a project initiated by Docent

Karel D. Klika from the University of Turku. The project, in par-

ticular, focuses on complex formation involving chiral compounds.

Certain molecules possess the property of chirality. This means

that the molecules are not superimposable upon their mirror im-

ages just as our left and right hands are not superimposable upon

each other although they are quintessentially one and the same

thing. The study of chiral molecules is challenging, none the least

because of the great similarities between molecule mirror images,

known as enantiomers. The chemistry of life itself is intrinsically a

study of chirality since many biomolecules are chiral. Drugs can al-

so be chiral, and moreover, the two enantiomers of a drug can of-

ten vary greatly in their efficacy, even to the point that whilst one is

beneficial, the other can be toxic. Thus, chirality studies can poten-

tially afford great practical benefits.

The molecular modeling method used in the studies at the Uni-

versity of Turku is density functional theory (DFT). The target ob-

jectives in the project are the understanding of chiral phenomena

and chiral interactions, but also to ultimately find and develop

new methods of enantiodifferentiation, i.e. the identification of

enantiomers, their quantification, and their physical separation.

Theprojectextendsnowoverseveralcountries:Slovakia,USAand

Germany.

The calculations require the use of the very latest and sophisti-

cated theoretical methods to attain high accuracy, demanded in

part by the small energy differences that are involved as a result of

the similarity of the two enantiomers. The computational methods

available at CSC and the powerful hardware infrastructure are able

to meet the demands necessitated by the work, and to do so in a

timely manner, such that a large number of structures can be dealt

with simultaneously.

A great deal of experimental structural information in this re-

search can also be obtained on the complexes under study by the

application of nuclear magnetic resonance (NMR) spectroscopy.

Computational calculations can reveal much about the structure of

the complexes too, as well as the energy of the molecular com-

plexes and thus the structural preferences.

Together, these two methods provide a powerful combination

for investigating chiral phenomena and the interactions of chiral

molecules, potentially for beneficial tangible returns in addition to

the accumulation of inherently interesting knowledge. n

STUDIeS AboUT ChIrAL CoMPLexeS AnD enAnTIoDIfferenTIATIon

Tomasz Malkiewicz has completed his doctoral thesis work, Tools for

PhysicswithLHCandRIB,attheUniversityofJyväskylä.Thefirstpartof

the thesis concerns the T0 detector for use in the ALICE experiment with

the world’s largest particle collider LHC at CERN. The LHC Large Hadron Collider

is a particle accelerator contained in a circular tunnel approximately 27 kilome-

ters long, located at CERN, European Organization for Nuclear Research in Swit-

zerland. The T0 is the fast timing and trigger detector for the Large Ion Collider

(ALICE) experiment. Tomasz Malkiewicz utilized CSC’s computing resources in

his research.

Technical requirements set for the detector are tough, for it has to endure

high radiation levels, handle high operating frequencies, and remain functional in

a strong magnetic field. The detector has to be able to detect not only the exact

time but also the position of the collisions. Malkiewicz’s thesis describes simula-

tions, design, construction, tests, installation and commissioning of the T0 detec-

tor as well as how these technical requirements for the detector were solved.

In the second part of the thesis Malkiewicz concentrates on neutron yield

measurements. Acceleration laboratory facilities like SPES and SPIRAL2 will use

neutrons to yield radioactive atoms. Malkiewicz studied neutron yields at the

AcceleratorLaboratoryoftheUniversityofJyväskyläbetween2004and2008.The

experimental results were compared with theoretical Monte Carlo calculations.

The results indicated that the yield expectations were too high. The results led to

changesbothintheSPESandSPIRAL2projects.Basedontheresultsofthethesis

the SPES project implemented the direct neutron yield method. A re-evaluation of

the converter and fission target module has been recommended by the SPIRAL 2

Technical Advisory Committee following the outcome of the measurements. n

DISSerTATIon: LhC AnD rIb – Two fronTLIne ProjeCTS In nUCLeAr AnD PArTICLe PhySICS

© C

ERN



Researcher Dario Greco’s study at the

University of Helsinki consisted of in-

creasing the performance of microar-

rays, and was measured by the successful vali-

dation of the results by independent tech-

niques. In the dissertation CSC’s computing and

software resources were utilized.

The time of the large sequencing proj-

ects has enabled unprecedented possi-

bilities of investigating more complex as-

pects of living organisms. Among the

high-throughput technologies based on

the genomic sequences, the DNA mi-

croarrays are widely used for many pur-

poses, including the measurement of the

relative quantity of the messenger RNAs.

However, the reliability of microarrays has

been strongly doubted as robust analysis

of the complex microarray output data

has been developed only after the tech-

nology had already been spread in the

community.

An objective of this study consisted of in-

creasing the performance of microarrays, and

was measured by the successful validation of

the results by independent techniques. To this

end, emphasis has been given to the possibility

of selecting candidate genes with remarkable

biological significance within specific experi-

mental design. Along with literature evidence,

the re-annotation of the probes and model-

based normalization algorithms were found

to be beneficial when analyzing Affymetrix

GeneChip data.

Typically, the analysis of microarrays aims at

selecting genes whose expression is significant-

ly different in different conditions followed by

grouping them in functional categories, en-

abling a biological interpretation of the results.

Another approach investigates the global dif-

ferences in the expression of functionally relat-

ed groups of genes. Here, this technique has

been effective in discovering patterns related

to temporal changes during infection of human

cells.

Another aspect explored in this thesis is re-

lated to the possibility of combining indepen-

dent gene expression data for creating a cata-

log of genes that are selectively expressed

in healthy human tissues. Not all the genes

present in human cells are active; some in-

volved in basic activities (named housekeep-

ing genes) are expressed ubiquitously. Other

genes (named tissue-selective genes) provide

more specific functions and they are expressed

preferably in certain cell types or tissues. Defin-

ing the tissue-selective genes is also important

as these genes can cause disease with pheno-

type in the tissues where they are expressed.

The hypothesis that gene expression

could be used as a measure of the relat-

edness of the tissues has been also

proved.

Microarray experiments provide

long lists of candidate genes that are of-

ten difficult to interpret and prioritize.

Extending the power of microarray re-

sults is possible by inferring the rela-

tionships of genes under certain condi-

tions. Gene transcription is constantly

regulated by the coordinated binding of

proteins, named transcription factors,

to specific portions of the promoter se-

quence. In this study, the analysis of

promoters from groups of candidate genes has

been utilized for predicting gene networks and

highlighting modules of transcription factors

playing a central role in the regulation of their

transcription. Specific modules have been

found regulating the expression of genes se-

lectively expressed in the hippocampus, an ar-

ea of the brain having a central role in the Major

Depression Disorder. Similarly, gene networks

derived from microarray results have elucidat-

ed aspects of the development of the mesen-

cephalon, another region of the brain involved

in Parkinson Disease. n

DISSerTATIon on gene exPreSSIon: froM MICroArrAyS To fUnCTIonAL genoMICS

© J

yrki

Ho

kkan

en

In nanostructures carbon exists in several

different forms, including spherical fulle-

renes, nanotubes and graphene sheets.

The diversified properties of carbon nanotu-

bes and graphene make them promising

materials for different applications. In ideal

carbon nanotubes and graphene, carbon

atoms form a hexagonal, honeycomb-like

structure. A cross section of the honeycomb

sheet has either a zigzag or an armchair pat-

tern. At the same time, the rolling direction

of the graphene sheet determines the chira-

lity of the carbon nanotube that is formed.

In order to develop applications it is es-

sential to understand the structures and

their behavior. Various defects affect the

structural properties and producing comp-

letely ideal structures is difficult. In his doc-

toral dissertation work at the University of

Jyväskylä,Sami Malola used computational

methods to investigate the impacts and pro-

perties of different defects. A significant fac-

tor affecting the properties of graphene rib-

bons is the edge structure.

One of the main observations was disco-

vering a new edge structure for graphene.

The edge energy of the reconstructed struc-

ture is more favorable than that of the pre-

viously known zigzag and armchair edges,

which makes it superior under high vacuum

conditions. The reconstruction is characteri-

zed by triple bonds between carbon atoms

that form at the edge. The studies on vibrati-

on modes show that the reconstruction also

makes the edge more rigid.

Malola also presents an experimental ob-

servation of the novel edge structure made

after the computation. Previously, graphene

edges have been assumed to appear either

in the form of a zigzag or an armchair, or a

combination of them. n

DISSerTATIon: A new grAPhene eDge foUnD In ADDITIon To zIgzAg AnD ArMChAIr



The focus of Marko Matikainen’s (Lap-

peenranta University of Technology)

dissertation is to develop finite ele-

ments based on the absolute nodal coordinate

formulation. The absolute nodal coordinate

formulation is a nonlinear finite element for-

mulation, which is introduced for special re-

quirements in the field of flexible multibody

dynamics. In this formulation, a special defini-

tion for the rotation of elements is employed

to ensure the formulation will not suffer from

singularities due to large rotations. The ab-

solute nodal coordinate formulation can be

used for analyzing the dynamics of beam, pla-

te and shell type structures.

The improvements of the formulation are

mainly concentrated towards the description

of transverse shear deformation. Additionally,

the formulation is verified by using conventio-

nal iso-parametric solid finite element and

geometrically exact beam theory. Previous

claims about especially high eigenfrequencies

are studied by introducing beam elements

based on the absolute nodal coordinate for-

mulation in the framework of the large rotati-

on vector approach. Additionally, the same

high eigenfrequency problem is studied by

using constraints for transverse deformation.

It was determined that the improvements

for shear deformation in the transverse direc-

tion lead to clear improvements in computa-

tional efficiency. This was especially true when

comparative stress must be defined, for

example when using elasto-plastic material.

Furthermore, the developed plate element

can be used to avoid certain numerical prob-

lems, such as shear and curvature lockings. In

addition, it was shown that when compared to

conventional solid elements, or elements

based on nonlinear beam theory, elements

based on the absolute nodal coordinate for-

mulation do not lead to an especially stiff sys-

tem for the equations of motion. n

DISSerTATIon: DeVeLoPMenT of beAM AnD PLATe fInITe eLeMenTS bASeD on The AbSoLUTe noDAL CoorDInATe forMULATIon

© M

arko

Mat

ikai

nen

Distribution of axial stress of cantilever beam, computed with ABAQUS.

Katriina Pussi, who works at the Lappeenranta University of

Technology (LUT), and in collaboration with an international

research group, has determined the structure of fullerenes

on a silver surface. Pussi utilized CSC’s supercomputers and the

cluster machine of LUT.

Fullerene is one of the forms of carbon. Carbon-based nanoma-

terials are currently very popular research targets for the design of

new materials. In an article published in the leading physics journal,

Physical Review Letters, Katriina Pussi and her colleagues present

the results of their experimental and theoretical research.

The fullerene molecule (C60

) consists of 20 hexagons and 12 pen-

tagons, with carbon atoms at the vertices. There are several ele-

ments of symmetry. The carbon atoms bond with each other via

single or dual bonds, like in graphite. The high level of symmetry

and the bonding structure make the electronic properties of C60

qui-

te unusual. This is one of the reasons why many research groups are

striving to “build” molecular-scale electronic devices using the C60

molecules. n

fULLerene STrUCTUre DeTerMIneD on SILVer SUrfACe ©

Kat

ariin

a Pu

ssi



TheBrutusscreeningmethod,deve-

loped at the University of Kuopio as

a result of Toni Rönkkö’s doctoral

thesis work, helps researchers to find new

and different drug candidates for the

needsofnewdrugdevelopment.CSC–IT

Center for Science Ltd. has collaborated in

the project and the Brutus software has

been run on CSC’s computing equipment.

Molecular screening is the most impor-

tant method for finding new drug candida-

tes. However, one of the problems concer-

ning the currently used virtual screening

methods is their tendency to find molecu-

les that are structurally similar or resemble

known drug compounds. These molecules

have usually been patented or studied by

other companies, so they do not provide a

favorable starting point for the develop-

ment of a completely new drug. One of the

primary goals in a new drug development

project is to discover a previously unkno-

wn, active “lead” molecule, on which the

dedicated drug development can be built.

TheBrutusscreeningmethodisdesig-

ned for discovering structurally different

lead molecules. The method is suitable for

use especially at the early phases of a drug

development project. The method is based

on computer-based modeling of intra-mo-

lecular electronic interactions. Electronic

interactions are vitally important when a

drug molecule binds with receptors within

the body. Brutus searches for molecules

with suitable electronic properties and the

search may produce new and structurally

different lead molecules.

Brutus complements thecurrentlyus-

ed virtual screening methods and can help

researchers to develop new drugs against

various diseases. The method has been

successfully utilized in drug development

projects at the University of Kuopio as well

as in industrial projects. The rights for the

method have been sold to Visipoint Oy, a

company in Kuopio, to introduce the met-

hod for implementation by international

pharmaceutical companies. n

DISSerTATIon: CoMPUTATIonAL SCreenIng for new DrUgS ©

To

mm

i Nyr

ön

en



Computational methods are very im-

portant when researchers try to find

out, why catalytic properties of nano-

sized particles are quite different compared

to the characteristics of larger particles of the

same material.

Recent progresses in nanoscience and

nanotechnology open new possibilities for

technological applications in many fields, in-

cluding magnetism, electronics and catalysts.

Metallic nanoparticles show unique catalytic

properties that may differ considerably from

those of the corresponding crystalline surfac-

es. Often the good catalytic activity can be re-

lated to catalytic sites, like atomic size steps,

on the cluster.

Due to the high curvature of the clusters,

the special site density and distribution is

much higher than on almost flat surfaces.

Furthermore, nanoclusters have several

unique active sites like facets and vertexes

between the facets which can have catalytic

properties that differ drastically from the

ones on almost flat surfaces of larger particles

or bulk material.

For example, it is well known that gold,

which is rather inert as a bulk metal, shows

high reactivity when in the form of nanosized

clusters. Although nanoparticles have excited

much interest owing to their unusual and

somewhat unexpected catalytic properties,

the origin of the catalytic activity is still not

fully understood.

The group has observed that small clus-

ters exhibit new active sites that complement

the stepped surface calculations. A new im-

portant effect has been observed: the in-

creased reactivity of low-coordinated mole-

cule on the vertexes. Such sites are particu-

larly abundant on the small nanosized

particles, and they very likely explain the cat-

alytic activity of them.

Experimentally many investigators have

studied the catalytic effect of nanoclusters

on different reactions of industrial relevance,

using a wide range of surface science tech-

niques. These studies have been done with

rather arbitrary size of clusters because it is

very difficult to prepare fixed size clusters.

However, if we want to model properly the

catalytic activity of nanoclusters it is impor-

tant to know the geometrical characteristics

of the clusters used in the research or appli-

cations. Even then, each cluster has several

different active sites and it is very difficult to

identify experimentally which of them is the

most active one.

For this reason the computational ap-

proach, where precise sites can be studied, is

very attractive. The group of researchers

Jarkko Vähäkangas, Dr. Giorgio Lanzani and

prof. Kari Laasonen from the University of

Oulu are studying the mechanism of catalytic

activity of nanosized gold and iron clusters.

Giorgio Lanzani and Kari Laasonen are partici-

pating in an EU project devoted to develop a

model for continuous CVD based synthesis

method for three dimensional regular nano-

structures in the form of hetero-atomic nan-

otubes (NTs) composed of boron, nitrogen

and carbon: BN, N-doped carbon, B-doped

carbonandmixedBNCnanotubes.n

geoMeTry of nAnoSIzeD CLUSTerS exPLAInS DIfferenCeS In reACTIVITy

© J

yrki

Ho

kkan

en



Ahti Jaatinen showed in his doctoral thesis that energy

consumption in industrial processes can be reduced by

using a suitable diffuser. Diffusers are used in the radial

compressors commonly present in process industries, effluent ae-

ration, and superchargers of combustion engines. A diffuser is us-

ed to slow down the gas flow to convert most of the its kinetic

energy into pressure. CSC’s computing resources were utilized in

the dissertation.

In the thesis work numerical modeling was applied to five diffe-

rent vaneless and six vaned diffusers in a low pressure high-speed

radial compressor. In four of the five vaneless constructions the

diffuser geometry was pinched from its original height - in other

words, the diffuser width was decreased. The vaned diffusers had

better efficiency but a considerably narrower operating range than

that of the vaneless unpinched diffuser. The best pinched diffu-

sers had better efficiency than the vaned ones, but the pinch had

no significant effect on the operating range.

Reducing the diffuser width is very simple to do. Improved effi-

ciency means reduced energy consumption in the process. Addi-

tionally, reducing the diffuser width also enables designing longer

diffusers, which means that more of the kinetic energy is recove-

red as pressure. This makes it possible to run the compressor with

a lower rotation speed, which further reduces the energy need. n

reDUCTIonS In InDUSTrIAL ProCeSSeS’ energy ConSUMPTIon

Due to the demanding working envi-

ronment highly specialized robots

are needed both in the manufactur-

ing and maintenance of the ITER (Internation-

al Thermonuclear Experimental Reactor). The

purpose of Pekka Pessi’s (Lappeenranta Uni-

versity of Technology) thesis was to develop

special parallel robots for the assembly, ma-

chining and repairing of the vacuum vessel of

the ITER. The vacuum vessel consists of nine

sectors that are to be welded together. In addi-

tion to the initial vacuum vessel assembly, af-

ter a limited running period, sectors need to

be replaced for repair. Pessi utilized CSC’s ap-

plication services in his thesis work.

The process of the assembly and machin-

ing of the vacuum vessel needs a special robot.

Bystudyingthestructureofthevacuumves-

sel, two novel parallel robots were designed

and built; they have six and ten degrees of

freedom driven by hydraulic cylinders and

electrical servo motors. Kinematic models for

the proposed robots were defined and two

prototypes built.

The design and testing processes of the

robots are complex tasks due to the high spe-

cialization of the manufacturing technology

needed in the ITER reactor. The results dem-

onstrate the applicability of the proposed so-

lutions quite well. The results offer not only

devices but also a methodology for the as-

sembly and repair of ITER by means of parallel

robots.

Mechanisms with closed-loop kinematic

chains are used in the design of robots in this

work. One version is a purely parallel manipu-

lator and another is a hybrid manipulator

where parallel and serial structures are com-

bined. Traditional industrial robots that gen-

erally have the links actuated in series are in-

herently not very rigid and have poor dynamic

performance in high speed and high dynamic

loading conditions. Compared with open chain

manipulators, parallel manipulators have high

stiffness, high accuracy and a high force/

torque capacity in a reduced workspace. Par-

allel manipulators have a mechanical architec-

ture where all of the links are connected to

the base and to the end-effector of the robot.

Experiments for machine cutting and laser

welding with the 6-DOF robot were carried

out. It was demonstrated that the parallel ro-

bots are capable of holding all necessary ma-

chining tools and welding end-effectors in all

positions accurately and stably inside the vac-

uum vessel sector.

The kinematic models appeared to be com-

plex especially in the case of the 10-DOF robot

because of its redundant structure. Multibody

dynamics simulations were carried out, ensur-

ing sufficient stiffness during the robot mo-

tion. n

DISSerTATIon: noVeL roboT SoLUTIonS for ConSTrUCTIng fUSIon reACTorS



nUCLeAr MAgneTIC reSonAnCe (nMr) PArAMeTerS of grAPhene frAgMenTS eVALUATeD CoMPUTATIonALLy

Recently developed experimental

techniques have made it possible

to produce two-dimensional sheets

of graphene, a carbon nanostructure with

many interesting characteristics. Graphene

is composed of a single layer of carbon at-

oms arranged in a honeycomb lattice, and

has been shown to have a gapless semicon-

ductor band structure. Its properties in-

clude high current-carrying capacity and

thermal conductivity, making it a poten-

tially advantageous material for electronic

devices.

First-principles electronic structure stud-

ies on nuclear magnetic resonance (NMR)

properties of increasingly large planar hy-

drocarbons, which can be related to finite

graphene fragments, have been carried

out by collaboration between the Molecu-

lar Magnetism and NMR Research groups at

the Universities of Helsinki and Oulu, re-

spectively, and CSC. NMR provides a pow-

erful tool for characterization of materials.

This study showed that the isotropic and

anisotropic chemical shifts and one-, two-

and three-bond spin-spin coupling tensors

converge rather quickly as the number of

carbon atoms in the molecule is increased,

which allows extrapolation of the parame-

ters to the large-system limit. Hence, these

results constitute a plausible starting point

of the analysis of eventual NMR experi-

ments for graphene.

High predictive value of the data was

ensured by calibrating the density-func-

tional theoretical methods by correlated ab

initio wave functions for small model sys-

tems, as well as by using the novel com-

pleteness-optimized basis-set paradigm

developed earlier by two of the authors.

With these novel basis sets, results close to

the basis-set limit are attainable with rela-

tively fewbasis functions: thesavingbya

factor of three in the dimension of the ba-

sis set means a reduction of the computa-

tional resources by two orders of magni-

tude. The calculations carried out in the

study would not have been feasible using

traditional basis sets, as the number of

functions would have been too high for the

larger molecules.

Large-scale density-functional linear re-

sponse calculations using up to 128 parallel

cores were carried out in the supercomput-

ers of CSC and the local Linux cluster facili-

ties in Helsinki and Oulu.

The work was part of the Ph.D. project

of Suvi Ikäläinen under the supervision of

Prof. Juha Vaara. The academic teams be-

long to the Finnish Center of Excellence in

Computational Molecular Science (CMS)

funded by the Academy of Finland. n

© J

yrki

Ho

kkan

en



DISSerTATIon: SIMULATIonS of weT fIber neTworkS CAn IMProVe PAPer ProDUCTIon MeThoDS

In his doctoral thesis in the field of ap-

plied physics, Pasi Miettinen, MSc (Uni-

versity of Jyväskylä) studied computer

simulations on the structural and rheologi-

cal properties of wet fiber networks. The

research deployed the supercomputing re-

sourcesofCSC–ITCenterforScience,Ltd.

In paper manufacturing, water is added

to pulp mass to create a suspension that

consists mainly of fibers and water. The

suspension is taken into a paper machine

to form a continuous paper web. At this

point the web contains more than 90 per-

cent of water. Water is gradually removed

by pressing and drying before the paper is

fed onto large rolls.

It is increasingly important to under-

stand the properties of wet paper web, be-

cause the web has a major effect on the

performance of a paper machine.

In his thesis Miettinen shows that the

models and parameters applied to dry pa-

per are not appropriate for describing wet

paper. Understanding the properties of wet

paper web would help to prevent wasting

expensive fiber raw material and the extra

material costs due to the waste. This would

also allow raising the production rates of

paper machines.

The aim of the study was to understand

the physical mechanisms covering the

formation of the paper structure and its

properties in the paper manufacturing pro-

cess. Miettinen investigated the properties

of fiber webs by utilizing a previously de-

veloped computational model for fiber sus-

pensions. Miettinen developed the model

further by adding the inter-fiber adhesion

forces present in the water-air wet fiber

web.

Fiber web simulations represent a re-

search tool gaining popularity in paper sci-

ences. They are particularly useful for

studying phenomena that are difficult to

study empirically. n

In his doctoral thesis in the field of

physics, Pentti Frondelius (University

ofJyväskylä)investigatedtheproper-

ties of gold nanoparticles, with a diame-

ter sometimes even smaller than a mil-

lionth part of a millimeter, on metal oxide

films supported by metal carriers.

The macroscopic gold items that

we encounter in our day-to-day lives are

chemically inactive, and hence, they main-

tain their luster finish almost forever. For

example, unlike a bronze statue, the sur-

face of a golden ring does not become

oxidized. Surprisingly, however, gold

nanoparticles, which are a billion times

smaller, are chemically active. Among

other things, they can catalyze chemical

reactions, or in other words, they reduce

the activation energy required by a cer-

tain reaction. The use of catalysts is ex-

tremely common in the chemical indus-

try. In fact, it has been estimated that as

much as 20% of the gross national prod-

uct of the industrial countries is linked,

either directly or indirectly, with chemical

catalysis.

One of the main results attained in

Frondelius’ work is the fact that the struc-

ture of gold nanoparticles depends on

the oxide film thickness. If the oxide film

is thinner than two nanometers, the gold

nanoparticles interact with the metal un-

derneath the oxide film, with the result

that the particles are transformed, elec-

tronically charged and stick to the sur-

face tighter than on thicker films.

The very smallest ones, clusters con-

sisting of 2−6 atoms, become chain-like

on thin films. Slightly bigger ones, clus-

ters of about 20 atoms, become planar

against the surface. On thick films, even

the smallest of clusters are not chain-like

and larger clusters form three-dimen-

sional polyhedral structures.

The atom clusters studied are too

small to see. Observing them requires

special empirical methods, such as scan-

ning tunneling microscopy. With this

method it is possible to measure the spa-

tial probability of density of occurrence

of electrons tied around a cluster of atom

nuclei. The computational method used

by Frondelius can be used to predict the

shape of the density distribution for a

certain size and form of a gold atom

cluster. n

DISSerTATIon: enVIronMenT CAUSeS goLDen nAnoPArTICLeS To TrAnSforM

In his Grand Challenge project, Alex Bun-

ker used long time molecular dynamics

simulations to study protein Prolyl Oligo-

peptidase (POP). POP is a very important pro-

tein involved in a wide range of metabolic

functions and it has a very important role for a

wide range of neurological function.

Bunker’s group used an extremely large

scale umbrella sampling simulation to study

the inhibitor molecule’s (Z-Pro-pronylol) en-

trance route to POP’s active site and exit path-

ways from POP’s active site. The study was

performed by calculating a number of simula-

tions, each with the inhibitor bound at a dif-

ferent site along the route. At each site, the

inhibitor was held in place with a force to al-

low effective sampling of adjacent conforma-

tions (umbrella sampling).

Since the system size was extensive and

several long simulations had to be run, a con-

siderable amount of computing time was re-

quired.AlexBunker’sGrandChallengeproject

used roughly one million processor hours of

CSC’s computing resources. n

InhIbITor’S roUTeS To ProTeIn PoP



Man-induced climate change has

raised the need to predict the

future climate and its feedback

to vegetation. These are studied with glob-

al climate models; to ensure the reliability

of these predictions, it is important to have

a biosphere description that is based upon

the latest scientific knowledge.

Meteorological Thesis of Tea Thum

(University of Helsinki) concentrates on the

modelling of the CO2 exchange of the bo-

real coniferous forest, studying also the

factors controlling its growing season and

how these can be used in modelling. In ad-

dition, the modelling of CO2 gas exchange

at several scales was studied.

A canopy-level CO2 gas exchange model

was developed based on the biochemical

photosynthesis model. This model was first

parameterized using CO2 exchange data

obtained by eddy covariance (EC) measure-

ments from a Scots pine forest at Sodanky-

lä. The results were compared with a semi-

empirical model that was also parameter-

izedusing ECmeasurements. Bothof the

models gave satisfactory results. The bio-

chemical canopy-level model was further

parameterized at three other coniferous

forest sites located in Finland and Sweden.

At all the sites, the two most important bio-

chemical model parameters showed sea-

sonal behaviour, i.e., their temperature re-

sponses changed according to the season.

Modelling results were improved when

these changeover dates were related to

temperature indices. During summer-time

the values of the biochemical model pa-

rameters were similar at all the four sites.

Different control factors for CO2 gas ex-

change were studied at the four coniferous

forests, including how well these factors

can be used to predict the initiation and

cessation of the CO2 uptake. Temperature

indices, atmospheric CO2 concentration,

surface albedo and chlorophyll fluores-

cence (CF) were all found to be useful and

have predictive power. In addition, a de-

tailed simulation study of leaf stomata in

order to separate physical and biochemical

processes was performed. The simulation

study brought to light the relative contribu-

tion and importance of the physical trans-

port processes.

The results of this work can be used in

improving CO2 gas exchange models in bo-

real coniferous forests. n

DISSerTATIon: MoDeLLIng boreAL foreST Co2 exChAnge AnD SeASonALITy

In his doctoral thesis in the field of physics, Lauri Wendland

(University of Helsinki) describes methods for the reliable

identification of hadronically decaying tau leptons in the

search for heavy Higgs bosons of the minimal supersymmetric

standard model of particle physics (MSSM).

The Higgs boson(s), whose existence has not yet been exper-

imentally verified, are a part of the standard model and its most

popular extensions. They are a manifestation of a mechanism

which breaks the electroweak symmetry and generates masses

for particles.

Since the H->tautau and H+->tau nu decay channels are im-

portant for the discovery of the Higgs bosons in a large region of

the permitted parameter space, the analysis described in Wend-

land’s thesis serves as a probe for finding out properties of the

microcosm of particles and their interactions in the energy scales

beyond the standard model of particle physics.

The tau-jet identification is studied with methods based on a

signature of a low charged track multiplicity, the containment of

the decay products within a narrow cone, an isolated electro-

magnetic energy deposition, a non-zero tau lepton flight path,

the absence of electrons, muons, and neutral hadrons in the de-

cay signature, and a relatively small tau lepton mass compared

to the mass of most hadrons. n

DISSerTATIon: IDenTIfICATIon of hADronICALLy DeCAyIng TAU LePTonS In SeArCheS for heAVy MSSM hIggS boSonS wITh The CMS DeTeCTor AT The Cern LhC

Charged Higgs boson in reaction gg->tbH+, t->Wb->scb, H+->tau nu->hadr.

© L

auri

Wen

dla

nd



In her doctoral thesis in the field of

biochemistry, Siina Junnila (Univer-

sity of Helsinki) investigated the

complex genomic alterations of gastric

cancer.

Multiple chromosomal regions with

recurrent copy number alterations were

detected. Junnila used themicroarray

analysis program, Chipster in the stud-

ies. Chipster has been developed by

CSC − IT Center for Science Ltd.

Gastric cancer is the fourth most

common cancer and the second most

common cause of cancer-related death

worldwide. Due to lack of early symp-

toms, gastric cancer is characterized by

late stage diagnosis and unsatisfactory

options for curative treatment. Several

genomic alterations have been identi-

fied in gastric cancer, but the major fac-

tors contributing to initiation and pro-

gression of gastric cancer remain poor-

ly known. Gene copy number alterations

play a key role in the development of

gastric cancer, and a change in gene

copy number is one of the fundamental

mechanisms for a cancer cell to control

the expression of potential oncogenes

and tumor suppressor genes.

Siina Junnila’s thesis aimsat clarify-

ing the complex genomic alterations of

gastric cancer to identify novel molecu-

lar biomarkers for diagnostic purposes

as well as for targeted treatment.

Altogether 192 clinical gastric tissue

samples and 7 gastric cancer cell lines

were included in this study.

To highlight genes of potential bio-

logical and clinical relevance, scientists

carried out a systematic microarray-

based survey of gene expression and

copy number levels in primary gastric

tumors and gastric cancer cell lines. Re-

sults were validated using immunohis-

tochemistry, real-time qRT-PCR, and af-

finity capture-based transcript (TRAC)

assay. n

DISSerTATIon: genoMIC ProfILIng of gASTrIC CAnCer Group 16, or the Oxygen Family, of the

periodic table of elements consists

of oxygen, sulfur, selenium, tellurium,

and polonium. These elements are also known

as chalcogens, or ore formers. Chalcogens and

their compounds are an important part of in-

organic chemical technologies. Especially sul-

fur and selenium have been found to be suit-

able materials for several industrial applica-

tions.

There are numerous studies on com-

pounds of chalcogen and sulfur. The interest

in these compounds is largely due to the poly-

meric sulfur nitride, which is supraconductive

at low temperatures. In contrast, until recent

decades very little information has been avail-

able on chalcogen-nitrogen compounds con-

taining selenium and tellurium, partly due to

the instability of these compounds and partly

due to the lack of suitable source materials.

At the University of Oulu, as part of her

doctoral research work, Maarit Risto has pre-

pared several new chalcogen-nitrogen ring

structures containing selenium and tellurium.

The structures were determined using NMR

spectroscopyandX-raycrystallography.Risto

investigated the formation of chalcogen-nitro-

gen complexes with transition metals and the

chemical and structural properties of the com-

pounds both in a solution and in the solid

state. The research results provided much

new basic information on the chemistry of se-

lenium-nitrogen and tellurium-nitrogen com-

pounds. The prepared compounds should be

suitable source materials both in inorganic and

organic syntheses, with possible applications

in the preparation of novel electronic materi-

als. Maarit Risto used CSC’s software services

in her thesis work. n

DISSerTATIon: PrePArATIon, STrUCTUre AnD bonDIng of noVeL ChALCogen-nITrogen rIng SySTeMS

In his dissertation, Tommi Mikkola has de-

veloped a numerical method for solving

time-dependent, frictionless free surface

flow problems, and systematically reviewed

the behavior of the error between the numeri-

cal and analytic model. The public defense of

the dissertation took place at the Helsinki Uni-

versity of Technology. In the development

stage of the solution method developed in the

dissertation, the heaviest test simulations

were run on CSC’s computing servers.

A free surface problem is a case where, be-

sides the flow of liquid, the interface between

two different substances, such as water and

air, are under review. The case is mathemati-

cally challenging because the shape of the in-

terface depends on the flow, which itself de-

pends on the shape of the interface. Typically,

the problems are separated from each other,

and the flow and the shape of the interface are

solved in turn. The approach is simple, but

computationally it is very intensive.

The first section of the dissertation pres-

ents two different ways to connect the flow

solution and the free surface solution. The

simple implementation of the methods pre-

sented is a considerable difference from the

connection methods presented in previous

literature. The second section of the disserta-

tion investigates the behavior of the error re-

lated to the computational solving of the

flow problem. This is challenging because the

problem’s precise solution, to which the com-

putational solution could be compared, is not

usually known.

The method presented in the dissertation,

based on the MMS method (method of manu-

factured solutions), differs from the method

based on approximate solutions typically used

in relation to free surface methods. The devel-

oped numerical method can be used, for ex-

ample, when investigating the behavior of

progressing waves or when determining the

forces that waves impose on structures, but

also as a research platform when developing

new solution methods. With the information

obtained about the behavior of the error, and

with the analysis method presented, it is pos-

sible to improve the reliability of simulation

results. n

A DISSerTATIon on The SIMULATIon of free SUrfACe fLowS



Chistian Achim’s (Helsinki University of Technology) thesis

deals with the static and dynamic properties of adsorbed

layers under the influence of a driving force using an exten-

ded version of the Phase Field Crystal Model. The supercomputing

resources of CSC, the Finnish IT center for science, were utilized in

the studies.

In the case of periodic potentials, the various commensurate

phases are described in detail and the complete phase diagram is

mapped out as a function of pinning strength and lattice mis-

match.

To investigate the microscopic origins of friction, these structu-

res were also driven under external driving force causing a depin-

ning transition that is characterized in detail. The research has appli-

cations in, for example, research on surface nanostructures and

supraconductors. Achim’s doctoral thesis, Studies of static and dri-

ven lattice systems with the Phase Field Crystal model, was inspected

at Helsinki University of Technology. n

DISSerTATIon on STATIC AnD DynAMICAL ProPerTIeS of Two DIMenSIonAL LATTICe SySTeMS

DISSerTATIon: CoMPUTATIonAL MoDeLS of CrUMPLIng of ThIn SheeTS AnD MeMbrAneS

The aim of Tuomas Tallinen’s doc-

toral thesis in physics (University of

Jyväskylä) was to investigate the

crumpling of thin sheets and membranes

using computational methods. The discrete

element simulations were carried out in

collaborationwithCSC– ITCenter for Sci-

ence Ltd., and the research provided de-

tailed information on the deformations in

crumpled thin sheets and membranes.

This type of crumpling occurs to paper

when it is crushed and to the sheet metal of

a car in a collision. The results help to

choose materials in which the crumpling

binds as much energy as possible.

Thin membranes are common also at

the microscopic scale. Examples of these

are, for example, a single-atom-thick gra-

phene layer and cell membranes. These

were modeled by taking into consideration

the thermal fluctuations and attractive in-

teractions that are commonly present in

microscopic systems. In this case, the im-

portance of computational research is em-

phasized, because corresponding empirical

research is extremely challenging.

The results can be used to predict the

conditions under which membranes will re-

main flat and when protein-like folding is

likely to occur due to attractive interac-

tions. However, this type of spontaneous

folding is uncharacteristic for biological

membranes and graphene. n

Automatic speech recognition is used in systems that convert

human speech into text or make other actions based on what

is said to the system. Typical applications include dictation,

automatic transcription of large audio or video databases, speech-

controlled user interfaces, and automated telephone services.

In his doctoral thesis defended at the Helsinki University of Tech-

nology, Teemu Hirsimäki presented methods that facilitate im-

provement of accuracy and efficiency of speech recognition in mor-

phologically rich languages, such as Finnish, Estonian and Turkish.

Instead of using a fixed vocabulary, Hirsimäki uses morpheme-like

units, referred to as morphs, which, in practice, may be used to iden-

tify an unlimited vocabulary. He uses speech recognition experi-

ments to show how statistical language models can be trained effi-

ciently, and presents efficient information structures for the mod-

els. The thesis also introduces methods for reducing recognition

errors made by the system and investigates the most significant

sources of error. In his work towards his dissertation, Teemu Hir-

simäkiusedthetextcorporaofCSC’sLanguageBankintraininghis

language models. n

DISSerTATIon on UnLIMITeD-VoCAbULAry SPeeCh reCognITIon

annual report 2009

editors: Ari Turunen Tiina Leiponen Sirpa Kotila

Statistics of CSC: Sirpa Kotila

layout: Up-to-Point Oy Paula Winter

translations: Pirkko Huuskonen

print: Painorauma Oy

Photographs unless marked otherwise Peter Forsgård, Studio IMG

dissertation news collected from news releases from the universities

CSC – IT CenTer for SCIenCe LTD.Life Science CenterKeilaranta 14, P.o. BoX 405fI – 02101 espoowww.csc.fi

Annual Report 2009

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