Zuse Institute Berlin | Annual Report 2013 ZIB 2017 Annual Report

SPATIAL AND SOFTWARE DYNAMIC MATHEMATICS SUSTAINABILITY SCALABILITY STRUCTURE OF MEETS IN THE AGE OF AND LIFE HUMANITIES OPEN SCIENCE CONCURRENCY PAGE 26 PAGE 36 PAGE 50 PAGE 66

Preface PREFACE

We are living in a rapidly changing world In its white paper SWD (2016) 106, the From a more scientific view, one has to At ZIB, we are guided by the belief In 2017, we worked frantically to open interdisciplinary projects in the fields with enormous opportunities, but also European Commission states: “High- add that MSO (modeling, simulation, and that a high-level approach to mod- new horizons, for example, into compu- of high-energy physics and the automo- many threats. Mastering complexity is performance computing (HPC) is at the optimization) is equally important for eling, simulation, and optimization tational social science and humanities, tive industry. “Dusting off Cometary becoming more and more important. The core of major advances and innovation the development of most innovations in (MSO), enriched by data analytics and we intensified our research activities Surfaces” shows how simulation and last decade has caused the digitization in the digital age. In the massively technology, health, energy, and finance. and high-performance computing in established application fields like life data analytics can be combined to model of almost every aspect of our daily lives connected digital economy, the expo- Although HPC, data analytics, and artifi- (HPC), delivers a considerable con- and materials sciences, nanophotonics, the gas and dust cloud around the comet and generated an avalanche of digital nential growth of data, networking, and cial intelligence offer new opportunities, tribution to solving the grand chal- and traffic and transport networks. Churyumov–Gerasimenko in order to data. What looks like an immense gain computing will continue to drive societal their impact on decision-making, tech- lenges, improving the scientific and This annual report provides insights extract relevant information from the in information for our networked society changes, scientific advances, and produc- nological and social innovation, and the industrial innovation capability, and into a variety of other success stories data gathered by a space mission to the at first, quickly turns out to be a curse. tivity gains. The nature of computing is improvement of products and services allowing better services for citizens and gives a general overview of ZIB’s comet. And, “Software Sustainability Data per se still is not information, and changing with an increasing number of will be limited without a massive effort and better decision-making. Major organization and key factors for its suc- in the Age of Open Science” reports on certainly is not knowledge. On the con- data-intensive critical applications, and on the MSO axes. This statement is opportunities rely on the connections cessful development. In particular, six research activities at ZIB regarding trary: intelligent questions about data the intertwining of HPC with a growing supported by various scientific studies at this interface across the whole feature articles highlight aspects of our sustainability methods that form part of diversity can only generate information number of industrial applications and that show that MSO methods have out- spectrum of the sciences and human- work: “Mathematics Meets Humanities” increasing efforts to conduct research in in the true sense of the term, and thus scientific domains makes HPC the paced computational power in terms of ities. Additionally, the convergence provides an insight for new fruitful accordance with open-science principles, allow for taming complexity. However, engine to power the new global digital capability over the past decades. It is well of MSO, HPC, and big data will enable interactions between mathematics, and demonstrates how these efforts may even the most reliable information is not economy. Mastering HPC technologies known that the performance of comput- traditional computational-intensive facing new challenges by integrating change the way research is done in the sufficient for decision-making, which has has become indispensable for supporting ing machines improves by a factor of two sectors to be more productive and the human factor into complex systems future. to be based on exploring several options policy making, maintaining national sov- every 18 months. Moore’s law describes move up into higher-value products modeling, and the humanities, seeking In summary, ZIB continues to be a place and trying to predict their consequences ereignty, and economic competitiveness. this trend. In the period from 1990 to and services, and will also pave the possible solutions to otherwise unsolv- booming with excellent research and (costs and benefits) in order to select The development of the next HPC gen- 2014, this resulted in a speedup of more way for new science, businesses, and able tasks. In “Spatial and Dynamic first-rate scientific services and infra- the best option or create new solutions eration has become a national strategic than a factor of 1,000,000. What is not applications that we are far from Structure of Life,” we report on recent structure. Against our own expectations, to grand challenges. The prediction of priority for the most powerful nations, known to the general public is that MSO being able to imagine now. ZIB is one research results at ZIB that provide we again broke several all-time records complex processes, however, requires including the USA, China, Japan, Russia, research has achieved similar or even of the places where this convergence insight into fundamental principles of in 2017, although present capacity limita- massive simulation based on efficient India, and Europe as well.” higher speedups in algorithms needed is happening now. biological processes, such as cell division, tion seemed to prevent this. For example, algorithms and high-performance com- for grand challenge simulations, so that protein regulation, and brain formation in total, €8 million worth of third-party puting infrastructures. the combined speedup is estimated to and activity. “20,000 Feet Above the funding was acquired, which marked an be larger than an expressive factor of Ground” sheds some light on one of increase for the sixth year in a row and a 1,800,000,000,000. This means that ZIB’s innovation projects with industry new record in ZIB’s history. computations that we can do in one sec- partners by showing how basic research ond today would have needed more than leads to new navigation systems for air- 50,000 years in 1990. craft that save both fuel and time. The Berlin, May 2018 article “Scalability and Concurrency” Christof Schütte features joint research problems in two President of ZIB

4 2017 Annual Report Zuse Institute Berlin 5 26 50 66 SOFTWARE SPATIAL AND DYNAMIC SUSTAINABILITY SCALABILITY AND STRUCTURE OF LIFE IN THE AGE OF CONCURRENCY Solving common problems Insight into fundamental OPEN SCIENCE in high-energy physics and principles of life the automotive industry Software as sustained 4 scientific output ZUSE INSTITUTE 36 58 BERLIN Preface | Executive Summary | MATHEMATICS Organization | ZIB Structure | 20,000 FEET ABOVE ZIB in Numbers | Kombiverkehr 2021 – Optimizing the Line MEETS HUMANITIES THE GROUND Network of Karlsruhe | ZIB's Illustrating the potential of New navigation systems Data Center | Economic enhanced collaboration Situation | Spin-Offs | for aircraft Number of Employees 76 84 DUSTING OFF ZIB PUBLICATIONS COMETARY SURFACES REFERENCES First realistic simulations of the IMPRINT CONTENTS dust and gas coma of a comet Executive Summary

PARALLEL AND DISTRIBUTED COMPUTING

MATHEMATICAL From the smallest structures at the sub-atomistic level to large-scale OPTIMIZATION cosmic matter: supercomputers are indispensable tools to simulate impor­ EXECUTIVE AND SCIENTIFIC tant real-world phenomena. Our feature article “Dusting off Cometary Surfaces” INFORMATION describes how the beautiful dust corona of the comet 67P/Churyumov– The ongoing digitization of industry Gerasimenko was investigated on the and society continues to open up new HLRN supercomputer. Taking the shape opportunities for optimization in many of the nucleus, the temperature distribu- applications, such as intermodal travel tion on the surface, the centrifugal, and or computational biology, and brings the Coriolis forces into account, the dust up exciting mathematical challenges distribution was predicted with a much on the interfaces to data and computer higher accuracy than previously possi- science, as well as economics. The ble. This project is also a good example computation of a new line plan for the of the new breed of mixed HPC/big-data city of Karlsruhe (see the respective projects, since our simulation results had report below) and for the ICE rotations to be correlated with a great deal of obser- SUMMARY vation data from the Rosetta mission. of Deutsche Bahn, as well as spectacular performance improvements in the gen- The two interdisciplinary projects of eral mixed-integer programming solver the feature article “Scalability and MATHEMATICS SCIP and the parallel computing frame- Concurrency” also combine high-per- work UG were particular highlights. formance computing with data-stream FOR LIFE AND FOR Networking and outreach was also in processing. A scalable software for the the focus of the department in 2017. real-time analysis of nucleus–nucleus MATERIAL SCIENCES inverse problems, and massive simula- Together with Freie Universität Berlin’s collisions at the FAIR particle accel- tion of particle-based and agent-based Department of Information Systems, erator was developed and parallel models allowed for novel insights in ZIB’s Optimization department co-orga- algorithms were designed for testing This year was marked by the prepara- such diverse areas as biomedicine or nized the 55th International Conference and verifying software components tion of the Cluster of Excellence initia- archaeology. on Operations Research (OR2017), in that are used in cars for the real-time tive MATH+, which fueled work on new analysis of sensor data. As in the years These new developments are comple- which more than 900 participants from application directions, in particular in before, research at ZIB was focused on mented by a successful continuation 44 countries contributed almost 600 the framework of collaborations with improving scalability and fault toler- of activities in modeling, simulation, presentations in 21 parallel streams. the existing excellence clusters TOPOI ance in dynamic systems with failing and optimization as well as visual data Two international workshops in Tokyo (digital humanities and computational components. analysis. They resulted, for instance, and Berlin, jointly organized with the social sciences) and Neurocure (ana- in the development of a nonaddictive Institute of Statistical Mathematics Our next supercomputer, the HLRN-IV, lyzing and interpreting life microscopy painkiller (with a publication in Science in Tokyo, the Institute of Mathematics will make it much easier to conduct the data). and emergence of a spin-off company), for Industry of Kyushu University, and most challenging research projects. Many research activities that were the first reconstruction and analysis MODAL AG, explored the fascinating The European procurement lead by ZIB started in previous years have been the- of entire microtubule spindles of C. interface of mathematical optimization was successfully finalized in 2017 and matically extended, such as augmenting elegans (with a publication in Nature and data analysis. Successful activities the contract signed in early 2018. With UQ by optimal design of experiments Communication), the acquisition of for the upcoming extension of the 244,000 processor cores, the new system and empirical Bayesian approaches, EU projects on optical metrology and Research Campus MODAL focused on will provide a six-fold increase in appli- or moving from linear to nonlinear scientific cloud computing, an indus- the acquisition of new partners from cation performance. The supercomputer shape manifolds. The investigation and try project on cloth simulation and both industry and academia. will be operated on behalf of the North utilization of machine-learning tech- visualization, and the first prize in German HLRN consortium by ZIB in niques has increased, with applications the worldwide MICCAI segmentation Berlin and the University of Göttingen particularly in image segmentation and competition. in Lower Saxony.

8 2017 Annual Report Zuse Institute Berlin 9 Organization

THE STATUTES

The Statutes, adopted by the Board of Directors at its meeting on June 30, 2005, define the functions and procedures of ZIB’s bodies, determine ZIB’s research and development mission and its service tasks, and decide upon the composition of the Scientific Advisory Board and its role. ADMINISTRATIVE SCIENTIFIC BODIES ADVISORY BOARD

The bodies of ZIB are the President and DR. JUTTA KOCH-UNTERSEHER The Scientific Advisory Board advises the Board of Directors Der Regierende Bürgermeister von ZIB on scientific and technical issues, (Verwaltungsrat). Berlin Senatskanzlei – Wissenschaft supports ZIB’s work, and facilitates und Forschung ZIB’s cooperation and partnership with President of ZIB univer­sities, research institutions, and PROF. DR. CHRISTOF SCHÜTTE DR. JÜRGEN VARNHORN industry. Senatsverwaltung für Wirtschaft, Vice President Energie und Betriebe The Board of Directors appointed the N.N. following members to the Scientific PROF. DR. MANFRED HENNECKE Advisory Board: The Board of Directors was composed in Bundesanstalt für Materialforschung ORGANIZATION PROF. DR. JÖRG-RÜDIGER SACK 2017 as follows: und -prüfung (BAM) Carleton University, Ottawa, Canada PROF. DR. PETER FRENSCH THOMAS FREDERKING Vice President, Humboldt-Universität PROF. DR. ALFRED K. LOUIS Helmholtz-Zentrum Berlin für zu Berlin (Chairman) Universität des Saarlandes, Materialien und Energie (HZB) Saarbrücken PROF. DR. CHRISTIAN THOMSEN DR. HEIKE WOLKE President, Technische Universität Berlin PROF. DR. RAINER E. BURKARD SCIENTIFIC BOARD OF DIRECTORS Max-Delbrück-Centrum für Molekulare (Vice Chairman) Technische Universität Graz, Austria Medizin (MDC) CHAIRMAN: PROF. DR. PETER FRENSCH ADVISORY BOARD Humboldt-Universität zu Berlin (HUB) PROF. DR. BRIGITTA SCHÜTT PROF. DR. MICHAEL DELLNITZ The Board of Directors met on May 19, CHAIRMAN PROF. DR. JÖRG-RÜDIGER SACK Vice President, Freie Universität Berlin Universität Paderborn 2017, and December 4, 2017. | Ottawa PROF. DR. RAINER E. BURKARD | Graz LUDGER D. SAX PROF. DR. MICHAEL DELLNITZ | Paderborn Grid Optimization Europe GmbH PROF. DR. ALFRED K. LOUIS | Saarbrücken LUDGER D. SAX | Essen DR. ANNA SCHREIECK DR. ANNA SCHREIECK | Ludwigshafen PRESIDENT BASF SE, Ludwigshafen DR. REINHARD UPPENKAMP | Berlin PROF. DR. CHRISTOF SCHÜTTE DR. KERSTIN WAAS | Frankfurt am Main DR. REINHARD UPPENKAMP PROF. DR. DOROTHEA WAGNER | Karlsruhe Berlin Chemie AG, Berlin VICE PRESIDENT N.N. DR. KERSTIN WAAS Deutsche Bahn AG, Frankfurt am Main

PROF. DR. DOROTHEA WAGNER Karlsruher Institut für Technologie (KIT), Karlsruhe MATHEMATICS FOR LIFE AND MATHEMATICAL OPTIMIZATION AND PARALLEL AND ADMINISTRATION MATERIAL SCIENCES SCIENTIFIC INFORMATION DISTRIBUTED COMPUTING AND LIBRARY The Scientific Advisory Board met on Prof. Dr. Christof Schütte Prof. Dr. Ralf Borndörfer Prof. Dr. Alexander Reinefeld Annerose Steinke July 3 and 4, 2017, at ZIB. Prof. Dr. Thorsten Koch

10 2017 Annual Report Zuse Institute Berlin 11 ZIB Structure

MATHEMATICS FOR LIFE MATHEMATICAL OPTIMIZATION PARALLEL AND DISTRIBUTED COMPUTING ADMINISTRATION AND LIBRARY AND MATERIAL SCIENCES AND SCIENTIFIC INFORMATION A. Reinefeld A. Steinke C. Schütte R. Borndörfer, T. Koch

NUMERICAL VISUAL DATA MATHEMATICAL SCIENTIFIC DISTRIBUTED SUPERCOMPUTING MATHEMATICS ANALYSIS OPTIMIZATION INFORMATION ALGORITHMS T. Steinke M. Weiser H.-C. Hege R. Borndörfer, T. Koch (B. Rusch) F. Schintke T. Koch ZIB

COMPUTATIONAL VISUAL DATA MATHEMATICS OF WEB DISTRIBUTED DATA HPC CONSULTING MEDICINE ANALYSIS IN TRANSPORTATION TECHNOLOGY MANAGEMENT T. Steinke M. Weiser, SCIENCE AND AND LOGISTICS AND MULTIMEDIA F. Schintke S. Zachow ENGINEERING R. Borndörfer W. Dalitz H.-C. Hege

COMPUTATIONAL IMAGE ANALYSIS MATHEMATICAL DIGITAL PRESER‑ SCALABLE HPC SYSTEMS MOLECULAR IN BIOLOGY OPTIMIZATION VATION ALGORITHMS STRUCTURE C. Schimmel DESIGN AND MATERIAL METHODS W. Peters-Kottig T. Schütt M. Weber SCIENCE A. Gleixner S. Prohaska, D. Baum

COMPUTATIONAL THERAPY MATHEMATICS OF SERVICE CENTER MASSIVELY ALGORITHMS ZIB is structured into four divisions: NANO OPTICS PLANNING TELECOMMUNI‑ DIGITIZATION PARALLEL DATA FOR INNOVATIVE three scientific divisions and ZIB’s F. Schmidt S. Zachow CATION BERLIN ANALYSIS ARCHICTETURE Since May 1, 2017 Until June 30, 2017 A. Müller F. Schintke T. Steinke administration. S. Burger R. Borndörfer Each of the scientific divisions is composed of two departments that are further subdivided into research groups COMPUTATIONAL BIOINFORMATICS ENERGY KOBV LIBRARY SYSTEMS BIOLOGY IN MEDICINE NETWORK NETWORK – (darker bluish color) and research service S. Röblitz T. Conrad OPTIMIZATION RESEARCH AND groups (lighter bluish color). J. Zittel DEVELOPMENT J. Schweiger B. Rusch

UNCERTAINTY MACHINE MATHEMATICS OF KOBV LIBRARY QUANTIFICATION LEARNING FOR HEALTH CARE NETWORK – T. Sullivan TIME SERIES Since July 1, 2017 OPERATING Since June 1, 2017 G. Sagnol S. Lohrum H. Wu

FRIEDRICH‑​ ALTHOFF‑​ KONSORTIUM U. Kaminsky

CORE FACILITY IT AND DATA SERVICES C. Schäuble LEGEND SCIENTIFIC DIVISIONS AND DEPARTMENTS RESEARCH GROUPS

RESEARCH SERVICE GROUPS BRAIN BERLIN RESEARCH AREA CORE FACILITY INFORMATION NETWORK C. Schäuble

12 2017 Annual Report Zuse Institute Berlin 13 ZIB in Numbers DATA ARCHIVE AT ZIB TOTAL CAPACITY ON 65 PB 16,600 TAPES ZIB IN NUMBERS 13,986 SEMINARS GIVEN BY ZIB SCIENTISTS AT UNIVERSITIES 15 OUTREACH EVENTS FOR 2,004 SCHOOL CLASSES AND THE GENERAL PUBLIC ¤7,896,000 ¤6,147,000 58 PROJECT-RELATED PUBLIC 9 VISITORS SCIP THIRD-PARTY FUNDS LECTURES LONG NIGHT OF THE SCIENCES GIVEN BY ZIB SCIENTISTS AT UNIVERSITIES OF MIP SOLVER SCIP ¤1,749,000 INDUSTRIAL THIRD-PARTY PROJECTS PROMOTION OF YOUNG SCIENTISTS: DISSERTATIONS MASTER’S PROFESSORSHIPS OFFERED TO ZIB RESEARCHERS 6,150 99 18 INTERNATIONAL GUESTS CONFERENCES AND 4 AT ZIB IN 2017 WORKSHOPS AT ZIB SCIENTIFIC 230TALKS 136 IN JUNE 2017: PEER-REVIEWED PUBLICATIONS IN ZIB SUPERCOMPUTER IS INTERNATIONAL SCIENTIFIC JOURNALS 65 DISTINGUISHED 165 INVITED NO.140 IN TOP500 LIST

14 2017 Annual Report Zuse Institute Berlin 15 Kombiverkehr 2021 – Optimizing the Line Network of Karlsruhe KOMBIVERKEHR 2021 – 1 OPTIMIZING THE LINE NETWORK OF KARLSRUHE ZIB’s research group Mathematics around 20,000 people, such that the certain transportation modes, mini- of Transportation and Logistics Kombi plan was no longer adequate. In mum frequency requirements for each supported the design of a new line a joint project with Verkehrsbetriebe station, or maximum frequency bounds network for Karlsruhe. The optimized Karlsruhe GmbH (VBK), PTV Transport on tracks. A solution of the optimiza- solution reduces costs by around 5% Consult GmbH, and TTK Transport tion model implies a set of line routes while travel times remain constant. Technology Consult GmbH, our goal together with frequencies of operations, was to investigate the potentials in cost such that the given passenger demand Kombiverkehr 2021 (combined traffic and efficiency improvements by using can be routed with respect to the result- 2021) is currently one of the largest mathematical optimization methods, ing line capacities. Using bi-criteria inner-city construction projects in in order to find the best compromise optimization, the whole potential and Germany. It aims at increasing the over- between travel-time improvements and the interdependencies between cost all traffic flow and the attractiveness cost efficiency. and travel-time minimization can be of the city of Karlsruhe by tunneling investigated by computing the entire public transport under the pedestrian The mathematical basis of our Pareto front of efficient solutions. Potentials for travel-time improvements zone of Karlstrasse. In this way, the line-planning optimization system is and cost savings were illustrated by tramway network is expanded, such a mixed-integer linear optimization The focus in Karlsruhe was on the computing different solutions address- that it becomes necessary to redesign model that considers all possible line redesign of the tramway network. All ing cost minimization, travel-time the complete line network. As early routes and passenger paths simulta- other transportation systems (e.g. bus minimization, and some compromise as 2002, a line plan (“Kombi”, see fig- neously. To favor traveling without and regional traffic) were considered for solutions (see table 1). In several rounds ure 2) was designed using the so-called transfers, the model is based on a novel passenger routing as well, however, the of computation, evaluation, and discus- “Standardisierte Bewertung” method. concept of metric inequalities for direct line routes of these systems remained sion, the infrastructure, operational, Kombi was supposed to be operated in connections, for further details see [1]. unchanged. The computation was done service-related, etc. constraints and 2021 after all construction works were All kinds of practical and technical for the peak hour. requirements of VBK, as well as a suit- finished. The population of Karlsruhe, requirements can be included in the able cost model, were incorporated into however, has increased since then by model, e. g. minimum cycle times for both the line-planning optimizer and the accompanying micro-simulation model VISUM of PTV. In this way, realistic line plans could be computed. Total travel time [T h] 2 Assessing many alternatives (which Cost (incl. eight-minute Total no. are all Pareto optimal, i.e. realize “best No. tram [% Kombi] transfer penalty) transfers possible compromises”), in the end, VBK Kombi 9 100.0% 131.78 124,259 decided on a network that yields similar travel times as the Kombi line network, C+ 8 83.1% 133.82 125,302 but reduces costs by around 5%. This 1 Karlsruhe. Source: VBK/Uli Deck. line plan is illustrated in figure 3. The C 7 86.8% 132.27 128,482 Verkehrsbetriebe Karlruhe GmbH are 2 Kombi: line plan computed for the currently evaluating the implementa- Final 8 95.1% 131.71 126,138 Standardisierte Bewertung. tion of either plan for the year 2021. T 9 95.2% 131.42 126,130 3 Optimized solution. T+ 9 102.0% 130.77 122,730

Table 1: Overview of some solutions.

16 2017 Annual Report 3 Zuse Institute Berlin 17 ZIB’s Data Center ZIB’S DATA CENTER VIRTUAL OPEN SOURCE 100 SCALABLE VIRTUAL INFRASTRUCTURE GBIT/S FIREWALLS DATA MANAGEMENT FILE SYSTEM DATA CENTER – TENANT MODEL

After the presentation of ZIB’s open The Berlin Research Area Information Since the beginning of 2017, the data ser- The handling of petabytes of user data in A complete renewal of ZIB’s data-center Parallel to the transformation of the data science infrastructure project Network (BRAIN) and ITDS are work- vice infrastructure has been updated: the management for direct data access operating area was started in August data center, a new multi-tenant virtu- in October 2016, the institute’s core ing closely together to create a 100 Gbit cache systems have been upgraded with on a multiuser level is a challenge that 2017. All server racks, the cooling, the alization solution was introduced. The facility “IT and Data Service” (ITDS) firewall solution based on standard the latest design SSDs, the Oracle HSM repeatedly produces previously unre- cabling have been updated and provided system now consists of 144 processors, started to rebuild and modernize the hardware with open-source software is now available in the latest version, solved problems for ITDS and our users with a modern and variable cooling and 3.5 TB RAM, and more than 200 TB entire IT infrastructure at ZIB. From components. This implements a highly additional protocols such as CIFS in searching, accessing, authorizing, alignment concept combined with a hot- SSD memory connected with a 40 Gbit the infrastructure of the data center to flexible firewall system with horizontal and NFS are now directly available and analyzing the data. In response, aisle air containment. We now operate network. This allows us to combine virtual file systems and server environ- scaling and building redundancy. In for cooperation partners with BRAIN ITDS introduced a virtual file system 50 directly cooled server racks with a about 200 virtual servers in a common ments, all IT services have been revised other words, this is a step from active/ connection, and additional services that implements data migration, data total capacity of 2,350 height units with infrastructure. and reviewed since 2016. We introduced passive standby to an active/active like Nextcloud or a scalable file-system hierarchy (HSM), metadata handling a theoretical peak cooling capacity of The virtual infrastructure tenant model new operating and development models system. integration are possible. The connection and capture, role-based management, 900 kW. In addition, redundant systems implements a combined environment for IT services. ZIB’s new life-cycle of our largest service consumer is now backup and duplication, as well as such as network and fiber channels have for software projects. These tenants management system transforms the available with 80 Gbit/s sustainable versioning transparently to the user. In been strategically distributed to build a consist of virtual servers, a firewall, IP IT deployment processes from crafting data rate. addition to the established access pro- high-availability data center. segments, network management like to automation. The hardware basis is tocols, a Web interface will enable user DNS and DHCP, and deployment proce- now strongly geared toward commodity self-service for Windows, Linux, and dures for virtual machine installations. hardware. Universal servers can be used Mac OS X. Automation interfaces are for specific software configurations. added to build data-related applications. The specifics of IT services will no Before, users had to interact with many longer be implemented in hardware but different storage and data management in software and thus at runtime of the systems. With the introduction of the systems. new paradigm, ITDS realized a new convergent view upon the virtual file The integration and operational density system. in the data center with more than 15 kW per server rack is close to the maximum This is a shift in paradigm away from cooling capacity when using in-row file-system management to data man- coolers. NOW FUTURE agement. Central aspects are automatic data classification, storage inventory VM VM and classification, storage analysis, VM WINDOWS (CIFS) user groups and project quota, storage USERS USERS LINUX (NFS) WEB (HTTPS) analysis, and storage pools that can VM … METADATA, HANDLING, be expanded dynamically and vendor SEARCH, REVISIONING HPC SCRATCHDATA ZIB independently.

BACKUP HPC SCRATCHDATA ZIB BACKUP

CONVERGENCE

18 2017 Annual Report Zuse Institute Berlin 19 Economic Situation in 2017

In 2017, the total income of ZIB comprised €18.5 million. The main part of this was made available by the Federal State of Berlin as the basic financial stock of ZIB (€8.4 million), including investments and Berlin’s part of the budget of HLRN at ZIB. A similarly large part resulted from third-party funds (€8.0 million) acquired by ZIB from public funding agencies (mainly DFG and BMBF) and via industrial research projects. This was complemented by a variety of further grants like the budgets of ECONOMIC BRAIN (State of Berlin) and KOBV (mixed funding) as well as the part of the HLRN budget made available by other German states. ¤2,100,000 SITUATION

¤8,400,000 IN 2017 ¤8,000,000 ZIB INCOME

45% Core budget by State of Berlin 43% Third-party funds 12% Further grants

20 2017 Annual Report Zuse Institute Berlin 21 Economic Situation in 2017

ZIB THIRD- ECONOMIC PARTY FUNDS SITUATION IN 2017 IN EUROS

The Zuse Institute Berlin (ZIB) finances INDUSTRY its scientific work via three main sources: the basic financial stock of the PUBLIC FUNDS Federal State of Berlin and third-party ¤9,000,000 funds from public sponsors and those of industrial cooperation contracts. In 2017, ZIB raised third-party funding by a large number of projects. Project- related public third-party funds raised ¤8,000,000 from €5.487 thousand in 2016 to €6.147 thousand in 2017, industrial third-party projects declined from €2.371 thousand to €1.749 thousand. In total, €7.896 ¤7,000,000 thousand third-party funding marked a new record in ZIB’s history, an increase for the sixth year in a row. ¤6,000,000

¤1,748,496 ¤2,992,033 ¤5,000,000 Industry BMBF incl. FC MODAL

¤4,000,000 ¤1,945,551 Other public funds

¤1,102,968 DFG ¤3,000,000

¤106,628 EU ¤2,000,000 ZIB THIRD- PARTY FUNDS ¤1,000,000 BY SOURCE 1% EU ¤0 14% DFG 25% Other public funds 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 22% Industry 38% BMBF incl. FC MODAL

22 2017 Annual Report Zuse Institute Berlin 23 Spin-Offs | Number of Employees

COMPUTING IN BIT-SIDE GMBH LAUBWERK GMBH In 2017, 231 people were TECHNOLOGY GMBH 2000 | www.bit-side.com 2009 | www.laubwerk.com employed at ZIB; of these, 171 (CIT) Telecommunication applications Construction of digital plant models positions were financed by 1992 | www.cit-wulkow.de and visualization third-party funds. Mathematical modeling and develop- 1000SHAPES GMBH ment of numerical software for technical DRES. LÖBEL, BORNDÖRFER & 2010 | www.1000shapes.com chemistry WEIDER GBR / LBW OPTIMIZATION Statistical shape analysis GMBH RISK-CONSULTING 2000 | www.lbw-berlin.de TASK – Berthold Gleixner Heinz Koch NUMBER PROF. DR. WEYER GMBH Optimization and consulting in GbR 1994 | www.risk-consulting.de public transport 2010 Database marketing for insurance LBW Optimization GmbH was founded Distribution, services, and consulting for companies in 2017 and is a spinn-off of LBW GbR ZIB’s optimization suite

INTRANETZ GMBH LENNÉ 3D GMBH QUOBYTE INC. 1996 | www.intranetz.de 2005 | www.lenne3d.com 2013 I www.quobyte.com Software development for logistics, 3-D landscape visualization, Quobyte develops carrier-grade storage database publishing, and e-government software development, and services software that runs on off-the-shelf OF EMPLOYEES hardware AKTUARDATA GMBH JCMWAVE GMBH 1998 | www.aktuardata.de 2006 | www.jcmwave.com KEYLIGHT GMBH Development and distribution of risk- Simulation software for 2015 I www.keylight.de evaluation systems in health insurance optical​ components Keylight develops scalable real-time Web services and intuitive apps. The focus VISAGE IMAGING GMBH ONSCALE SOLUTIONS GMBH is on proximity, marketing, iBeacon, (Originating from the ZIB spin-off 2006 | www.onscale.de and Eddystone for interactive business Visual Concepts GmbH) Software development, consulting, and models 1999 | www.visageimaging.com services for parallel and distributed Advanced visualization solutions for storage and computing systems DOLOPHARM BIOSCIENCES UG diagnositic imaging 2017 A specialty pharmaceutical company 1/1/2017 1/1/2018 ATESIO GMBH focused on the clinical and commercial 2000 | www.atesio.de development of new products in pain Development of software and consulting management that meet the needs of 3 0 3 3 0 3 MANAGEMENT for planning, configuration, and optimi- acute and chronic care practitioners and zation of telecommunication networks their patients 15 99 114 15 100 115 SCIENTISTS 38 10 48 34 10 44 SERVICE PERSONNEL 8 8 16 8 9 17 KOBV HEADQUARTERS SPIN- 0 55 55 0 52 52 STUDENTS 64 172 236 60 171 231 TOTAL Temporary Temporary Permanent Permanent OFFS TOTAL TOTAL

24 2017 Annual Report Zuse Institute Berlin 25 Dr. Steffen Prohaska | [email protected] | +49-30-84185-337 SPATIAL AND DYNAMIC STRUCTURE OF LIFE How cells organize patterns in space and time Researchers at ZIB develop data analysis and mathematical modeling techniques and apply them in cooper- ation with biologists in order to gain insight into fundamental principles of biological processes, such as cell division, protein regulation, and brain formation and activity. Spatial and Dynamic Structure of Life a

1 The mitotic spindle during the metaphase of cell division in C.elegans: a Schematic of the microtubule spindle (green) and the chromosomes (blue). b Electron-microscopy image of the full cell. c Complete stitched UNDERSTANDING electron-tomography serial-section stack (120 GB). d Segmented microtubules (green, MICROTUBULE red) and chromosomes (blue).

Microtubules are tube-like polymers ORGANIZATION DURING that play an important role in cell divi- sion. They form the spindle, which is a b microtubule assembly that segregates the chromosomes, see figure 1 (a,b). Electron tomography is the preferred technique to acquire most detailed spatial infor- CELL DIVISION 1 mation about microtubules. The cells are prepared for electron microscopy as 300 nm thick serial sections (slices). With the application of image-processing techniques, we are able to automatically extract the microtubules within a sec- tion [1,2,3] (see figure 1). Furthermore, we have been developing reconstruction methods for joining multiple sections to create a geometric model of the entire spindle [4], see figure 1 (c,d). Our integra- c tion of automated techniques with real- time user interactions allows handling of practical challenges during day-to-day research, such as varying tomogram quality. In cooperation with TU Dresden, we visually and quantitatively analyzed entire microtubule spindles of C. ele- gans for the first time [5]. We identified different classes of microtubules and analyzed geometrical properties, such as length and density distributions. In particular, we investigated potential microtubule interactions based on their spatial arrangement. One major finding is that microtubules do not directly con- nect chromosomes and centrosomes, but form an interactive dynamic network. Currently, the full reconstruction and analysis pipeline is adapted for upcoming d experiments that will study spindles in different phases of cell division, spindles in mutant organisms, meiotic spindles, and spindles of different species.

28 2017 Annual Report Zuse Institute Berlin 29 Spatial and Dynamic Structure of Life

3 Gene expression in a eukaryotic cell. In the nucleus, the DNA is transcribed into messenger RNA (mRNA), which is then exported to the cytoplasm and translated into proteins. Such cellular reaction kinetics can appropriately be characterized by the spatiotemporal chemical CELLULAR master equation [8].

NUCLEUS REACTION DNA

Transcription KINETICS mRNA CYTOPLASM Export 2 Protein mRNA

 2 Chemical master equation (CME) for well-mixed stochastic reaction kinetics. It defines the temporal evolution of the Translation probability P(x,t) to find the system at time t in a certain state x, given the reaction propensities k.

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Accurate modeling of reaction kinetics is approximative mathematical formula- than all other involved reactive species. important to understand how biological tions of the cellular dynamics. Especially In collaboration with the DFG research cells work. Spatially well-mixed reaction multiscale reaction systems, which often center CRC 1114 “Scaling cascades in 3 dynamics can be modeled by the chemi- appear in real-world applications, are in complex systems,” we applied new hybrid cal master equation (CME, see formula the focus of our investigations because methods to efficiently simulate the gene 2), an infinite set of ordinary differential they require new combinations of exist- expression process and showed that, in equations, which is, in general, too com- ing approximation methods. contrast to classical uniform approxima- plex to be solved analytically. There are tion methods, advanced hybrid schemes An example for a cellular reaction pro- accurate numerical simulation schemes are able to reproduce the characteristic cess that involves cascades of particle for solving the CME indirectly, like patterns of the cellular dynamics [7]. numbers is the process of gene expres- Gillespie’s stochastic simulation algo- the spatiotemporal CME [8], to include plasm (see figure 3), which both have a models form the basis for the simula- sion, which is relevant for all known But what can we do if the central well- rithm [6]. For many relevant realistic the necessary spatial information, central meaning for the process of gene tion of cellular reaction kinetics in all life. See figure 2 for an illustration. The mixed assumption underlying the CME settings, however, even our high-perfor- with the level of detail adapted to the expression. By making use of this natu- relevant details; their use in massive information encoded in a gene is used for is broken and some spatial resolution is mance computers fail to create reliable reactive system under consideration. A ral cellular structure, we obtain models simulation environments, however, still the synthesis of functional gene prod- needed to capture the dynamics? Based statistics within an acceptable amount eukaryotic cell, for example, naturally that are computationally practical and poses significant challenges that will be ucts, the proteins, which typically arise on mathematical theory, we have been of time. This is the motivation to reduce decomposes into several compartments at the same time close to the reality of the motivation for further research in in bursts with much higher abundance developing suitable extended models, like the model complexity by considering (e.g. the nucleus and parts of the cyto- a biological cell. Spatiotemporal hybrid this direction at ZIB.

30 2017 Annual Report Zuse Institute Berlin 31 Spatial and Dynamic Structure of Life

4 Single “spiny pyramid” neuron in a cortical column (transparent cylinder) in the rat brain, with its dendrites (red) and axons (gray). Synapse density (yellow) indicates where neurons of this type receive information through synaptic contacts. Data: 3-D BRAIN M. Oberlaender (CAESAR Bonn). 5 Modeling and analysis pipeline, consisting of an offline and an online part. The 3-D neural-network model is created using the Amira visualization software. The large connectome dataset is precomputed on a batch cluster. A Web application, intended for the research community and implemented using state-of-the-art Web frameworks and cloud technologies, provides a query interface to extract MODELING TO and analyze on the fly specific subsets of the large dataset. UNDERSTAND In the recent past, we developed meth- Based on this realistic model, neuron Within the Priority Programme ods to count the number of neurons in simulations can be performed, which “Computational Connectomics” of the the network from 3-D may provide insight into the function DFG (German Research Foundation) microscope images [9]. of each neuron type in the network [11]. starting 2018, we aim to use a data- SENSORY The synaptic connectivity Also, mathematical models, for example, driven Bayesian approach to investigate between them, called the “connec- describing population dynamics [12], can more in depth what anatomical proper- tome,” cannot, however, be directly be tested using this model, and may lead ties underlie synapse formation in order recovered from image data at this to a better understanding of biological to make even more accurate predictions scale. Therefore, we estimate the mechanisms involved. of network connectivity. number of synapses and their location Currently, we are developing a Web on the individual neurons based on mor- INFORMATION application to make this model publicly phological features, in particular spatial available to the research community. overlap between signal-sending axons Neuroscientists can perform in-silico and signal-receiving dendrites (figure 5) experiments by interactively defining [10]. This predicted connectivity turned queries that extract specific information out to match available measurements 4 from this large dataset on the fly (figure 5). PROCESSING well. 5 OFFLINE MODELING AND BATCH PROCESSING ONLINE INTERACTIVE QUERYING AND ANALYSIS

3-D NEURAL-NETWORK CONNECTOME COMPUTATION COMPUTE SERVER WEB BROWSER How does the brain process informa- Amira HTC cluster tion from our senses, and how does Openstack Meteor, D3, ThreeJS this ultimately lead to specific behav- ior? To investigate this question, we, together with our collaborators at WEB SERVER CAESAR Bonn, created an anatom- Galaxy ically realistic model of the part of the rat brain that processes informa- tion from the whisker hairs on the animal’s snout. The model consists STORAGE, DB SERVER of a large network of interconnected S3, MongoDB neurons.

32 2017 Annual Report Zuse Institute Berlin 33 BEFORE SYNAPTOGENESIS DURING SYNAPTOGENESIS 3 3 Spatial and Dynamic Structure of Life Wild type Mutant Wild type Mutant [] 2 [] 2 7 1 1 Average length length Average STOCHASTICITY length Average <8 8-30 >30 <8 8-30 >30 Filopodia lifetime classes [min] Filopodia lifetime classes [min] DRIVING PATTERN AXON GUIDANCE LOOKING FOR REVISITED SIMPLICITY

For the last 70 years, the dominant model The genome is too small for encoding and retraction of filopodia as well as FORMATION IN of axon guidance has been based on the brain wiring explicitly. Thus, the release of guidance molecules [14]. global concentration gradients of guid- pattern must emerge from rather simple For simulating such models, solvers for ance molecules. During axon growth, regulatory mechanisms encoded in the deterministic partial differential equa- filopodia, small extrusions of the growth genome [13]. One compelling hypothesis tions describing diffusion, reaction, and cone, sprout in different directions, as is that these developmental rules do not transport processes need to be coupled is visible in microscopy images. The only tolerate randomness in the axons’ to a stochastic simulation algorithm [6] general assumption has been that the environment, but use stochasticity as a BRAIN WIRING capturing the random events of guidance filopodia sample the surroundings driving force and to achieve robustness. Neurons form specific patterns in a molecule reception and filopodia growth. for chemical gradients of guidance very robust and reliable way during In a joint Matheon project with M. von molecules, allowing them to find One of the simplest models of this type, brain development. How axons and Kleist (FU), we aim at identifying mech- the right direction despite the containing just a single type of guidance dendrites find the appropriate syn- anistic models that are both physically stochasticity of molecule sensing. molecule, can already create robust and aptic partners has been studied for plausible and able to reproduce observed quasi-regular space-filling axon struc- decades. But the question is posed With new microscopy technology, the wiring patterns and the statistics of tures that avoid self-contact as well as today with a new twist. group of R. Hiesinger (FU) is able to filopodia dynamics (figure 7). The sim- neighbor contact (figure 8). acquire in-vivo 4-D movies of axons pler and more general the mechanisms growing in drosophila brains, which forming such a model are, the more one shed new light on the brain wiring can expect that structurally similar process. The filopodia dynamics processes are actually driving 6 Four examples of growth cones feature a much richer structure the neural development. with extending filopodia of varying than would be necessary for As a first candi- number and shape, displayed as stochastic gradient sampling date, we con- volume renderings for individual (figure 6). Currently, the role sider a model time points from in-vivo microscopy of these complex dynamics comprising image time series. Data courtesy R. for brain wiring is essentially three essential com- Hiesinger. unknown. ponents. First, dif- fusion and decay of 7 Statistics of filopodia dynamics guidance molecules extracted from 4-D microscopy in the extracellular data. Length, a characteristic space seem neces- quantity, appears to be correlated 6 sary for inter-axon with filopodia lifetime, and differs communication. between mutants (green) and wild Second, reception of type (blue) for growth cones during guidance molecules by synaptogenesis. Data courtesy of R. the filopodia is a stochastic Hiesinger. process due to the low concentra- 8 tion. Finally, nonlinear reactions 8 25 axons in a spatially periodic within the axons, affected setting growing to a robust and by the sensing of guidance quasi-regular space-filling but molecules, control growth contact-avoiding pattern.

34 2017 Annual Report Zuse Institute Berlin 35 Dr. Daniel Baum | [email protected] | +49-30-84185-293

MATHEMATICS © mapsland.com MEETS HUMANITIES

Examples from ancient studies and psychology For many years, the humanities and mathematics were considered as two sciences that have little to do with one another. During the last decade, however, researchers on both sides realized the potential lying in the respective other field. In this article, we present four examples illustrating this potential. Mathematics Meets Humanities

a

1 MODELING ? THE PAST: ? INNOVATION SPREADING IN THE PREHISTORIC WORLD How can we understand processes and provides new links in our modeling and its usage was passed on from one b that happened in prehistoric times approach. person to another, we can expect the when there were no written records spreading path to be strongly connected Let us consider a more specific problem: of events? One possibility is to use to the human mobility dynamics. In order How did innovations spread in the available archaeological findings and to study this, we built a mathematical prehistoric world? One of the impact- build a good mathematical model that we model that allows us to simulate both ful innovations that spread from the can study. However, most of the existing human migration and innovation spread- Near East to Europe between 6200 and archaeological data is sparse and uncer- ing. These simulations can be used to 3000 BC, was the wool-bearing sheep. 1 Geographical area of our interest for wooly sheep spreading. tain; lots of information is unknown analyze dynamical properties of the two The change from herding hairy sheep to a Suitability landscape constructed from environmental data; and there is no procedure to repeat the processes, explore how they are coupled, woolly sheep was an essential driving the assumed origin of the woolly sheep is around Tell Sabi Abyad history and obtain new data. To deal and discover the important factors that force for the later textile production. But (star). b Agents move in the suitability landscape and adopters with these problems, we work closely could have affected this innovation the exact spreading path is unknown. (red) of the innovation can pass on the innovation to neighboring with researchers from the humanities, spreading. Since the knowledge of an innovation non-adopters (yellow) with a certain probability. whose expertise enhances our studies

38 2017 Annual Report Zuse Institute Berlin 39 Mathematics Meets Humanities

Where are we from? 3

Through a fruitful collaboration with experts from the Cluster of Excellence TOPOI, we gained access to the archaeo- INFO BOX logical and environmental data. We used this data to build a suitability landscape This research is done in collaboration that indicates how suitable a particular with Brigitta Schütt (Freie Universität region was for herding woolly sheep in 6200 BC Berlin, FB Geowissenschaften and the respective period (see figure 1a). TOPOI, Berlin, Germany), Wolfram Then, we constructed an agent-based Schier (Freie Universität Berlin, FB model (ABM) in order to simulate Geschichts- und Kulturwissenschaften possible spreading scenarios. An ABM and TOPOI, Berlin, Germany), Daniel consists of a set of rules describing the Fürstenau (Freie Universität Berlin, behavior of agents and their interaction FB Wirtschaftswissenschaft and patterns with each other and the environ- Einstein Center Digital Future, Berlin, ment. In our model, an agent represents Germany), and their coworkers. It has a group of people in the ancient world. 5900 BC been partially funded by the Cluster Agents move in the suitability landscape of Excellence TOPOI – The Formation by following the so-called dynamical and Transformation of Space and equation, according to which they move Knowledge in Ancient Civilizations freely but with a bias toward regions that and ECMath (Einstein Center for are attractive for herding woolly sheep. Mathematics Berlin). At the same time, agents can interact socially with other agents in their vicin- ity and pass on the innovation with a cer- tain probability. By applying this abstract 5000 BC model to the example of the woolly sheep (figure 2), we can generate time series for the spreading process (see figure 3)[1]. This opens up new research questions like: What are the best parameters of our model? How did the innovation spread between different geographical regions? With our research, we try to answer such questions and, thus, help understand 4000 BC processes in prehistoric times. © Georg Mittenecker

Snapshots of one realization of the wool- 3000 BC bearing sheep innovation spreading in 2 the prehistoric world.

40 2017 Annual Report Zuse Institute Berlin 41 Mathematics Meets Humanities 5 b

ACCESSING HIDDEN TEXTS 4 Left: Photograph of sealed legal texts. Right: Physically unfolded package. (ÄMP Berlin, SMB)

5 a Volume rendering of CT scan of rolled mock-up papyrus. b Virtually unfolded mock-up from CT scan seen on the left.

IN EGYPTIAN PAPYRI 6 Virtual unrolling of a papyrus roll. Right: Red contours are interactively set; yellow and blue contours are computed by inter- and extrapolation. Left: Depiction of a cross section.

7 Left: Computer-tomographic (CT) scan of folded mock-up One of the best sources of information figure 4). However, for papyri that are method depicts the writing with a suf- papyrus. Right: Virtually unfolded papyrus from CT scan seen about our cultural origin is provided too fragile to be physically unfolded or ficiently high contrast. For documents on the left. by written texts. unrolled, the writings are inaccessible. written with ferrous ink, this is the case when using X-ray-based tomography. For example, excavations in Elephantine, Our aim is to make such papyri readable. a small island in the Nile in Egypt, For this, we acquire a 3-D tomographic For virtual unrolling, we depict cross a brought to light large quantities of papyri, image of it, reconstruct the papyrus sections in high detail, allowing the user telling us 4,000 years of cultural history geometrically on the computer, virtually to define manually closed polylines that INFO BOX of various religious, ethnic, and linguistic unfold and unroll it, and finally visualize approximate the contours (figure 6, left); groups that lived there [2,3]. The papyri the writing on it [4]. A prerequisite is that using interpolation and extrapolation, This project was carried out in collaboration with are typically rolled or folded (see the tomographic similar contours are computed in EXTRAPOLATION the archaeologist Verena M. Lepper (Ägyptisches other planes (figure 6, right). SLICE i Museum und Papyrussammlung (ÄMP) – Ensuring that the number Staatliche Museen zu Berlin (SMB) – Stiftung of points in each polyline INTERPOLATION Preußischer Kulturbesitz), the physicists Heinz- is equal, a quadrangular Eberhard Mahnke (Freie Universität Berlin, FB 2-D mesh is implicitly SLICE j Physik and TOPOI, Berlin, Germany) and Ingo defined, repre- 6 Manke (Helmholtz-Zentrum Berlin), and their senting a surface; INTERPOLATION coworkers. It was financially supported by the this surface is Starting Grant ELEPHANTINE of the European flattened such that SLICE k Research Council (ERC), the Beauftragte der differences in the EXTRAPOLATION Bundesregierung für Kultur und Medien (BKM), distances between the Cluster of Excellence TOPOI (The Formation n e i g h b o r e d and Transformation of Space and Knowledge 4 contour points in Ancient Civilizations) of the Deutsche are minimized Forschungsgemeinschaft (DFG). (figure 5).

For virtual unfold- ing, each step of the physical folding process is virtually undone. 7 After a series of steps, the unfolded papyrus becomes rent state using volume rendering (see virtually been undone, we unroll the Only some papyri are described with topologically figure 7, left); furthermore, we display roll as described previously. In a final ferrous ink; for the majority, soot ink equivalent to a cross sections in high detail in which the step, an equalization is performed that was used. For this case, alternative role, which is then user can interactively draw polylines. largely eliminates all distortions that tomographic procedures are currently unrolled, as described For the actual unfolding, Moving Least accumulated during the whole proce- being investigated, in the hope of finding before. In each step, Squares deformation is applied based on dure. Then the writing is visualized one that offers sufficient contrast. we provide the user with these polylines to unfold the package as using contrast-enhancing techniques an overview of the cur- rigidly as possible. After all folds have (figure 7, right).

42 2017 Annual Report Zuse Institute Berlin 43 Mathematics Meets Humanities INFO BOX 10 The project is done in collaboration with the biologist Gerhard Scholtz (HU Berlin) and the psychologists Torsten Schubert (University Halle) and Antonia Reindl (Cluster of Excellence Image Knowledge Gestaltung). It is financially 3-D MESH supported by the Cluster of Excellence “Image Knowledge Gestaltung”.

MORPHING FOR 8 Global morphing from a lobster (far left) to a crab (far right).

9 Even though only the carapace is modified, the images show a smooth PSYCHOLOGICAL transition of the whole object without any noticeable artifacts at the joints between the carapace and other parts of the body. Local morphing of the carapace from a lobster (far left) to the carapace of a crab (far right) while EXPERIMENTS keeping all other parts fixed as in the lobster.

9 8

Understanding how object recognition Therefore, in an interdisciplinary ware. This resulted (see figure 8). Controlled psychological and categorization is performed by the project, perceptual psychol- in intermediate experiments, however, require local human brain is a topic that has been ogists and biologists in the images between a mesh morphing that transforms one part studied in psychology for many years. As Cluster of Excellence “Image crab and a lobster (e.g. the carapace) of the animal at a time. a result, it is widely believed that for this Knowledge Gestaltung” have that were then used To achieve this goal, we developed an task our brain builds up a mental repre- been investigating object catego- to study the adaptation approach that combines two previously sentation of objects. Studies have shown rization on the biological categories effect [5]. Unfortunately, proposed methods for mesh morphing to that such mental representations are not of crabs and lobsters. In particular, they these images showed a rather poor obtain a natural-looking transformation fixed but remain flexible and are subject are investigating how a previously seen resemblance with real crabs and of selected parts of the mesh, while keep- to continuous short- and long-term input stimulus influences the categoriza- lobsters, which may bias the experi- ing the rest of the mesh as stable as pos- adaptation. The majority of such studies tion decision of a test person. This effect mental results. sible (see figure 9). From the interpolated have so far concentrated on human faces, is known as adaptation effect and has representations, standardized images To create more realistic-looking the recognition of which plays a very been shown to exist for the recognition were created that much better resemble images, we utilize 3-D shape morphing essential role in our daily life. Hence, it of human faces [6]. For their study, they real crabs and lobsters even though 10 Overlay of images using state-of-the-art methods from is not clear how these findings generalize produced images in which categoriza- artificial. Currently, new psychological representing a differential geometry. This allows us to to the recognition and categorization of tion-relevant features of crabs and lob- experiments are being carried out using global morphing easily create natural-looking 3-D shapes other objects. sters were systematically morphed using these new images, thus greatly improving from a lobster to that are in between a crab and a lobster standard 2-D image-processing soft- a crab. the experimental conditions.

44 2017 Annual Report Zuse Institute Berlin 45 Mathematics Meets Humanities FACIAL MORPHOLOGY 11 AND ITS APPLICATIONS

They suffer from so-called Together with our collaborators from face blindness (pro- anthropology, we have studied regular Our face has an immense significance sopagnosia), which facial development in male and female for interpersonal communication. is a neurological children. Nonlinear growth trajectories Sympathy and antipathy for others disorder of the were determined for the use in the early often depend on our first impression. Already within milliseconds, stereotypes brain that needs diagnosis of syndromes. Similarly, may have been triggered by an opponent’s to be identified typical aging effects like facial sagging face. The perception of facial expres- and thor- have been investigated morphometric­ sions determines our interpretation of https://twitter.com/realdonaldtrump o u g h l y ally. For the analysis and synthesis of statements (see figure 10). Similarly, tested facial expressions (computational facial we always use facial expressions – con- for any morphology), we have established a 3-D sciously or unconsciously – to emphasize Image source: treat- morphable model that is able to synthe- what we say. Therefore, the face and its ment. size various individual nuances beyond perception have been the subject of art typical expression categories [6]. Their significance for expression perception is and science for centuries and are still A small percentage of 10 being investigated in a broad user study intensively researched. the population suffers as part of the Mimik-Explorer shown from an autism-spec- People with congenital or acquired facial at the German Hygiene Museum in trum disorder. Those malformations, or palsy due to nerve Dresden. damage, are often stigmatized. An aim people often have diffi- of facial plastic surgery is to correct such culties in interpreting In collaboration with psychologists, we dysplasia in view of a normal or natural facial expressions. It are developing novel experiments for facial anatomy. To plan and perform is difficult for them to the investigation of self-representation surgical modifications of faces in such imagine what other peo- based on virtual-reality techniques. Our a way that both desired aesthetic visual ple think or feel, which goal is to gain understanding of the role appearance and expressions are consid- causes impairments of of facial identity in (virtual) communi- ered is still a challenge. social interaction. The train- cation. For the planning of facial sur- ing of expression interpretation gery, our work allows the assessment of and production therefore supports expressions before and after treatments their social skills. Another small group [7]. For example, in facial palsy, a detailed of the population has difficulties in rec- planning of facial nerve reanimation ognizing familiar faces. along with an objective follow-up evalu- ation method can be established.

INFO BOX 10 We have probably all encountered the experience of drawing conclusions from interpreting other people’s facial expressions. Disputes up to serious conflicts may have arisen from a (mis)interpretation of facial expressions. Hence, facial expressions and With applications in anthropology, medicine, psychology, and affective computing in mind, we target questions like: (a) How their deliberate use are intensively trained, not only in acting but also for successful negotiations (e.g. in business and politics). do facial proportions vary in a normal or healthy range, (b) what kinds of growth and aging trajectories can be observed during childhood or in elderly people, (c) are there characteristic patterns for facial expressions giving rise to an objective classification 11 Expressions are formed by the actions of facial muscles. In our research, we are studying the resulting effects on the facial scheme, and (d) is it possible to employ such a scheme to artificially synthesize plausible expressions? These are all driving surface. questions in research that motivate an in-depth analysis of the almost endless diversity of real faces.

46 2017 Annual Report Zuse Institute Berlin 47 Mathematics Meets Humanities DIGITAL FACIAL 14 MORPHOLOGY 12

13 CAMERA FACIALIS – 15 12 The 3-D portrait studio Camera Facialis uses multiview 3-D FACIAL photogrammetry to capture high- COMPUTATIONAL PERFORMANCE resolution 3-D facial performances. ZIB 3-D FACE DIGITAL 3-D FACIAL 13 Expression scans from the ZIB 3-D CAPTURE Face Database with photographic ANALYSIS OF FACIAL DATABASE MORPHOLOGY texture containing high-resolution Human face perception is particularly skin details. MORPHOLOGY AND sensitive to the subtlest details. For Photometric reconstruction of 3-D faces The statistical analysis of shape and the acquisition of high-resolution is usually a tedious manual process even appearance requires a well-defined 14 Nuances of facial expressions EXPRESSIONS facial details including small wrinkles for expert users. To establish a compre- mathematical framework. Descriptors synthesized using expression resulting from micro expressions, the hensive large-scale 3-D face database, we are needed to transform a face into a patterns determined by statistical Computational facial morphology offers appearance due to expressions can be 3-D portrait studio Camera Facialis have developed a fully automated recon- typically high-dimensional space, where shape analysis. the opportunity to apply mathematical precisely extracted and quantified from (see figure 12) has been established at struction pipeline for high-throughput similarities or distances, correlations, methods for the analysis of facial shape a representative set of facial perfor- ZIB [8]. In contrast to expensive and data acquisition. This has been achieved or clusters can be analyzed. At ZIB, we 15 In the Camera Facialis, 3-D face and proportions as well as skin appear- mances. Our research comprises (1) the laborious commercial setups common by consequent integration of statistical are developing correspondence-based scans in dense correspondence to ance and expression. Based on image development of new techniques for the in entertainment productions and media shape templates. Detailed 3-D facial descriptors that take the Riemannian an animatable surface mesh are and geometry processing, statistics, acquisition of high-resolution 3-D faces, art, Camera Facialis has been built on scans result from specifically optimized structure of shape spaces into account acquired. On top of a neutral face and machine learning, the relation of (2) their integration into a large-scale top of affordable optical devices and algorithms [9]. That way, several thou- [10]. We enable the analysis of facial scan (left), arbitrary expression facial morphology to attributes like sex, database, and, using this, (3) establishing commodity hardware to enable ultrafast, sand faces have already been integrated features up to the level of wrinkles and patterns extracted from the ZIB age, culture, and so forth, can be stud- a foundation of morphological analysis high-fidelity measurements for a very into the 3-D face database, which is skin pores by establishing accurate dense face database can be transferred, ied. Similarly, characteristic patterns as well as applications in psychology and detailed capture of facial performances continuously extended for digital facial correspondence with our techniques (see for instance, the smile expression describing the change in shape and medicine. in a large-scale manner (see figure 14). morphology. figure 15) [6]. shown on the right.

48 2017 Annual Report Zuse Institute Berlin 49 Prof. Dr. Thorsten Koch | [email protected] | +49-30-84185-213 © pixabay SOFTWARE SUSTAINABILITY IN THE AGE OF OPEN SCIENCE

When mathematicians combine mathematical theory and real-world applications, then mathematical research software complements chalk and blackboard, or pencil and paper. Today, mathematical software plays a central role in research and key technologies and has an increasing impact on mathematical education. Software Sustainability in the Age of Open Science

Since its creation more than 30 years ago, ZIB has promoted this combination as a significant extension of scientific work. This has resulted in many software pack- ages, some of which are of outstanding importance to the scientific community. Prominent examples today include SCIP in the area of optimization, KASKADE for numerical mathematics, and AMIRA for scientific visualization and data anal- SOFTWARE ysis. An overview of software developed at ZIB can be found here: http://www.zib. de/software. Software Sustainability is a new working area that has been gaining momentum in SUSTAINABILITY AT ZIB the past few years. With the continuing In order to establish sustainable soft- shift toward data-centric science, the ware development practices, a variety software utilized to produce the scien- of infrastructure and organizational 1 tific output is increasingly regarded as measures have to be addressed. The an equally important “product of science” following approaches, services, and itself. project results form the basis and start- A general understanding is evolving that ing point for these measures. In recent ciples of Open Access, software should it very difficult to define an encapsulated not only a publication, but also the doc- years there have been several activities also be made publicly available, ideally status as a datum. In addition, software umented and available datasets should to promote research-data management. corresponding to the FAIR principles of is a living entity that evolves over time. get scientific credit. Moreover, there is a One of the essential first steps was the research-data management: data should The concept of Software Sustainability growing consensus in the research-da- formation of a focus group supporting be Findable, Accessible, Interoperable, involves development, deployment, main- ta-management community that the handling of research data, composed and Reusable. tenance, and publication efforts, with the research software could be considered as of researchers from different divisions aim to ensure the ongoing functionality datasets (i.e. research data). Publication To transfer these principles to the man- and departments at ZIB. This group has of research software. The incorporation and reuse of software is necessary to agement of research software is a true started to identify common needs across of Software Sustainability methods ensure validity, reproducibility, and to challenge, especially because software is all departments and divisions. It acts as OPUS is utilized to present landing pages ital preservation system EWIG at ZIB, at ZIB is part of increasing efforts to drive further discoveries. Since a com- characterized by an exceptional variety a contact point concerning all questions (called front doors in OPUS) for specific which is composed of freely available conduct research in accordance with mon research-data-management prac- of dependencies on other entities (hard- related to research-data management, software with an additional set of meta- open-source components, is used as a open-science principles. tice fosters publication along the prin- ware, OS, algorithms, etc.), which renders including the generation of data-man- data and a download link. The software research-software source-code archive, agement plans. Its most important action packages will reside on a dedicated accompanied by extensive metadata. item is publication of research data and download server. OPUS itself is an open- To date, the incorporation of digital research software. A twofold strategy is source product of ZIB, published under preservation strategies within the con- being pursued to increase the visibility a GNU General Public License. Current text of software sustainability has not of produced software. In addition to the work on OPUS involves other important been straightforward. There is a gap to project page (i.e., the product page of the features with regard to open-science be closed between software archiving research software, which is maintained principles: automatic DOI minting and and maintenance approaches on the one by the respective research group), all ORCID implementation. hand, and long-term aspects of digital released versions of a software are curation of software on the other. intended to be published as research A further step to achieve software data with the institutional repository sustainability at ZIB involves the use OPUS (https://opus4.kobv.de/opus4-zib/ of the swMATH portal that analyzes home). In this context, the Kooperativer mathematical publications for software Bibliotheksverbund Berlin-Brandenburg citations. The aim is to identify the (KOBV), part of ZIB since 1997, provides connection of research software and support for OPUS. scientific articles that present results based on the use of this software. Another aspect of the long-term availability of research software is being addressed by the experimental 1 Figure 1: Search interface application of digital preservation of ZIB OPUS institutional techniques. The OAIS-compliant dig- repository

52 2017 Annual Report Zuse Institute Berlin 53 Software Sustainability in the Age of Open Science

SWMATH – WEB-BASED FINDING SOFTWARE HOW TO CITE APPROACH IN SWMATH SOFTWARE?

the websites related to the software, in swMATH offers several ways to find When analyzing zbMATH articles, you AN OPEN-ACCESS DATABASE repositories, or on portals, which provide software. Based on the referenced publi- will find different citation styles for information about and access to software cations, swMATH analyzes the abstracts software. Software companies, repos- for a special subject. Therefore, some and the MSC classification for each itories, and publishers give different concepts for capturing and analyzing software entry. This allows software to recommendations for citing software or further information about software be searched by key word (e.g. “integer research data. swMATH will close this FOR MATHEMATICAL from websites, software repositories, programming”) or by browsing through gap. In cooperation with related commu- and Internet archives have been devel- the MSC classification scheme (e.g. nities, e.g. the Software Citation Working oped. In principle, we are faced with the “90C10”). Additionally, swMATH clas- Group of the FORCE11 Initiative, we are same tasks as in the publication-based sifies all entries by types, for example, working on standards for citing software approach: identification of the relevant programming languages, benchmarks, and research data. SOFTWARE information and analyzing and struc- data collections, or Web services. Last turing the information about a software. but not least, you also have access to But instead of publications, we have to documentation and manuals wherever extract it from information on the Web. it is accessible. How does one find software for a The swMATH pages represent an online An important side effect of analyzing specific mathematical problem? Is CENTRAL IDEA: portal to retrieve information regarding research papers is the discovery of there already a solution or an imple- mathematical software: they provide related software: if software S1 is mentation? What is the mathematical PUBLICATION- general information about the software, referred by paper P1 and paper P2 refers background? Who are the authors? namely the profile of a software derived not only to software S1, but also software What hardware do you need? Is there BASED APPROACH ANALYZING ZBMATH from the publication-based approach and S2, we conclude that S1 is related to S2. any documentation? Is it free for edu- links to other relevant Web resources This helps to identify more than one cational use or do you need a license? The most informative and relevant The manual maintenance of Web data- that contain more detailed information. possible software solution for solving a Moreover, it is also a real problem secondary source for information about bases is an effort that is both expensive Each swMATH page has a unique iden- given problem. to cite software when writing a mathematical software is the corre- and time-consuming. Therefore, the tifier, which can be used for the citation scientific paper. Where to find the sponding scientific literature. Therefore, use of machine-based methods for the of a software. software? Which version was used? the most complete bibliographic database data analysis and content generation Is it accessible? Can you reproduce of mathematical literature, zbMATH has been a significant aspect in the the results? (the former Zentralblatt MATH), is used design of the swMATH service from The project swMATH (www.swmath. as a basis to extract information about its beginning. Heuristic methods have org) is an attempt to develop and estab- mathematical software. The fact that been developed for identification and lish an information service for mathe- zbMATH covers almost all mathematical to analyze software information in matical software and mathematical journals with a focus on mathematical zbMATH entries. The information research data. It started as a project of software is of crucial importance. regarding publications citing a software Mathematisches Forschungsinstitut is aggregated and provides a profile of zbMATH provides a review or a sum- Oberwolfach (MFO) and FIZ Karlsruhe, the software and its context involving mary, characteristic key phrases, the and is presently continued as a project of use cases, mathematical background, references lists, and classification of the the Research Campus MODAL at ZIB. acceptance, life cycle, related software, mathematical subjects and application swMATH provides information about and a list of publications citing the soft- areas of mathematical publications. mathematical software and its mathe- ware. The publication-based approach is Also, information about the authors, the matical background. It will improve the the basic step in the swMATH workflow sources, and the language of the publica- visibility of software and strengthen the and provides general information about tion are presented. Today, the database role of software within mathematics. mathematical software. But details, such zbMATH stores the bibliographic data of swMATH is focused on software, but as source code, versions, the technical nearly four million peer-reviewed mathe- also benchmarks, data collections, and environment, license information, doc- matical publications with an increase of manuals are listed. umentation, manuals, or installation 10,000 items per month. In general, this guides, as well as links to related bench- approach ensures quality control. marks or data collections, are missing. This kind of information can be found on

54 2017 Annual Report Zuse Institute Berlin 55 Software Sustainability in the Age of Open Science

VISIBILITY OF 2,000,000 3 AUTHORS STATE OF THE ART Careers in the scientific community are 1,500,000 based on the visibility of papers pub- AND CHALLENGES lished in peer-reviewed journals. But what about the contributions of software Currently (i.e. December 2017), swMATH developers? Do they get any credit for 1,000,000 contains information about more than writing software while helping to find 20,000 software entries with nearly solutions to a mathematical problem? 270,000 software references in publica- Software developers play a different role tions. swMATH is an innovative service to the authors of publications. swMATH 500,000 for mathematical software citations lists the authors of a software and builds and has unique features. The swMATH a citation graph presenting the annual service is largely based on the automatic numbers of publications citing the processing of information and requires software. This also characterizes the 0 little effort for maintenance. Usage development stage and reflects the dis- 07 07 07 statistics reveal increasing interest in tribution and acceptance of the software. 2015 2016 2017 the service. A large number of publications indicate that the software has been widely used PAGES Software information is challenging and can be considered as an indicator for because it is highly dynamic and stan- the quality of the software. dards for software information, e.g. for software citations and metadata If you take, for example, the SCIP schemes, have been missing until now. Optimization Suite, you find more than The swMATH project working group 250 bibliographical entries in zbMATH will participate in the development of that cite the software. The software standards and will work on both new packages with most citations are concept algorithms for a more complete MATLAB (8,000 references), CPLEX, recording of mathematical software MAPLE, MATHEMATICA, and R, each and on improved content analysis of the with more than 4,000 references. information about a software. 24,000 2 160,000 18,000 140,000 12,000 120,000 6,000 100,000 0 80,000 2 Figure 2: swMATH figures for software and 2015 07 2016 07 2017 07 zbMATH references 2015–2017

3 Figure 3: Usage statistics for swmath.org SOFTWARE (20,000) ZBMATH REFERENCES (150,000) 2015–2017 (Apache log file, Webalizer pages, no robots).

56 2017 Annual Report Zuse Institute Berlin 57 Prof. Dr. Ralf Borndörfer | [email protected] | +49-30-84185-243 20,000 FEET ABOVE THE GROUND

New navigation systems for aircraft save fuel and time 20,000 Feet Above the Ground

1

are equally important. Here is where ZIB lifted into the air, requiring even more A representation of the airway network 2 comes into play. fuel. Too little, however, is even worse. over Germany can be seen in figure 2. Balancing safety and efficiency is Together with Lufthansa Systems After fixing a pair of airports as the therefore a delicate task, which must be GmbH & Co. KG, a leading provider of departure and the destination nodes in addressed with advanced mathematical IT solutions to the airline industry, this graph, the main objective of flight methods. This is also the way to deal with the Optimization department at ZIB is planning is to find a minimum cost path all the constraints of flight planning. working on the development of VOLAR, – a chain of airways – connecting them. a brand-new system for flight-trajectory Aircraft are not allowed to fly along the The problem of computing a minimum optimization, which will ultimately shortest curve between any two airports. cost/shortest path between two nodes become the core optimizer of Lufthansa Instead, they must adhere to airways, on a graph is well studied and also very Systems’ flight-planning software which are invisible roads in the sky span- relevant in real-world applications. Lido/Flight. Similar to a car navigation ning the entire planet. The set of all such Pedestrians in the city try to walk along system, many airlines use Lido/Flight airways and their intersections define paths with minimum distance. Car nav- to compute the most efficient routes for the airway network. In mathematics, igation systems seek to find the shortest their aircraft. Unlike in car navigation, such a construct is called a graph. The path to a destination by minimizing however, a plane cannot stop in midair set is not only defined on one altitude, but the total travel time, which may vary if something goes wrong. The weather on several layers stacked on top of each depending on traffic. The flight-planning plays a much more important role. And other. These layers, roughly 300 m apart, problem is similar in nature, but it has a fueling is really critical. Too much is not correspond to the possible altitudes on much more complex cost function. good, as every liter of kerosene must be which aircraft are allowed to cruise. 200 200 200 200 202 20 20

1 Specific fuel consumption for the Lufthansa fleet (source: [4]) 2

Cheap air transport has become a According to a recent forecast by the The past decades have witnessed a matter of course since the 1980s. It International Air Transport Association significant improvement regarding the allows us to see the world and visit (IATA) [1], the current number of four environmental impact. For example, in remote countries on vacations, as well billion air travelers per annum will figure 1, we can see how the Lufthansa as to attend multiple business meet- double by 2036. As air connectivity of Group managed to reduce the fuel ings per week around the country or countries is assumed to be a stimulus consumption of their fleet to 3.85 l per continent, and to still sit down for for growth and prosperity [2], such passenger and per 100 km during 2017. dinner with the family at home in the prognoses are good news. However, The most obvious factor contributing to evening. Because of these amenities, the increase in air-traffic volume also this is technical progress of aircraft, and the market for passenger transpor- presents challenges: the infrastructure particularly engines [3]. However, as air- tation has been and will be a growing needs to be constantly adapted to handle craft are often used for around 25 years, one. ever-larger numbers of passengers, the fleet renewal is a long-term task for an

safety of passengers and crews needs to airline. Therefore, short-term measures, 2 Airway network over Germany be ensured, and emissions of CO2 and such as minimizing fuel consumption (source: skyvector.com). other pollutants should be minimized. through efficient trajectory planning,

60 2017 Annual Report Zuse Institute Berlin 61 20,000 Feet Above the Ground

3 High-altitude wind over the American continent on a specific day. Blue is still air, strong wind is represented in red. (Representation: Google Earth) 3

The relevant cost components for flight-trajectory optimization are Besides the complex cost function, there are many other challenges to consider fuel consumption (which is usually correlated to flight time) and in the flight-planning problem. A good example is the diverse constraints. overflight fees. While the latter play a big role for airlines and are On the one hand, there are so-called aerodynamic constraints. These very interesting from the mathematical point of view [5], fuel are given by the flight dynamics, which determine, for example, how consumption is by far the most important factor. Its compu- steep the climb or descent angle can be. For instance, it is important tation is not straightforward, since it heavily depends on to know exactly at what moment to initiate the final descent, so the weather. This can be best understood by considering that the destination airport can be reached comfortably. Also, jet streams, which are currents of strong wind. The it is important to always have enough fuel onboard to reach an best-known example is the jet stream around the alternate airport in case of an emergency, such as an engine North Pole, which blows east and is particularly failure. rele­vant for aviation over the Atlantic. Flying along jet streams significantly decreases both On the other hand, there are less obvious operative con- flight time and fuel consumption. Similarly, fly- straints, which regulate how the airspace may be used. ing in the opposite direction should be avoided, These constraints have objectives such as avoiding con- which is why flights from Europe to North gestion, ensuring safety, and enforcing regional legisla- America often make a detour over Greenland. tion (such as night-flying restrictions to reduce noise). The jet stream is clearly visible over North These constraints are managed by air-navigation ser- America in figure 3. vice providers around the world (e.g. EUROCONTROL in Europe, through the monthly Route Availability In a sense, wind on airways is similar to Document publication). Such a restriction can, for traffic jams on roads, since it can reduce or example, forbid the usage of Belgian airways for increase an airway’s effective length, or even flights departing from Luxembourg on weekdays block it. Considering such time-dependent after 10 p.m. In this case, it is easy to imagine why factors during optimization is always a this restriction is published: aircraft would fly at low major challenge, as a lot of data has to be altitudes over the Belgian airspace, hence causing too processed. For instance, weather data is much noise at night. As of January 2018, the European needed not only on the horizontal level, but Route Availability Document consists of over 13,000 also on the vertical level and on a time horizon restrictions. Considering all of them during the search of more than 24 hours. for an optimal flight trajectory increases the problem’s Furthermore, fuel consumption at any given complexity considerably, since they make it NP-hard. time is dependent on the aircraft’s weight (which itself depends on the current fuel amount) and altitude. In general, lighter aircraft are more effi- cient than heavier ones, and flying at high altitudes is better than at low altitudes. However, given that the wind is stronger at high altitudes, it sometimes makes sense to fly lower to avoid strong headwinds.

62 2017 Annual Report Zuse Institute Berlin 63 20,000 Feet Above the Ground

4 The vertical profile of a flight computed between On that day, there was an unusually Frankfurt and Minneapolis. The final segment strong jet stream above the Northern follows a “zigzag” pattern, efficient with respect to Pacific. While for airlines it is common fuel consumption but probably uncomfortable for to fly routes that lie close to a geodesic the passengers. between the departure and destination airports, on this day, flying a big detour to 4 5 Adam Schienle at the award ceremony of the GFFT. take advantage of the unusual jet stream paid off. Figure 4 shows this phenome- 6 Two routes from Taipei to New York: the red one non. The yellow line represents the great was precomputed, the green one was computed by circle connection between Taipei and VOLAR. New York. The red line shows a common flight route between both cities and the green one was computed by VOLAR, tak- ing advantage of the jet stream described above. The shaded area (in gray) in fig- ure 6 shows the search space inspected by VOLAR (i.e, the regions in which the optimal route is looked for). To do so, VOLAR uses the Super-Optimal Wind. It is remarkable that the red route is not even considered by our algorithm, since it lies partially outside of the shaded area – it is simply not a potential candidate for the optimal trajectory. Indeed, as the table in figure 6 shows, the green route saves 5,665 kg of fuel and 5,335 USD compared to the red one, even though it is significantly longer. CASE STUDY: TAPEI–NEW YORK 6 Boeing B777-300ER, April 25, 2017, great circle distance = 12,565 km Another example of human-made con- Since both a short runtime and low Using dynamic Using typical search search space GAIN straints are comfort constraints, which memory usage are essential in real-world space reduction reduction are not easy to model but intuitively are flight planning, it is necessary to restrict clear. In particular, the most fuel-effi- the search space of our algorithms. 5 Distance flown (km) 13,385 14,635 –1,250 cient route sometimes results in a pattern Roughly speaking, this means that if Flight time (hours) that pilots are unlikely to follow, such as we want to fly from Berlin to Tenerife, 14:40 13:55 0:45 5,665 in figure 4. there is little sense in looking for a flight Fuel burn (kg) 95,524 89,859 = 17.8 t CO trajectory overflying Russia. This was 2 Currently, the VOLAR software devel- in part achieved after introducing the Overflight fees (USD) 2,291 1,139 1,152 oped at ZIB is capable of computing Super-Optimal Wind, which is based on a optimal trajectories that consider Total costs (USD)* simple observation: aircraft travel faster 76,453 71,118 5,335 weather, aircraft performance, overflight when being pushed along by tailwinds *based on: fuel price 500 USD/ton, flight time costs: 1,800 USD/hour fees, and traffic restrictions. It is based (wind from the back), and when there is on original research that has been well as little crosswind (wind from the side) received in the operations-research as possible. Hence, we can calculate the community. As an example, Adam “best” wind conditions we may expect Schienle’s master’s thesis [6], which for a given weather forecast. This allows focuses on minimizing flight time under the search space to be reduced drastic­ consideration of wind, won awards ally. Furthermore, it also ensures that both at the OR conference in Berlin and the optimal route is not cut off by this the Gemeinnützige Gesellschaft zur reduction. This is done by adapting the Förderung des Forschungstransfers e.V., well-known A* algorithm. both in 2017. Furthermore, the research paper [7] won the prestigious Best Paper The efficiency of this method can be Award at the international Algorithmic demonstrated at the following striking Approaches for Transportation example. On April 25, 2017, at 3:00 a.m. Modeling, Optimization, and Systems UTC, a flight leaving Taipei Taoyuan workshop (ATMOS 2017). The scope of Airport was scheduled to go to New York these works is as follows. John F. Kennedy International Airport.

64 2017 Annual Report Zuse Institute Berlin 65 Dr. Florian Schintke | [email protected] | +49-30-84185-306

SCALABILITY AND

CONCURRENCY Challenges from Two Interdisciplinary Research Projects How to chop and distribute hundreds of continuous high-bandwidth data streams efficiently in a network so that, for each time frame, the sensor data is collected in a particular analysis node? How to exploit modern network capabilities, like remote direct memory access, to improve the scalability of SAT solving on super- computers? How to effectively test shared-memory parallel programs for concur- rency bugs due to data races? These are three exemplary research questions we are currently tackling in two interdisciplinary research projects in the fields of high-energy physics and the automotive industry. Scalability and Concurrency

HIGHLY PARALLEL AUTOMATIC TESTING OF CONCURRENT PROGRAMS SOFTWARE VERIFICATION Concurrent applications are particularly hard to debug. Since multiple threads access the same memory locations, data races can Embedded software in modern cars formance software infrastructure to critical concurrency issues can be found lead to unintended program behavior and requirement violations. Data races may occur with multiple unordered accesses to the enables new opportunities regarding accelerate the verification and testing in the source code and SAT formulas same memory location by two or more threads, where at least one modifies the memory state. We developed Actul, a compile-time the passengers’ safety and comfort, process, tackle more complex problems, can be used to prove that the predefined tool that detects data races. It checks data races for their harmfulness (i.e. whether they may cause a program violation). but it simultaneously presents great and also make the deployment of new and requirements are satisfied by the model. challenges for the automotive industry. more complex features possible. Both methods are completely automated The software has to guarantee high and thereby give the engineers precise In the software-engineering process, security standards. Unfortunately, the feedback with concurrency error reports statechart models are created according #include 1 #include complexity of the verification and testing and detailed proof pointing out where #include#include COMPILE-TIME CLASSIFYING to predefined requirements. The model #include grows exponentially with the size of the inconsistencies may remain in the model. #includeint main(int argc, char * argv[]) #include Source { formally describes the behavior of the #include Source std::string str = “hello, world!”; int main(int argc, char * argv[]) software. Hence, parallel methods are To allow testing and verification as a #include Code {#include Source INSTRUMENTATION DATA RACES software and can be directly parsed #include if( argc > 1 ) std::string str = “hello, world!”; Code int main(int argc, char * argv[]) needed. In the BMBF project Highly service model in this highly competitive #include str = “The users says: “ + argv[1]; Code { Source std::cout << std << std::endl; if( argc > 1 ) into source code or translated into std::string str = “hello, world!”; Actul is based on the LLVM compiler Data-race detectors often report false int main(int std::cout. str argc,= flush()“The char users; * argv[]) says: “ + argv[1]; Parallel Software Verification (HPSV), field, the models are obfuscated during SourceCode { std::coutstr.clear() <<; std << std::endl; if( argc > 1 ) SAT formulas. Combined with formal std::string str = “hello, world!”; infrastructure. Source code is translated positives (i.e. potential data races std::cout.flush(); str = “The users says: “ + argv[1]; partners from the automotive industry the testing and verification process. The Code str.clear()clang; -emit-llvm std::cout << std << std::endl; if( argc > 1 ) requirements, the correctness of the std::cout.flush(); into the intermediate representation lan- that never happen in practice because str = “The users says: “ + argv[1]; work together with researchers from resulting feedback is then deobfuscated clang -emit-llvm str.clear()clang; -emit-llvm @.str std::cout = internal << constant std << std::endl; [14 x i8] c"hello, world\0A model can be verified. Two alternative \00" std::cout.flush(); guage (IR) of LLVM. Then each memory- of user-defined synchronizations or Christian-Albrechts-Universität Kiel to make it interpretable in the automotive @.strdeclare str.= internali32clear() @printf(i8*,clang ;constant ...) -emit-llvm[14 x i8] c"hello, world\0A model representations are used to expose IR \00"define i32 @main(i32 %argc, i8** %argv) nounwind { and concurrency-relevant instruction implicit orderings in the program work- entry: and ZIB. We are developing a high-per- industry. @.strdeclare = internali32 @printf(i8*,clang constant ...) -emit-llvm[14 x i8] c"hello, world\0A %tmp1 = getelementptr [14 x i8]* @.str, i32 0, i32 0 potential faults in the modeling process: CodeIRIR \00"define i32 @main(i32 %argc, i8** %argv) nounwind { in the IR code is modified to allow Actul flow). Actul excludes false positives by entry: %tmp2 = call i32 (i8*, ...)* @printf( i8* %tmp1 ) @.strdeclare = internali32 @printf(i8*, constant ...) [14 x i8] c"hello, world\0A nounwind %tmp1 = getelementptr [14 x i8]* @.str, i32 0, i32 0 Code \00"define i32 @main(i32 %argc, i8** %argv) nounwind { CodeIR %tmp2 = call i32 (i8*, ...)* @printf( i8* %tmp1 ) to monitor all memory accesses and replaying data races in additional test declareentry: i32 @printf(i8*, ...) nounwind opt -actul Code de %tmp1fine i32 =@main(i32 getelementptr %argc, [14 i8** x i8]*%argv) @.str, nounwind i32 0, i32 { 0 IR to control the thread execution order. runs, with a different access order. For entry: %tmp2 = call i32 (i8*, ...)* @printf( i8* %tmp1 ) nounwind opt -actul Code @.str %tmp1 = internal = getelementptr constant [14 [14 x x i8] i8]* c"hello, @.str, world\0Ai32 0, i32 0

\00" %tmp2 = call i32 (i8*, ...)* @printf( i8* %tmp1 ) Thus, the OS scheduler is overwritten further analysis, the reorderable data nounwinddeclareopt i32-actul @printf(i8*,opt -actul ...) TESTING AND @.str = internal constant [14 x i8] c"hello, world\0A \00" de fine i32 @main(i32 %argc, i8** %argv) nounwind { by a user-level, deterministic scheduler, races are permuted with other such entry: [email protected] = internali32 @printf(i8*,opt constant -actul ...) [14 x i8] c"hello, world\0A call funcEntry(%entry) Extended de\00"fine i32 @main(i32 %argc, i8** %argv) nounwind { which records and replays executions data-races. Based on these test runs, each entry: call write(%tmp1) @.strdeclare = internali32 @printf(i8*, constant ...) [14 x i8] c"hello, world\0A %tmp1 = getelementptr [14 x i8]* @.str, i32 0, i32 0 APPLICATION ENGINEERING VERIFICATION ExtendedIR Code calldefi nefuncEntry(%entry) i32 @main(i32 %argc, i8** %argv) nounwind { \00" call call write(%tmp2))write(%tmp1) and can reorder events in a subsequent data-race access order is correlated with declareentry: i32 @printf(i8*, ...) IRExtended Code %tmp1%tmp2 == getelementptrcall i32 (i8*, ...)* [14 @printf( x i8]* @.str, i8* %tmp1 i32 0, )i32 0 Extended decallfi nefuncEntry(%entry) i32 @main(i32 %argc, i8** %argv) nounwind { callnounwind write(%tmp2)) execution. The instrumented IR code is appearing program violations. Therefore, entry: call write(%tmp1) IR Code %tmp2%tmp1 = callgetelementptr i32 (i8*, ...)* [14 @printf( x i8]* @.str, i8* %tmp1 i32 0, )i32 0 ExtendedIR Code call funcEntry(%entry) deobfuscate nounwind call call write(%tmp2))write(%tmp1)clang -lactul compiled and linked against the Actul harmful data races can be identified as a IR Code %tmp1%tmp2 = getelementptrcall i32 (i8*, ...)* [14 @printf( x i8]* @.str, i8* %tmp1 i32 0, )i32 0 Software demands Error report nounwind call write(%tmp2))clang -lactul test 00000000111000000011101110110111101010100000 runtime library, which provides the func- root cause of a violation without the need %tmp2 = call i32 (i8*, ...)* @printf( i8* %tmp1 ) requirements 00000000011111111111011110000000000111011110 nounwind clang -lactul 0000000011100000001110111011011110101010000000110010101010011111110000000001111110000000 tionalities of the scheduler and the test to check each false positive or benign Instrumented 0000000001111111111101111000000000011101111000000001111111100110011001100110110001000010 Binary clang0011001010101001111111000000000111111000000000000000000111111111110111100011000000001110 -lactulclang -lactul feedback 00000000111000000011101110110111101010100000 environment. Executing the resulting data race manually, as typically would Instrumented 00000011101110110111101010100000000000000111 0000000111111110011001100110011011000100001000000000011111111111011110000000000111011110 00000000000111111111110111100011000000001110 Binary 0000000011100000001110111011011110101010000000110010101010011111110000000001111110000000 Instrumented 00000011101110110111101010100000000000000111 binary starts the testing, where Actul be necessary with other tools. 0000000001111111111101111000000000011101111000000001111111100110011001100110110001000010 parse InstrumentedBinary 0011001010101001111111000000000111111000000000000000000111111111110111100011000000001110 Instrumented 00000011101110110111101010100000000000000111 automatically starts and analyzes mul- obfuscate Code 00000001111111100110011001100110110001000010 Binary 00000000000111111111110111100011000000001110 Model Binary 00000011101110110111101010100000000000000111 tiple test cases in parallel. translate feedback Benign data race on 0x1279814 on threads 1 (w) and 2 (w) appearances:68, crash rate:7.3529% validation Function stack from thread 1 SAT #0 updateAccess(void) in /pthread/benchmark_hart1.cpp:17 1 Instrumentation workflow of #1 workerUpdate1(void) in /pthread/benchmark_hart1.cpp:39 Function stack from thread 2 Actul using the LLVM compiler #0 workerUpdate2(void*) in /pthread/benchmark_hart1.cpp:58 infrastructure and the Clang Harmful data race on 0x1279818 on threads 0 (w) and 1 (w) appearances:5, crash rate:100% Verified software deobfuscate Function stack from thread 0 solve compiler. #0 updateData(void) in /pthread/benchmark_hart1.cpp:10 #1 mainUpdate(void) in /pthread/benchmark_hart1.cpp:33 Proof #2 main(void) in /pthread/benchmark_hart1.cpp:64 2 Example error report of Actul’s Function stack from thread 1 #0 workerUpdate1(void*) in /pthread/benchmark_hart1.cpp:39 concurrency analysis for one benign Random search: crashes/done/maxTests/maxSchedules: 5/300/300/17496 2 and one harmful data race.

68 2017 Annual Report Zuse Institute Berlin 69 FASTER DEBUGGING PROCESS DEBUGGING FASTER Scalability and Concurrency 70 control). cruise of the specification the match should speed the point, some at (e.g. system of the requirements the representing connections all with whole model the represent clauses car). All of the speed actual the and control a cruise by yield regulation the between interaction the (e.g. other each with connected are that components of these agroup describes of acar). Aclause speed current the (e.g. of amodel of components ferent states dif describe literals different context, our In clauses. and of literals consists problem (SAT) satisfiability Boolean The VALIDATION MODEL OF CONTEXT IN SOLVING SAT COMMUNICATION ASYNCHRONOUS SCALING WITH UNSTRUCTURED 2017 Annual Report BENCHMARK DynMatMul2 TaskQueue3 stringbuffer queue_bad ping_pong HARMFUL DATAHARMFUL RACES 0 0 1 1 1 - space by introducing new clauses. These These clauses. new introducing by space search of the areduction to ment leading assign this with acontradiction get we or found is literals of all assignment valid a either assignments, different checking approach (cdcl). clause-learning While conflict-driven the with reduced is assignment of avalid space search The complete. NP is SAT solutions Finding cruise control and cannot be reached). be cannot and control cruise the of specification the than less is speed maximum the (e.g. system the correct to back reported be then can defects indicates system defects. These system which unsatisfiability, or its model of the correctness the prove globally either can we assignments, such With problem. the to solution a finding to key the are clauses SERIAL RUNTIME 245.2s 8.2s 4.7s 1.0s 2.1s PARALLEL RUNTIME 53.7s 0.6s 0.8s 4.8s 1.7s - ­ 4 3 5 FOUND DATA RACES

Accumulated runtime characteristic characteristic runtime Accumulated Offering data (MPI_Compare_and_ and Actul of analysis Runtime competition 2013. competition SAT the from problems of classes fortypes two different problem clause of combinations different for clauses exchanged of amount correlated with the accumulated RMA. via (MPI_Accumulate) transfer data finishing and (MPI_Get) receiving situational swap) with node. one on parallel in tests independent by running generated is runtime parallel The benchmark. the in races harmful only the are by Actul found race data harmful The GHz. 1.4 cores, 68 CPU: 7250 Phi Xeon Intel an on LLVM-ThreadSanitizer THREADSANITIZER 0 0 3 5 2 RUNTIME 0.05s 0.01s 0.9s 0.5s 1.2s 3 FUTURE WORK FUTURE AND RESULTS on the overall runtime. overall on the distributions clause heuristic of different effect the study further We will cesses. pro the among distributed be should runtime the reducing help that clauses those only systems, parallel to problem the scaling When time. solution overall the influences greatly of clauses type The scheme. offer–select an on based clauses exchange to way flexible and effective an need we Therefore, data. much too handling due to solver of each effectiveness the reduce can clauses sible pos of amount a huge because beneficial necessarily not is clauses many of too exchange up, the scaling While improve. to solvers other help will clauses these Exchanging space. search its reduce to clauses own its learns solver Each SCALING SAT Clause offerer 4 MPI_Compare_and_swap MPI_Accumulate MPI_Get - - APPROACH COMMUNICATION RDMA of offers each solver then actually takes. actually then solver each of offers number the and distributes solver each that of offers number the adjust can we process, problem-solving of the state and capabilities, network size, system on the Depending pattern. nication commu asynchronous unstructured, this establish to us allows RDMA when done. offerers the informs and them, retrieves value, scoring on the based packages of these number limited a selects solver Each value. a scoring including solvers, other to a package such offers solver each First, of solvers. a set to clauses of learned packages distribute asynchronously to way efficient an offers (RDMA) access memory direct Remote

Normalized values Normalized values Clause receiver 0.5 0.5 1.5 1.5 0 0 2 2 1 1 all all 2 2 3 3 4 4 Academic benchmark Academic 5 5 benchmark Industrial

runtime 6 6 7 7 - Exchanged clauseExchanged types 8 clauseExchanged types 8 23 23 VIA SCORING SCHEME SCORING VIA SELECTION CLAUSE 34 34 exchanged. of clauses amount the reduce to fetching for of packages subset best the select can we So, packages. of potential scores other all it to comparing score on this depends apackage or declining fetching of decision The of apackage. scoring the on depending of clauses packages the rate now can scheme Ascoring clauses. distinguish between different types of can we Thus, generated. is clause the indicating under what circumstances (LBD)) distance block literal (e.g. values Clauses have different characteristic 45 45 imported clauses imported 56 56 67 67 78 78 234 234 Zuse Institute Berlin 456 456 678 678 2,345 2,345 5,678 5,678 23,456 23,456 45,678 45,678 5 71 Scalability and Concurrency SCALING HIGH-BANDWIDTH FLESNET ARCHITECTURE DATA STREAMS ... ts#3 ts#2 ts#1 ts#0 ... ts#3 ts#2 ts#1 ts#0 ... ts#3 ts#2 ts#1 ts#0 sensor sensor sensor Fiber Fiber Fiber COMPRESSED- BARYONIC-MATTER Input node #0 Input node #1 Input node #2 EXPERIMENT

The compressed-baryonic-matter time. The overall data rate from the Approximately 600 nodes will be used (CBM) experiment at the Facility for sensors is expected to exceed 1 TB/s to spread and group data streams. This Antiproton and Ion Research (FAIR) (1,000,000,000,000 bytes per second). is done by the First-Level Event Selector in Darmstadt aims to explore the quan- (FLES), a high-performance compute The CBM data streams from about 600 Input node #0 Input node #0 Input node #0 tum-chromodynamics (QCD) phase cluster. The software to build time input channels have to be spread and diagram in the region of high baryon den- slices for the analysis, called FLESnet, grouped to form views of time intervals. sities using high-energy nucleus–nucleus must be scalable, highly available, and The grouped data is analyzed to detect collisions. Many sensors surround the fault-tolerant. and discover different phenomena. experiment to collect data during beam The high-level design of FLESnet consists of two kinds of processes (called nodes in the following): input and compute nodes. Input nodes receive data from the sensor links via a custom FLESNET CHALLENGES FPGA-based input interface and chop the stream into time intervals, called micro time slices, before distributing FLESnet faces several challenges in its design: them for time-slice building. Compute Portability: FLESnet was implemented Scalability: Due to the limited buffer nodes receive micro time slices of a cor- using the API of InfiniBand Verbs and space, each compute node should receive responding time interval from all input relied on connection-oriented commu- the contributions from all input nodes nodes to form complete time slices before nication. To also exploit other modern for a particular time slice in a small time analyzing them further. interconnects, we ported FLESnet to the frame. As a result, input nodes should open-source framework OpenFabrics send their data coordinated to not over- Each compute node reserves one buffer Interface (OFI) Libfabric. This widens load individual network links or become in its memory for each input node. Input the spectrum of clusters FLESnet can blocked due to full buffers at compute nodes use remote direct memory access run on and keeps future decisions on the nodes. On the other hand, FLESnet's (RDMA) to write their contribution actual computer and networking hard- aggregate bandwidth should scale lin- directly to the compute nodes' memory ware flexible. early with the number of nodes. and inform them accordingly. Before overwriting the same memory address Synchronization: Although each input Monitoring, scheduling, and fault in the buffer, input nodes wait for an node can fill its buffer space at each com- tolerance: FLESnet has to avoid net- acknowledgement from the compute pute node, buffer space cannot be reused work congestion, node failures, and load node that the time slice was processed until contributions from all input nodes imbalances on heterogeneous hardware. and the buffer is free for reuse. are received to complete the time slice It must be able to tolerate node and link and the analysis is finished. Therefore, failures because the beam time is costly a single lazy node or slow connection and each physics experiment is unique would cause input nodes to be out of syn- and cannot be repeated. chronization and slow down the entire cluster.

72 2017 Annual Report Zuse Institute Berlin 73 Scalability and Concurrency

7,000 Without scheduler With scheduler 6,000 6 DISTRIBUTED RESULTS 5,000 4,000

Waiting d uration (ms) 3,000 DETERMINISTIC SYNCHRONIZATION 2,000 1,000

OVERHEAD 0 0.0 500.0 k 1.0 M 1.5 M 2.0 M 2.5 M Time slice no. DDS minimizes the duration needed for SCHEDULER a compute node to receive a complete time slice. Figure 6 depicts the time gap between the first and last arrival of 2.5 million time slices with/without our COMPUTE SCHEDULER INPUT SCHEDULER scheduler on 192 nodes, 96 input nodes, and 96 compute nodes. This figure shows To address the outlined challenges, The compute scheduler stores the history The input scheduler receives the pro- how the DDS helped in minimizing the FLESnet is supposed to transmit data of the transmitted intervals and proposes posed starting time and duration of an duration needed to receive a complete time slice. in high throughput and low latency. It the needed information for the upcoming interval, and then schedules the trans- 300 Without scheduler should minimize the time gap between intervals. It consists of four modules: mission accordingly. It consists of three With scheduler Figure 7 depicts the variance with and Machine limit the first and last delivered contributions receiver, history manager, proposer, and modules: sender, receiver, and scheduler. without the scheduler compared with 250 8 of each time slice to compute nodes. clock synchronizer. The receiver module The sender module updates the trans- the minimum and maximum waiting FLESnet should not congest a single node collects the actual starting times and mitted messages to compute nodes and duration of each. It shows that 90% of the or link at a time or leave other nodes or durations from input schedulers. After includes the actual starting time and needed waiting duration is exceptionally 200 links idle. Our distributed deterministic that, it sends them to the history-man­ duration of the completed interval. The small when DDS is used. scheduler (DDS) synchronizes the input a­g­er module to calculate statistics and receiver module receives the proposed 150 s) nodes to send their contributions within storage. The proposer module calculates interval information from the compute a particular time interval. Furthermore, the expected starting time and duration scheduler. The scheduler module sched­ Agg. bandwidth (G B 100 it attempts to eliminate the end-point of up coming intervals based on the ules the transmission according to the congestion at compute nodes. To do so, statistics from the history manager receiver information from the receiver 7 DDS proposes a start time and duration and sends it to input schedulers. The module. It informs the sender module 50 for each interval of time slice distribution clock-synchronizer module considers once a complete interval is transmitted. 7,000 Min, max (bar: 10th–90th percentile)

that input nodes should follow. DDS con- different clock drifts between different 0 32 64 192 sists of two schedulers, one at the input machines for higher accuracy. 6,000 # of nodes nodes and another at the compute nodes.

5,000

INPUT SCHEDULER COMPUTE SCHEDULER 4,000 duration(ms) HISTORY 3,000 SENDER RECEIVER Waiting MANAGER 2,000 SCHEDULER FUTURE WORK 1,000 We plan to further enhance the scheduler to achieve an aggregated bandwidth as 0 SCALABILITY Withoutscheduler With scheduler close as possible to the machine limit. SENDER PROPOSER CLOCK SYNC. DDS also enhanced the performance of Furthermore, we aim to design and FLESnet. Figure 8 shows how the aggre- implement a fault-tolerance mechanism gated bandwidth is enhanced using DDS so that FLESnet can tolerate faults in compared with no scheduler. nodes and the underlying network.

74 2017 Annual Report Zuse Institute Berlin 75 Dr. Tobias Kramer | [email protected] | +49-30-84185-360 Photo: ESA/Rosetta/NavCam Photo: DUSTING OFF Modeling gas and dust around comet Churyumov-Gerasimenko COMETARY The European Space Agency Rosetta mission to comet 67P/Churyu- mov-Gerasimenko (67P/C-G) sent back millions of observations during its journey around the sun. ZIB contributed to the scientific analysis of the space mission by modeling the gas and dust environment around the comet on the HLRN SURFACES supercomputer. Dusting off Cometary Surfaces

COMETS: VISITORS ROSETTA'S LONG / Freepik kjpargeter © Designed by FROM OUTER SPACE JOURNEY TO COMET AND ANCIENT TIMES 67P/CHURYUMOV-

A spectacular and beautiful show space to get very close to the comet. Mass of a bright comet with long tail and spectrometers, developed for the Rosetta mission at the University of Bern, allow GERASIMENKO large coma is a rare experience for observers from earth. Most comets Prof. Kathrin Altwegg's (University of The comet 67P/C-G has been expelled pass at a safe distance from earth Bern) team to obtain a detailed inventory by Jupiter from the cold, outer regions of around the sun on highly elongated of molecular abundances and isotopic our solar system and is presently losing orbits and are active only during a ratios. about 1/2000 of its total mass on each of couple of months at closest approach its 6.4-year round-trips. to the sun (the perihelion). Periodic Rosetta followed the path of 67P/C-G comets, designated with the suffix P from close distance (20–200 km) to find in astronomical literature, are faith- out how water and dust are distributed ful visitors and have been regularly on the comet and which factors drive the observed starting with comet 1P/ development of the dust and gas tail and Halley (orbital period 75 years). inner atmosphere (coma). Astronomers What makes comets so interesting, apart have a difficult task predicting the from the spectacular appearance of the 2 activity of a specific comet and to link glowing tail that emerges through out- the often million-kilometer-long tail to gassing and ionization in the near-solar specific physical processes at the surface parts of the comet's path? of the only few-kilometer-sized nuclei. Comets are messengers from the early stages of the solar system's formation bil- lions of years ago and provide important clues about the early formation of com- plex molecules. Furthermore, collisions of comets with earth over millions of 2 The nucleus of 67P/Churyumov-Gerasimenko: years provided our planet with organic a space potato sized 4 km x 3.5 km x 3.5 km, materials and water. consisting of dust (carbon-rich compounds and Earthbound telescopes have no chances silicates) and ice. The complex shape of the to resolve the kilometer-sized nucleus, rotating nucleus requires high-resolution mesh- surrounded by a tenuous gas atmosphere based models for the dust and gas emission (figure 2); this can be revealed only by across the surface [1]. Simplified shape models satellites making a long journey through help to pin down the sources of gas and dust emitted from the surface.

78 2017 Annual Report Dusting off Cometary Surfaces

tions of dust in space, imaged as brighter taking into account the acceleration of strikes around the nucleus and referred dust grains by the evaporating gas and to as "jets." Before Rosetta's encounter, the gravitational pull of the odd-shaped PREDICTING THE it was hypothesized that the dust jets are nucleus. An effective parallelization is caused by isolated patches of activity on required, which allows us to simulate TAILS OF COMETS the surface (pointing to a large heteroge- different scenarios. One unexpected THE SHAPE OF neity of the surface composition). outcome of the simulations performed at the HLRN supercomputer facility At ZIB, we developed a detailed dust and To analyze this in detail requires the hosted at ZIB is that it is possible to pre- gas forecast for 67P/C-G that has been development and implementation of dict the near-surface dust distribution of compared with the downlinked images. models for simulating millions of dust 67P/C-G with high accuracy just based Of particular interest are agglomera- particles around the rotating nucleus, on the shape of the nucleus. THE NUCLEUS AND 3 THE OBSERVER PERSPECTIVE In a collaboration between the How can our findings be reconciled with 3 Simulation of dust trajectories Supercomputing and Visual Data the rapidly changing appearance of "jets" from the sunlit and shaded Analysis departments at ZIB, we used around 67P/C-G seen in many images? surface. Dust is accelerated the Amira software to deform a mesh The 3-D visualization of the modeled within the gas field (arrows) representation of the nucleus to study dust cloud reveals that the imaged dust and is lifted off the surface. The how the curvature of the surface affects concentrations are highly sensitive to the rotation of the comet during the the dust release. The best match between perspective of the observer (Rosetta's travel time of the dust results in the model and Rosetta's observation is camera). Higher intensities in the images curved trajectories due to the obtained if we consider globally uniform ("jets") are caused by multiple concave Coriolis force [1]. dust emission from the entire sunlit areas aligned along the line of sight (fig- nucleus, instead from localized patches. ure 4). Our simulations take into account 4 Image analysis of the brightest This suggests a rather homogeneous the 12-hour rotation of the nucleus, point in the Rosetta image composition of the surface of 67P/C-G. which lead to the curved appearance of taken on April 12, 2015, 12:12, Higher dust levels are stemming from dust jets further away from the nucleus: decomposed into all contributing concave areas on the surface, which any observer standing on the cometary dust sources along the line of act as a lense, leading to a convergence surface would get firsthand confirmation sight (yellow line) from Rosetta's of dust trajectories several kilometers of the Coriolis effect. perspective. The bright jet seen above the surface (figure 3). from Rosetta's perspective originates from multiple sources and, in addition, from background contributions from all sunlit surface areas [2]. 4

80 2017 Annual Report Zuse Institute Berlin 81 Dusting off Cometary Surfaces

COLLABORATIONS AND FUNDING:

• Prof. Kathrin Altwegg, University of Bern, Switzerland, responsible for the Rosina: Rosetta THE GAS ATMOSPHERE Orbiter Spectrometer for Ion and Neutral Analysis instrument onboard Rosetta and the COmetary 5 Pressure Sensor (COPS) • Dr. Martin Rubin, University of Bern, Switzerland • Mattias Malmer, Stockholm, Sweden (reconstruction of the shape of the nucleus based on navigation camera images) • Prof. Eric J. Heller, Department of Physics, Harvard University, USA • Simulations were performed on the HLRN supercomputing facilities at ZIB Bright, short-living outbreaks resulting in very bright localized dust jets, have PREPARING THE also been observed in the weeks around perihelion (August 12, 2015). In collabo- NEXT RENDEZVOUS ration with the Rosina/COPS team at the University of Bern, data points from the WITH 67P/C-G cometary pressure sensor instrument onboard Rosetta allowed us to recon- For the first time, Rosetta and simulta- struct the most likely gas sources linked neous telescopic observations provide to the observed outbreaks. As it turns out, a unified picture of the evolution of the dust outbreaks are not happening at the surface and the coma of a comet. A random locations, but are highly cor- follow-up mission to comet 67P/C-G at related with carbon-dioxide-rich areas its next visit to the inner solar system (figure 5). This is interesting because for has been proposed and might lead to an the total gas emission on 67P/C-G, the unexpected reunion with Rosetta and its water emission tops the carbon-dioxide lander Philae. If the theoretical models release. pan out, next time we might be able to predict what the images of the dust tail and coma of 67P/C-G will look like.

AUTHORS: 5 Reconstruction of carbon-dioxide sources on the surface of 67P/C-G and locations Tobias Kramer, [email protected], +49 30 841 85-360 of observed dust outbreaks [3], [4]. Matthias Läuter, [email protected], +49 30 84185-421 Matthias Noack, [email protected], +49 30 84185-328 Hans-Christian Hege, [email protected], +49 30 84185-141 Daniel Baum, [email protected], +49 30 84185-293

82 2017 Annual Report Zuse Institute Berlin 83 ZIB Publications ZIB PUBLICATIONS

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Muluneh G. Abebe, Guillaume Gomard, Lin Carlo Barth, Sebastian Roder, Daniel Brod- Mascha Berg, Julia Plöntzke, Sabine Leon- Ralf Borndörfer, Oytun Arslan, Ziena Elija- Kevin K.H. Cheung, Ambros Gleixner, Daniel E. Jose Coutinho, Mark Stillwell, Katerina Argy- Zschiedrich, Carsten Rockstuhl, Ulrich W. oceanu, Tobias Kraus, Martin Hammerschmidt, hard-Marek, Kerstin Elisabeth Müller, Susanna zyfer, Hakan Güler, Malte Renken, Guvenc Steffy (2017). Verifying Integer Programming raki, George Ioannidis, Anca Iordache, Chris- Paetzold, Aimi Abass (2017). Thermodynam- Sven Burger, Christiane Becker (2017). Röblitz (2017). A dynamic model to simulate Sahin, Thomas Schlechte (2017). Line Planning Results. In F. Eisenbrand and J. Koenemann, toph Kleineweber, Alexandros Koliousis, John ics of Photon Recycling in Four Terminal Increased fluorescence of PbS quantum dots potassium balance in dairy cows. 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Journal of Engineering in Medicine, 232(1):67- Discrete Mathematics, 340(10):2499-2506. (epub ahead of print 2017-10-12) Christian Gils, Ambros Gleixner, Dmitry Sparse Proteomics Analysis – a compressed Special Matrices 5(1): 73–81. https://doi. 79. https://doi.org/10.1177/0954411917743274 https://doi.org/10.1016/j.disc.2017.05.005 Khabi, Thorsten Koch, Daniel Rehfeldt, Man- sensing-based approach for feature selec- org/10.1515/spma-2017-0006 (epub ahead of print 2017-11-02) Marco Blanco, Ralf Borndörfer, Nam Dung uel Wetzel (2017). Optimizing Large-Scale tion and classification of high-dimensional Andreas Benn, Christian Hiepen, Marc Hoang, Anton Kaier, Pedro Maristany de las Linear Energy System Problems with Block proteomics mass spectrometry data. BMC Konstantin Fackeldey, Marcus Weber (2017). Felix Ambellan, Alexander Tack, Dave Wil- Osterland, Christof Schütte, An Zwijsen, Petra Casas, Thomas Schlechte, Swen Schlobach Diagonal Structure by Using Parallel Interi- Bioinfomatics, 18(160). https://doi.org/10.1186/ GenPCCA – Markov State Models for son, Carolyn Anglin, Hans Lamecker, Stefan Knaus (2017). Role of bone morphogenetic (2017). Cost Projection Methods for the or-Point Methods. In Operations Research s12859-017-1565-4 (Joint publication: Numeri- Non-Equilibrium Steady States. In H.-J. Mucha, Zachow (2017). Evaluating two methods for proteins in sprouting angiogenesis: differen- Shortest Path Problem with Crossing Costs. In Proceedings 2017. (accepted for publication cal Mathematics, Visual Data Analysis) ed., Big data clustering: Data preprocessing, Geometry Reconstruction from Sparse Sur- tial BMP receptor-dependent signaling path- Gianlorenzo D'Angelo, Twan Dollevoet, eds., 2017-12-08) variable selection, and dimension reduction. gical Navigation Data. In Proceedings of the ways balance stalk vs. tip cell competence. 17th Workshop on Algorithmic Approaches for Tim Conrad, Barbara Rath, Puja Myles, Maren https://doi.org/10.20347/WIAS. REPORT.29 Jahrestagung der Deutschen Gesellschaft für FASEB Journal, 31(11):4720–4733. https://doi. Transportation Modelling, Optimization, and Jan Brüning, Leonid Goubergrits, Werner Alchikh, Xiaolin Ma, Christian Hoppe, Fran- Computer- und Roboterassistierte Chirurgie org/10.1096/fj.201700193RR Systems (ATMOS 2017), 59. Heppt, Stefan Zachow, Thomas Hildebrandt ziska Tief, Xi Chen, Patrick Obermeier, Bron Frank Fischer, Boris Grimm, Torsten Klug, (CURAC), 16:24-30. (2017). Numerical Analysis of Nasal Kisler, Brunhilde Schweiger (2017). Influenza Thomas Schlechte (2017). A Re-optimization Ralf Borndörfer, Boris Grimm, Markus Breathing – A Pilot Study. Facial Plastic and other respiratory viruses: standardizing Approach for Train Dispatching. In Operations Reuther, Thomas Schlechte (2017). 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Frank Fischer, Thomas Schlechte (2017). Robert Lion Gottwald, Stephen J. Maher, Yuji Boris Grimm, Ralf Borndörfer, Markus Rieke Heinze, Anurag Dipankar, Cintia Benjamin Hiller, René Saitenmacher, Tom Robert Joachimsky, Felix Ambellan, Stefan Strong Relaxations for the Train Timetabling Shinano (2017). Distributed Domain Propa- Reuther, Stanley Schade, Thomas Schlechte Carbajal Henken, Christopher Moseley, Walther (2017). Analysis of operating modes of Zachow (2017). Computerassistierte Auswahl Problem using Connected Configurations. In gation. In 16th International Symposium on (2017). A Propagation Approach to Acyclic Odran Sourdeval, Silke Trömel, Xinxin Xie, complex compressor stations. In Proceedings und Platzierung von interpositionalen Spacern Gianlorenzo D'Angelo, Twan Dollevoet, eds., Experimental Algorithms (SEA 2017), volume Rolling Stock Rotation Optimization. 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Blahak, Sebastian Bley, Slavko Brdar, Matthias Gesellschaft für Computer- und Roboterassist- and Systems (ATMOS 2017), 59. https://doi. org/10.4230/LIPIcs.SEA.2017.6 Pooja Gupta, Annika Gramatke, Ralf Einspan- Brueck, Susanne Crewell, Hartwig Deneke, René Hoffmann, Robert Lemanis, Janina ierte Chirurgie (CURAC), 16:106-111. org/10.4230/OASIcs.ATMOS.2017.11 ier, Christof Schütte, Max von Kleist, Jutta Paolo Di Girolamo, Raquel Evaristo, Jürgen Falkenberg, Steffen Schneider, Hendrik Niels Gregersen, Jakob Rosenkrantz de Sharbati (2017). In silico cytotoxicity assess- Fischer, Christopher Frank, Petra Friederichs, Wesendonk, Stefan Zachow (2017). Integrat- Klaus Jäger, Grit Köppel, David Eisenhauer, Lisa Fischer, Sebastian Götschel, Martin Lasson, Lars Hagedorn Frandsen, Oleksiy ment on cultured rat intestinal cells deduced Tobias Göcke, Ksenia Gorges, Luke Hande, ing 2-D and 3-D shell morphology to disen- Duote Chen, Martin Hammerschmidt, Sven Weiser (2017). Lossy data compression S. Kim, Olav Breinbjerg, Fengwen Wang, from cellular impedance measurements. Moritz Hanke, Akio Hansen, Hans-Christian tangle the palaeobiology of ammonoids: A Burger, Christiane Becker (2017). Optical reduces communication time in hybrid Ole Sigmund, Aliaksandra Ivinskaya, Andrei Toxicology in Vitro, 41:179-188. Hege, Corinna Hose, Thomas Jahns, Norbert virtual approach. Palaeontology, 61(1):89–104. simulations of advanced light management for time-parallel integrators. Comput. Vis. Sci.. Lavrinenko, Philipp Gutsche, Sven Burger, Kalthoff, Daniel Klocke, Stefan Kneifel, Peter https://doi.org/10.1111/pala.12328 liquid-phase crystallized silicon thin-film solar (accepted for publication 2017-09-22) http:// Teppo Häyrynen, Jesper Merk (2017). Com- Tobias Günther, Alexander Kuhn, Hans-Chris- Knippertz, Alexander Kuhn, Thriza van Laar, cells. Proc. SPIE, 10356:103560F. https://doi. dx.doi.org/10.1007/s00791-018-0293-2 parison of five numerical methods for comput- tian Hege, Markus Gross, Holger Theisel Andreas Macke, Vera Maurer, Bernhard Ulrike Homberg, Daniel Baum, Steffen Pro- org/10.1117/12.2273994 ing quality factors and resonance wavelengths (2017). Progressive Monte Carlo rendering of Mayer, Catrin I. Meyer, Shravan K. Muppa, haska, Jens Günster, Stefanie Krauß-Schüler Roeland A. J. Neggers, Emiliano Orlandi, Gerald Gamrath, Thorsten Koch, Stephen in photonic crystal membrane cavities. In atmospheric flow features across scales. Physi- (2017). Adapting trabecular structures for Max von Kleist, Christof Schütte, Wei Zhang Florian Pantillon, Bernhard Pospichal, Niklas Maher, Daniel Rehfeldt, Yuji Shinano (2017). CLEO/Europe-EQEC. https://doi.org/10.1109/ cal Review Fluids, 2:09050-1-09050-3. https:// 3-D printing: an image-processing approach (2017). Statistical analysis of the first passage Röber, Leonhard Scheck, Axel Seifert, Patric SCIP-Jack – A solver for STP and variants with CLEOE-EQEC.2017.8087750 doi.org/10.1103/PhysRevFluids.2.090502 based on µCT data. Biomedical Physics & path ensemble of jump processes. Journal of Seifert, Fabian Senf, Pavan Siligam, Clemens parallelization extensions. Mathematical Pro- Engineering Express, 3(3):035027. https://doi. Statistical Physics. (accepted for publication Simmer, Sandra Steinke, Bjorn Stevens, Kath- gramming Computation, 9(2):231–296. https:// Niels Gregersen, Jakob Rosenkrantz de Martin Hammerschmidt, Martin Weiser, org/10.1088/2057-1976/aa7611 2017-12-22) doi.org/10.1007/s12532-016-0114-x Lasson, Lars Hagedorn Frandsen, Teppo rin Wapler, Michael Weniger, Volker Wulf- Xavier Garcia Santiago, Lin Zschiedrich, meyer, Günther Zängl, Dan Zhang, Johannes Häyrynen, Andrei Lavrinenko, Jesper Moerk, Bernd Bodermann, Sven Burger (2017). Kai Hoppmann, Robert Schwarz (2017). On Marco Klindt (2017). PDF/A considered harm- Fengwen Wang, Ole Sigmund, Oleksiy S. Kim, Quaas (2017). Large-eddy simulations over Gerald Gamrath, Christoph Schubert (2017). Quantifying parameter uncertainties in opti- Germany using ICON: a comprehensive eval- Finding Maximum Minimum Cost Flows. ful for digital preservation. In Proceedings of Measuring the impact of branching rules for Olav Breinbjerg, Aliaksandra Ivinskaya, Philipp cal scatterometry using Bayesian inversion. In . uation. Quarterly Journal of the Royal Meteo- Operations Research Proceedings 2017 iPres – 14th International Conference on Dig- mixed-integer programming. In Operations Gutsche, Sven Burger (2017). Benchmarking Proc. SPIE, 10330:1033004. https://doi. (accepted for publication 2017-11-01) ital Preservation / Kyoto, Japan / September five computational methods for analyzing rological Society, 143(702):69-100. https://doi. Research Proceedings 2017. (accepted for org/10.1117/12.2270596 org/10.1002/qj.2947 25–29, 2017, volume 14 of iPres Proceedings. publication 2017-11-10) large photonic crystal membrane cavities. Rudolf Huttary, Leonid Goubergrits, Christof In Numerical Simulation of Optoelectronic Carsten Hartmann, Christof Schütte, Marcus Michael Hengartner, Tillmann H.C. Krüger, Schütte, Stefan Bernhard (2017). Simulation, Stefan Klus, Patrick Gelß, Sebastian Peitz, Brady Gilg, Torsten Klug, Rosemarie Mar- Devices (NUSOD), IEEE, page 89. https://doi. Weber, Wei Zhang (2017). Importance sam- Identification, and Statistical Variation in Christof Schütte (2017). Tensor-based org/10.1109/NUSOD.2017.8010005 Kirsten Geraedts, Enrico Tronci, Toni Mancini tienssen, Joseph Paat, Thomas Schlechte, pling in path space for diffusion processes with Mancini, Fabian Ille, Marcel Egli, Susanna Cardiovascular Analysis (SISCA) – a Software dynamic mode decomposition. SIAM Journal Christof Schulz, Sinan Seymen, Alexander slow-fast variables. Probability Theory and Röblitz, Rainald Ehrig, Lanja Saleh, Katharina Framework for Multi-compartment Lumped on Scientific Computing. (accepted for publi- Tesch (2017). Conflict-Free Railway Track Andreas Griewank, Richard Hasenfelder, Related Fields, 1–52. https://doi.org/10.1007/ Modeling. Computers in Biology and Medi- cation 2017-04-03) Manuel Radons, Lutz Lehmann, Tom Streubel Spanaus, Cordula Schippert, Yuanyuan Zhang, Assignment at Depots. In Proceedings of the s00440-017-0755-3 Brigitte Leeners (2017). Negative affect is cine, 87:104–123. IAROR conference RailLille. (2017). Integrating Lipschitzian dynamical Stefan Klus, Feliks Nüske, Peter Koltai, Hao systems using piecewise algorithmic differen- unrelated to fluctuations in hormone levels Carsten Hartmann, Lorenz Richter, Christof across the menstrual cycle: evidence from Sinaida Igde, Susanna Röblitz, Anne Müller, Wu, Ioannis Kevrekidis, Christof Schütte, tiation. Optimization Methods and Software. Ambros M. Gleixner, Timo Berthold, Ben- Schütte, Wei Zhang (2017). Variational a multisite observational study across two Katharina Kolbe, Sophia Boden, Claudia Frank Noé (2017). Data-driven model reduc- jamin Müller, Stefan Weltge (2017). Three https://doi.org/10.1080/10556788.2017.13786 characterization of free energy: theory and Fessele, Thisbe Lindhorst, Marcus Weber, tion and transfer operator approximation. 53 (epub ahead of print 2017-10-03) successive cycles. Journal of Psychosomatic Enhancements for Optimization-Based Bound algorithms. Entropy, 19(11), 626. https://doi. Research, 99:21-27. https://doi.org/10.1016/j. Laura Hartmann (2017). Linear Precision Gly- Journal of Nonlinear Science. (accepted for Tightening. Journal of Global Optimization, org/10.3390/e19110626 jpsychores.2017.05.018 comacromolecules with Varying Interligand publication 2017-12-21) 67(4):731–757. https://doi.org/10.1007/s10898- Andreas Griewank, Tom Streubel, Lutz Leh- Spacing and Linker Functionalities Binding to mann, Manuel Radons, Richard Hasenfelder 016-0450-4 Felix Hennings (2017). Benefits and Limita- Concanavalin A and the Bacterial Lectin FimH. (2017). Piecewise linear secant approximation Marcomolecular Bioscience, 17(12):1700198. via algorithmic piecewise differentiation. tions of Simplified Transient Gas Flow Formu- lations. . (accepted for https://doi.org/10.1002/mabi.201700198 Optimization Methods and Software. https:// OR Proceedings 2017 doi.org/10.1080/10556788.2017.1387256 publication 2017-11-01) (epub ahead of print 2017-10-27)

86 2017 Annual Report Zuse Institute Berlin 87 ZIB Publications

Helge Knoop, Tobias Gronemeier, Matthias Christoph Kreisbeck, Tobias Kramer, Rafael Juliane Lube, Natasha Flack, Sebastian Cotof- Jan Müller, Sebastian Götschel, Christiane Thomas Orgis, Matthias Läuter, Dörthe Han- Daniel Rehfeldt, Thorsten Koch (2017). SCIP- Sühring, Peter Steinbach, Matthias Noack, Molina (2017). Time-dependent wave packet ana, Orkun Özkurtul, Stephanie Woodley, Ste- Maierhofer, Martin Weiser (2017). Determining dorf, Klaus Dethloff (2017). Baroclinic waves JACK – a solver for STP and variants with Florian Wende, Thomas Steinke, Christoph simulations of transport through Aharanov– fan Zachow, Niels Hammer (2017). Pelvic and the material parameters for the reconstruction on the β plane using low-order Discontinuous parallelization extensions: An update. In Oper- Knigge, Siegfried Raasch, Klaus Ketelsen Bohm rings with an embedded quantum lower extremity physiological cross-sectional of defects in carbon fiber reinforced polymers Galerkin discretization. Journal of Compu- ations Research Proceedings 2017. (accepted (2017). Porting the MPI-parallelized LES model dot. Journal of Physics: Condensed Matter, areas: An MRI study of the living young and from data measured by flash thermography. tational Physics, 339:461–481. https://doi. for publication 2017-11-01) PALM to multi-GPU systems and many inte- 29(15):155301. https://doi.org/10.1088/1361- comparison to published research literature. In AIP Conference Proceedings, 1806. https:// org/10.1016/j.jcp.2017.03.029 grated core processors: an experience report. 648X/aa605d Surgical and Radiologic Anatomy, 39(8):849- doi.org/10.1063/1.4974671 Zully Ritter, Daniel Belavy, Wolfgang Bau- International Journal of Computational Sci- 857. https://doi.org/10.1007/s00276-016- Chavdar Papazov, Hans-Christian Hege mann, Dieter Felsenberg (2017). In-vivo ence and Engineering. Special Issue on: Novel Alexander Kuhn, Wito Engelke, Markus 1807-6 Benjamin Müller, Renke Kuhlmann, Stefan (2017). Blue-noise Optimized Point Sets Based bone remodeling rates determination and Strategies for Programming Accelerators. Flatken, Hans-Christian Hege, Ingrid Vigerske (2017). On the performance of NLP on Procrustes Analysis. In SIGGRAPH Asia compressive stiffness variations before, (accepted for publication 2017-04-29) Hotz (2017). Topology-based Analysis for Lars Lubkoll, Anton Schiela, Martin Weiser solvers within global MINLP solvers. In Oper- 2017 Technical Briefs, 20:1–20:4. https://doi. during 60 days of bed rest and a two‑year Multimodal Atmospheric Data of Volcano (2017). An affine covariant composite step ations Research Proceedings 2017. (accepted org/10.1145/3145749.3149442 follow‑up: a micro-FE-analysis from HR-pQCT David Knötel, Ronald Seidel, Steffen Prohaska, Eruptions. Topological Methods in Data Anal- method for optimization with PDEs as equality for publication 2017-12-20) measurements of the Berlin bed rest study-2. Mason N. Dean, Daniel Baum (2017). Auto- ysis and Visualization IV, 35–40. https://doi. constraints. Optimization Methods and Soft- Jannes Quer, Luca Donati, Bettina Keller, Acta Astronautica, 132:67–77. https://doi. mated Segmentation of Complex Patterns in org/10.1007/978-3-319-44684-4_2 ware, 32(5):1132-1161. https://doi.org/10.1080/ Matthias Noack, Florian Wende, Georg Zit- Marcus Weber (2017). An automatic adaptive org/10.1016/j.actaastro.2016.12.002 Biological Tissues: Lessons from Stingray Tes- 10556788.2016.1241783 zlsberger, Michael Klemm, Thomas Steinke importance sampling algorithm for molecular sellated Cartilage. PLOS ONE 12(12):e0188018. Alexander Lange (2017). A mathematical (2017). KART – A Runtime Compilation Library dynamics in reaction coordinates. SIAM Ulrich-Peter Rohr, Pia Herrmann, Katharina https://doi.org/10.1371/journal.pone.0188018 framework for predicting lifestyles of viral Stephen J. Maher, Guy Desaulniers, Francois for Improving HPC Application Performance. Journal on Scientific Computing. (accepted for Ilm, Hai Zhang, Sabine Lohmann, Astrid Reiser, pathogens. In Modelling Biological Evolution Soumis (2017). The daily tail assignment prob- In High Performance Computing: ISC High publication 2017-11-17) Andrea Muranyi, Janice Smith, Susen Burock, Thorsten Koch (2017). The ZIMPL modeling 2017: Developing Novel Approaches. lem under operational uncertainty using look- Performance 2017 International Workshops, Marc Osterland, Katherine Leith, Shalini language. Optima, 103:8–9. ahead maintenance constraints. European DRBSD, ExaComm, HCPM, HPC-IODC, Jannes Quer, Han Lie (2017). Some connec- Singh, Patrick Brunhoeber, Rebecca Bower- Nikolay Ledentsov, Vitaly Shchukin, Jörg-R. Journal of Operational Research, 264(2):534- IWOPH, IXPUG, P^3MA, VHPC, Visualization tions between importance sampling and master, Jeanne Tie, Michael Christie, Hui-Li *Tobias Kramer, Matthias Noack, Daniel Baum, Kropp, Nikolay Ledentsov, Lin Zschiedrich, 547. https://doi.org/10.1016/j.ejor.2017.06.041 at Scale, WOPSSS, Frankfurt, Germany, enhanced sampling methods in molecular Wong, Paul Waring, Kandavel Shanmugam, Hans-Christian Hege, Eric J. Heller (2017). Frank Schmidt (2017). Resonant cavity light– (epub ahead of print 2017-06-20) June 18–22, 2017, Revised Selected Papers, dynamics. Journal of Chemical Physics. Peter Gibbs, Ulrike Stein (2017). Prognostic Dust and gas emission from cometary nuclei: emitting diodes based on dielectric passive volume 10524 of LNCS, pages 389–403, (accepted for publication 2017-10-31) value of MACC1 and proficient mismatch the case of comet 67P/Churyumov-Gerasi- cavity structures. Proc. SPIE, 10124:101240O. Gauri Mangalgiri, Makars Šiškins, Alina Arsla- Springer International Publishing. https://doi. repair status for recurrence risk prediction in menko. Advances in Physics: X, 3(1):1404436. https://doi.org/10.1117/12.2253089 nova, Martin Hammerschmidt, Phillip Manley, org/10.1007/978-3-319-67630-2_29 Barbara Rath, Tim Conrad, Puja Myles, Maren stage II colon cancer patients: the BIOGRID https://doi.org/10.1080/23746149.2017.1404 Wiebke Riedel, Martina Schmid (2017). Highly Alchikh, Xiaolin Ma, Christian Hoppe, Fran- studies. Annals of Oncology, 28(8):1869-1875. 436 (Joint publication: Visual Data Analysis, B. Leeners, T. H. C. Kruger, K. Geraedts, E. Transmittive Broadband Dielectric Nanoholes. Matthias Noack (2017). OpenCL in Scientific ziska Tief, Xi Chen, Patrick Obermeier, Bron https://doi.org/10.1093/annonc/mdx207 Distributed Algorithms and Supercomputing) Tronci, T. Mancini, F. Ille, M. Egli, S. Röblitz, L. In CLEO, OSA Tech. Dig., page JTu5A.117. High Performance Computing: The Good, Kisler, Brunhilde Schweiger (2017). Influenza (accepted for publication 2017-10-23) Saleh, K. Spanhaus, C. Schippert, Y. Zhang, https://doi.org/10.1364/CLEO_AT.2017. the Bad, and the Ugly. In Proceedings of the and other respiratory viruses: standardizing Manish Sahu, Anirban Mukhopadhyay, Ange- M. P. Hengartner (2017). Lack of association JTu5A.117 5th International Workshop on OpenCL, disease severity in surveillance and clinical lika Szengel, Stefan Zachow (2017). Addressing Tobias Kramer, Mirta Rodriguez (2017). between female hormone levels and visuospa- IWOCL 2017, pages 12:1–12:3. https://doi. trials. Expert Review of Anti-infective Therapy, multi-label imbalance problem of Surgical Tool Two-dimensional electronic spectra of the tial working memory, divided attention, and Matthias Miltenberger, Ted Ralphs, Daniel org/10.1145/3078155.3078170 15(6):545–568. https://doi.org/10.1080/147872 Detection using CNN. International Journal of photosynthetic apparatus of green sulfur cognitive bias across two consecutive men- Steffy (2017). Exploring the Numerics of 10.2017.1295847 Computer Assisted Radiology and Surgery, bacteria. Scientific Reports, 7:45245. https:// strual cycles. Front. Behav. Neurosci.. https:// Branch-and-Cut for Mixed-Integer Linear Andrey Novitsky, Jakob Rosenkrantz de 12(6):1013-1020. https://doi.org/10.1007/ doi.org/10.1038/srep45245 doi.org/10.3389/fnbeh.2017.00120 Optimization. In Operations Research Lasson, Lars Hagedorn Frandsen, Philipp Stefanie Redemann, Johannes Baumgart, s11548-017-1565-x Proceedings 2017. (accepted for publication Gutsche, Sven Burger, Oleksiy S. 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88 2017 Annual Report Zuse Institute Berlin 89 ZIB Publications

Stanley Schade, Ralf Borndörfer, Matthias Philipp-Immanuel Schneider, Xavier Garcia Borong Shao, Carlo Vittorio Cannistraci, Tim Avan Suinesiaputra, Pierre Albin, Xenia Alba, Ingmar Vierhaus, Armin Fügenschuh, Robert Stefanie Winkelmann, Christof Schütte Breuer, Boris Grimm, Markus Reuther, Santiago, Carsten Rockstuhl, Sven Burger Conrad (2017). Epithelial Mesenchymal Tran- Martino Alessandrini, Jack Allen, Wenjia Bai, Lion Gottwald, Stefan Grösser (2017). Using (2017). Hybrid models for chemical reaction Thomas Schlechte, Patrick Siebeneicher (2017). Global optimization of complex sition Network-Based Feature Engineering in Serkan Cimen, Peter Claes, Brett Cowan, Jan white-box nonlinear optimization methods in networks: Multiscale theory and application (2017). Pattern Detection For Large-Scale Rail- optical structures using Bayesian opti- Lung Adenocarcinoma Prognosis Prediction D'hooge, Nicolas Duchateau, Jan Ehrhardt, system dynamics policy improvement. System to gene regulatory systems. The Journal of way Timetables. In Proceedings of the IAROR mization based on Gaussian processes. Using Multiple Omic Data. Genomics and Alejandro Frangi, Ali Gooya, Vicente Grau, Dynamics Review, 33(2):138–168. https://doi. Chemical Physics, 147(11):114115-1-114115-18. conference RailLille. Proc. SPIE, 10335:103350O. https://doi. Computational Biology, 3(3):e57. https://doi. Karim Lekadir, Allen Lu, Anirban Mukhopad- org/10.1002/sdr.1583 https://doi.org/10.1063/1.4986560 org/10.1117/12.2270609 org/10.18547/gcb.2017.vol3.iss3.e57 hyay, Ilkay Oksuz, Nripesh Parajuli, Xavier Pen- Stanley Schade, Thomas Schlechte, Jakob nec, Marco Pereanez, Catarina Pinto, Paolo Stefan Vigerske, Ambros Gleixner (2017). Stefanie Winkelmann (2017). Markov Control Witzig (2017). Structure-based Decomposition Ingmar Schuster, Heiko Strathmann, Brooks Yuji Shinano, Stefan Heinz, Stefan Vigerske, Piras, Marc-Michael Rohe, Daniel Rueckert, SCIP: Global Optimization of Mixed-Integer with Rare State Observation: Average Opti- for Pattern-Detection for Railway Timetables. Paige, Dino Sejdinovic (2017). Kernel Sequen- Michael Winkler (2017). FiberSCIP – A shared Dennis Saring, Maxime Sermesant, Kaleem Nonlinear Programs in a Branch-and-Cut mality. Markov Processes and Related Fields, In Operations Research 2017. (accepted for tial Monte Carlo. Joint European Conference memory parallelization of SCIP. INFORMS Siddiqi, Mahdi Tabassian, Lusiano Teresi, Framework. Optimization Methods & Soft- 23:1-34. publication 2017-11-01) on Machine Learning and Knowledge Dis- Journal on Computing, 30(1):11–30. https:// Sotirios Tsaftaris, Matthias Wilms, Alistair ware. https://doi.org/10.1080/10556788.2017. covery in Databases, 390 –409. https://doi. doi.org/10.1287/ijoc.2017.0762 (epub ahead of Young, Xingyu Zhang, Pau Medrano-Gracia 1335312 (epub ahead of print 2017-06-14) *Jakob Witzig, Isabel Beckenbach, Leon Sebastian Schenker, Ingmar Vierhaus, Ralf org/10.1007/978-3-319-71249-9_24 print 2017-11-01) (2017). Statistical shape modeling of the left Eifler, Konstantin Fackeldey, Ambros Gleix- Borndörfer, Armin Fügenschuh, Martin ventricle: myocardial infarct classification Marcus Weber, Konstantin Fackeldey, Christof ner, Andreas Grever, Marcus Weber (2017). Skutella (2017). Optimization Methods Stephan Schwartz, Thomas Schlechte, Elmar Yuji Shinano (2017). The Ubiquity Generator challenge. IEEE Journal of Biomedical and Schütte (2017). Set-Free Markov State Model Mixed-Integer Programming for Cycle Detec- https://doi.org/10.1109/ in Sustainable Manufacturing. In Rainer Swarat (2017). Designing Inspector Rosters Framework: 7 Years of Progress in Parallelizing Health Informatics. Building. Journal of Chemical Physics, 146(12). tion in Non-reversible Markov Processes. JBHI.2017.2652449 Stark, Günther Seliger, Jérémy Bonvoisin, with Optimal Strategies. In Operations Branch-and-Bound. In Operations Research https://doi.org/10.1063/1.4978501 Multiscale Modeling and Simulation, 16(1):248– eds., Sustainable Manufacturing, 239–253, Research Proceedings 2016, 217–223. https:// Proceedings 2017. (accepted for publication 265. https://doi.org/10.1137/16M1091162 (Joint Springer International Publishing. https://doi. doi.org/10.1007/978-3-319-55702-1_30 2017-11-11) Tim Sullivan (2017). Well-posedness of Bayes- Martin Weiser, Simone Scacchi (2017). Spec- publication: Mathematical Optimization, org/10.1007/978-3-319-48514-0_15 ian inverse problems in quasi-Banach spaces tral Deferred Correction methods for adap- Numerical Mathematics) (accepted for publi- Jonas Schweiger, Frauke Liers (2017). A Viola Spahn, Giovanna Del Vecchio, Dominika with stable priors. In 88th Annual Meeting tive electromechanical coupling in cardiac cation 2017-10-18) *Sebastian Schenkl, Holger Muggenthaler, Decomposition Approach for Optimal Gas Labuz, Antonio Rodriguez-Gaztelumendi, N. of the International Association of Applied simulation. In G. Russo et al.(eds.) Progress in Mathematics and Mechanics (GAMM), Wei- Michael Hubig, Bodo Erdmann, Martin Network Extension with a Finite Set of Massaly, Julia Temp, Vedat Durmaz, Peggy Industrial Mathematics at ECMI 2014, 321–328. Jakob Witzig, Timo Berthold, Stefan Heinz mar 2017, volume 17 of Proceedings in Weiser, Stefan Zachow, Andreas Heinrich, Demand Scenarios. Optimization and Engi- Sabri, Marco Reidelbach, Halina Machelska, Applied https://doi.org/10.1007/978-3-319-23413-7_42 (2017). Experiments with Conflict Analysis in pages 871–874. Felix Victor Güttler, Ulf Teichgräber, Gita Mall neering. (accepted for publication 2017-11-25) Marcus Weber, Christoph Stein (2017). A Mathematics and Mechanics, Mixed–Integer Programming. In Integration of https://doi.org/10.1002/pamm.201710402 (2017). Automatic CT-based finite element nontoxic pain killer designed by modeling of Florian Wende, Martijn Marsman, Zhengji AI and OR Techniques in Constraint Program- model generation for temperature-based Lea Seeber, Tim Conrad, Christian Hoppe, pathological receptor conformations. Science, Zhao, Jeongnim Kim (2017). Porting VASP ming, volume 10335 of LNCS, pages 211-222. Tim Sullivan (2017). 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Educating Tom Streubel, Christian Strohm, Philipp and Imaging, OpenMP, IWOMP 2017, Stony Brook, NY, USA, Ryohei Yokoyama, Yuji Shinano, Yuki org/10.3934/ipi.2017040 publication: Numerical Mathematics, Visual parents about the vaccination status of their Trunschke, Caren Tischendorf (2017). Generic September 20–22, 2017, volume 8766 of LNCS, Wakayama, Tetsuya Wakui (2017). Multiobjec- Data Analysis) children: A user-centred mobile application. Construction and Efficient Evaluation of pages 107–122. https://doi.org/10.1007/978-3- tive Optimal Design of a Gas Turbine Cogen- Preventive Medicine Reports, 5:241–250. Network DAEs and Their Derivatives in the Alexander Tesch (2017). Improved Compact 319-65578-9_8 eration Plant by a Revised Hierarchical Opti- Frank Schmidt (2017). Photonics. In Joachim https://doi.org/10.1016/j.pmedr.2017.01.002 Context of Gas Networks. (accepted for publi- Models for the Resource-Constrained Project mization Method. In ASME Turbo Expo 2017: Piprek, ed., Handbook of Optoelectronic cation 2017-12-08) Scheduling Problem. In Operations Research David Wilson, Carolyn Anglin, Felix Ambellan, Turbomachinery Technical Conference and Device Modeling and Simulation, CRC Press. Ronald Seidel, Michael Blumer, Paul Zaslan- Proceedings 2016, 25–30. Carl Martin Grewe, Alexander Tack, Hans Exposition, 3:1–14. https://doi.org/doi:10.1115/ sky, David Knötel, Daniel R. Huber, James Lamecker, Michael Dunbar, Stefan Zachow GT2017-64296 Robert Schmidtke, Kenny Erleben (2017). C. Weaver, Peter Fratzl, Sidney Omelon, Christoph von Tycowicz, Felix Ambellan, Anir- (2017). Validation of three-dimensional Chunked Bounding Volume Hierarchies for Luca Bertinetti, Mason N. Dean (2017). ban Mukhopadhyay, Stefan Zachow (2017). An models of the distal femur created from Wei Zhang, Christof Schütte (2017). Reliable Fast Digital Prototyping using Volumetric Ultrastructural, material, and crystallographic Efficient Riemannian Statistical Shape Model surgical navigation point cloud data for approximation of long relaxation timescales Meshes. IEEE Transactions on Visualiza- description of endophytic masses – a possible using Differential Coordinates. Medical Image intraoperative and postoperative analysis of in molecular dynamics. Entropy, 19(7), 367. tion and Computer Graphics. https://doi. damage response in shark and ray tessellated Analysis, 43(1):1–9. https://doi.org/10.1016/j. total knee arthroplasty. International Journal https://doi.org/10.3390/e19070367 org/10.1109/TVCG.2017.2784441 calcified cartilage. Journal of Structural media.2017.09.004 (epub ahead of print 2017- of Computer Assisted Radiology and Surgery, Biology, 198(1):5–18. https://doi.org/10.1016/j. 09-14) 12(12):2097–2105. https://doi.org/10.1007/ jsb.2017.03.004 s11548-017-1630-5

90 2017 Annual Report Zuse Institute Berlin 91 ZIB Publications

NOT PEER- ZIB REVIEWED (14) DISSERTATIONS (4) REPORTS (74)

Zhengji Zhao, Martijn Marsman, Florian Jens Buchmann, Bernhard Kaplan, Steffen Jan Müller, Sebastian Götschel, Martin Weiser, Christian Tobias Willenbockel: Divisive Amal Aboulhassan, Ronell Sicat, Daniel Felix Binkowski (2017). On the convergence Wende, Jeongnim Kim (2017). Performance Prohaska, Jan Laufer (2017). Experimental Christiane Maierhofer (2017). Thermografie Variational Bayesian Algorithms for the Clus- Baum, Olga Wodo, Markus Hadwiger (2017). behavior of spectral deferred correction of Hybrid MPI/OpenMP VASP on Cray validation of a Monte-Carlo-based inversion mit optimierter Anregung für die quantitative tering of large and complex Networks with Comparative Visual Analysis of Structure-Per- methods for convection-diffusion equations. XC40 Based on Intel Knights Landing Many scheme for 3-D quantitative photoacoustic Untersuchung von Delaminationen in kohlen- Applications to Earthquake Networks. Freie formance Relations in Complex Bulk-Hetero- ZIB-Report 17-53. Integrated Core Architecture. In , CUG Con- tomography. In Proc. of SPIE, Photons Plus stofffaserverstärkten Kunststoffen. In NDT. Universität Berlin (2017). junction Morphologies. ZIB-Report 17-16. ference Proceedings. Ultrasound: Imaging and Sensing, volume net Proc. DGZfP 2017. Andreas Bittracher, Péter Koltai, Stefan 10064 of Proc. of SPIE, pages 1006416– Patrick Gelß: The Tensor-Train Format and Its Felix Ambellan, Alexander Tack, Dave Wil- Klus, Ralf Banisch, Michael Dellnitz, Christof Yulia Zhukova, Christian Hiepen, Petra Knaus, 1006416-8. https://doi.org/10.1117/12.2252359 Daisuke Sakurai, Hans-Christian Hege, Application. Modeling and Analysis of Chem- son, Carolyn Anglin, Hans Lamecker, Stefan Schütte (2017). Transition manifolds of com- Marc Osterland, Steffen Prohaska, John W. C. Alexander Kuhn, Henning Rust, Bastian Kern, ical Reaction Networks, Catalytic Processes, Zachow (2017). Evaluating two methods for plex metastable systems: Theory and data- Dunlop, Peter Fratzl, Ekaterina V. Skorb (2017). Carl Martin Grewe, Lisa Schreiber (2017). Dig- Tom-Lukas Breitkopf (2017). An Applica- and Brownian Dynamics. Freie Universität Geometry Reconstruction from Sparse Surgi- driven computation of effective dynamics. The role of titanium surface nanotopography ital Image Archive. The Archiving and Coding tion-Oriented Framework for Feature Track- Berlin (2017). cal Navigation Data. ZIB-Report 17-71. ZIB-Report 17-22. on preosteoblast morphology, adhesion of Emotions. In Nikola Doll, Horst Bredekamp, ing in Atmospheric Sciences. In Proceedings and migration. Advanced Healthcare Mate- Wolfgang Schäffner, eds., +ultra. Knowledge & of 2017 IEEE 7th Symposium on Large Data Jonad Pulaj (2017). Cutting Planes for Union- Kilian Amrhein, Tim Hasler, Marco Klindt, Elias Andreas Bittracher, Ralf Banisch, Christof rials, 6(15):1601244. https://doi.org/10.1002/ Gestaltung, 281–286. Analysis and Visualization (LDAV), 96–97. Closed Families. Technische Universität Oltmanns, Wolfgang Peters-Kottig (2017). Schütte (2017). Data-driven Computation of adhm.201601244 https://doi.org/10.1109/LDAV.2017.8231857 Berlin. Digitale Langzeitarchivierung: Mustervorlage Molecular Reaction Coordinates. ZIB-Report Carl Martin Grewe, Stefan Zachow (2017). für Übernahmevereinbarungen, Version 2. 17-77. Face-to-Face-Interface. In Nikola Doll, Horst Farouk Salem, Florian Schintke, Thorsten Jonas Schweiger (2017). Exploiting structure ZIB-Report 17-15. Bredekamp, Wolfgang Schäffner, eds., +ultra. Schütt, Alexander Reinefeld (2017). Support- in non-convex quadratic optimization and gas Marco Blanco, Ralf Borndörfer, Nam Dung Knowledge & Gestaltung, 320–321. ing various interconnects in FLESnet using network planning under uncertainty. Tech- Daniel Baum, Norbert Lindow, Hans-Christian Hoang, Anton Kaier, Pedro Maristany de las Libfabric. CBM Progress Report 2016, 159–160. nische Universität Berlin. Hege, Verena Lepper, Tzulia Siopi, Frank Kutz, Casas, Thomas Schlechte, Swen Schlobach Klaus Jäger, Grit Köppel, Martin Hammer- Kristin Mahlow, Heinz-Eberhard Mahnke (2017). Cost Projection Methods for the schmidt, Sven Burger, Christiane Becker Martin Schmidt, Denis Assmann, Robert (2017). Revealing hidden text in rolled and Shortest Path Problem with Crossing Costs. (2017). Accurate optical simulations of periodic Burlacu, Jesco Humpola, Imke Joormann, folded papyri. ZIB-Report 17-02. ZIB-Report 17-48. nanostructures on a thick glass substrate. Nikolaos Kanelakis, Thorsten Koch, Djamal In 29th Workshop on Quantum Solar Energy Oucherif, Marc E. Pfetsch, Lars Schewe, Isabel Beckenbach, Britta Peis, Oliver Ralf Borndörfer, Matthias Breuer, Boris Conversion – (QUANTSOL). Robert Schwarz, Matthias Sirvent (2017). Schaudt, Robert Scheidweiler (2017). A Com- Grimm, Markus Reuther, Stanley Schade, GasLib – A Library of Gas Network Instances. binatorial Proof of a König-type Theorem for Thomas Schlechte (2017). Timetable Sparsifi- Bernhard Kaplan, Jens Buchmann, Steffen Optimization Online. Unimodular Hypergraphs. ZIB-Report 17-27. cation by Rolling Stock Rotation Optimization. Prohaska, Jan Laufer (2017). Monte-Car- ZIB-Report 17-63. lo-based inversion scheme for 3-D quantita- Ingmar Schuster, Paul Constantine, Tim Sulli- Isabel Beckenbach (2017). A Hypergraph Net- tive photoacoustic tomography. In Proc. of van (2017). Exact active subspace Metropolis– work Simplex Algorithm. ZIB-Report 17-36. Ralf Borndörfer, Heide Hoppmann, Marika SPIE, Photons Plus Ultrasound: Imaging and Hastings, with applications to the Lorenz-96 Karbstein (2017). Umsteigen ohne Warten. Sensing 2017, volume 10064 of Proc. of SPIE, system. arXiv. https://arxiv.org/abs/1712.02749 Peter Benner, Sara Grundel, Christian ZIB-Report 17-05. pages 100645J–100645J–13. https://doi. Himpe, Christoph Huck, Tom Streubel, Caren org/10.1117/12.2251945 Feda Seblany, Ulrike Homberg, Eric Vincens, Tischendorf (2017). Gas Network Benchmark Thomas Breuer, Michael Bussieck, Karl-Kien Paul Winkler, Karl Josef Witt (2017). Merging Models. ZIB-Report 17-73. Cao, Felix Cebulla, Frederik Fiand, Hans Alexander Kuhn, Hans-Christian Hege (2017). criteria for the definition of a local pore and Christian Gils, Ambros Gleixner, Dmitry Khabi, Object-based visualization and evaluation the CSD computation of granular materials. In Mascha Berg, Julia Plöntzke, Sabine Leon- Thorsten Koch, Daniel Rehfeldt, Manuel of cloud-resolving simulations. In Book of Proceedings of the 25th meeting of the Work- hard-Marek, K.E. Müller, Susanna Röblitz Wetzel (2017). Optimizing Large-Scale Linear Abstracts, SCCS 2017 – Scaling Cascades in ing Group on Internal Erosion in embankment (2017). A dynamic model to simulate potassium Energy System Problems with Block Diagonal Complex Systems, Mar 27–29, 2017, Berlin, dams and their foundations, 150–159. balance in dairy cows. ZIB-Report 17-47. Structure by Using Parallel Interior-Point Germany. Methods. ZIB-Report 17-75. Cheng-Lung Wu, Stephen J. Maher (2017). Air- Timo Berthold, Michael Perregaard, Csaba Marian Moldenhauer, Martin Weiser, Stefan line scheduling and disruption management. Mészáros (2017). Four good reasons to use Hagen Chrapary, Wolfgang Dalitz, Winfried Zachow (2017). Adaptive Algorithms for In L. Budd, S. Ison, eds., Air transportation an Interior Point solver within a MIP solver. Neun, Wolfram Sperber (2017). Design, Optimal Hip Implant Positioning. PAMM, management: an international perspective, ZIB-Report 17-42. concepts, and state of the art of the swMATH 17(1):203–204. https://doi.org/10.1002/ 151–167, Routledge. service. ZIB-Report 17-11. pamm.201710071

92 2017 Annual Report Zuse Institute Berlin 93 ZIB Publications

Robert Clausecker (2017). Notes on the Con- Gerald Gamrath, Christoph Schubert (2017). Sebastian Götschel, Michael Minion (2017). Bernhard Kaplan, Jan Laufer, Steffen Pro- Lluis-Miquel Munguia, Geoffrey Oxberry, Ulrich-Peter Rohr, Pia Herrmann, Katharina struction of Pattern Databases. ZIB-Report Measuring the impact of branching rules for Parallel-in-Time for Parabolic Optimal Control haska, Jens Buchmann (2017). Monte-Car- Deepak Rajan, Yuji Shinano (2017). Parallel Ilm, Hai Zhang, Sabine Lohmann, Astrid Reiser, 17-59. mixed-integer programming. ZIB-Report Problems Using PFASST. ZIB-Report 17-51. lo-based inversion scheme for 3-D quantitative PIPS-SBB: Multi-Level Parallelism For Sto- Andrea Muranyi, Janice Smith, Susen Burock, 17-34. photoacoustic tomography. ZIB-Report 17-04. chastic Mixed-Integer Programs. ZIB-Report Marc Osterland, Katherine Leith, Shalini Peter Deuflhard (2017). The Grand Four. Martin Hammerschmidt, Sandra Döpking, 17-58. Singh, Patrick Brunhoeber, Rebecca Bower- ZIB-Report 17-70. Brady Gilg, Torsten Klug, Rosemarie Martiens- Sven Burger, Sebastian Matera (2017). Field David Knötel, Ronald Seidel, Steffen Prohaska, master, Jeanne Tie, Michael Christie, Hui-Li sen, Joseph Paat, Thomas Schlechte, Christof Heterogeneities and their Impact on Pho- Mason N. Dean, Daniel Baum (2017). Auto- Benjamin Müller, Renke Kuhlmann, Stefan Wong, Paul Waring, Kandavel Shanmugam, Belmiro P.M. Duarte, Guillaume Sagnol, Weng Schulz, Sinan Seymen, Alexander Tesch (2017). tocatalysis: Combining optical and kinetic mated Segmentation of Complex Patterns Vigerske (2017). On the performance of NLP Peter Gibbs, Ulrike Stein (2017). Prognostic Kee Wong (2017). An algorithm based on Conflict-Free Railway Track Assignment at Monte Carlo Simulations on the Nanoscale. in Biological Tissues: Lessons from Stingray solvers within global MINLP solvers. ZIB-Re- value of MACC1 and proficient mismatch Semidefinite Programming for finding mini- Depots. ZIB-Report 17-23. ZIB-Report 17-20. Tessellated Cartilage. ZIB-Report 17-62. port 17-35. repair status for recurrence risk prediction in max optimal designs. ZIB-Report 18-01. stage II colon cancer patients: the BIOGRID Ambros Gleixner, Leon Eifler, Tristan Gally, Martin Hammerschmidt, Martin Weiser, Péter Koltai, Christof Schütte (2017). A multi- Chavdar Papazov, Hans-Christian Hege studies. ZIB-Report 17-28. Belmiro P.M. Duarte, Guillaume Sagnol (2017). Gerald Gamrath, Patrick Gemander, Robert Xavier Garcia Santiago, Lin Zschiedrich, scale perturbation expansion approach for (2017). Blue-noise Optimized Point Sets Based Approximate and exact D-optimal designs for Lion Gottwald, Gregor Hendel, Christopher Bernd Bodermann, Sven Burger (2017). Markov state modeling of non-stationary on Procrustes Analysis. ZIB-Report 17-55. Guillaume Sagnol, Marco Blanco, Thibaut $2^k$ factorial experiments for Generalized Hojny, Thorsten Koch, Matthias Miltenberger, Quantifying parameter uncertainties in opti- molecular dynamics. ZIB-Report 17-49. Sauvage (2017). The Cone of Flow Matrices: Linear Models via SOCP. ZIB-Report 18-02. Benjamin Müller, Marc E. Pfetsch, Christian cal scatterometry using Bayesian inversion. Jannes Quer, Luca Donati, Bettina Keller, Approximation Hierarchies and Applications. Puchert, Daniel Rehfeldt, Franziska Schlösser, ZIB-Report 17-37. *Tobias Kramer, Matthias Noack, Daniel Baum, Marcus Weber (2017). An automatic adaptive ZIB-Report 17-32. Konstantin Fackeldey, Péter Koltai, Peter Felipe Serrano, Yuji Shinano, Jan Merlin Hans-Christian Hege, Eric J. Heller (2017). importance sampling algorithm for molecular Névir, Henning Rust, Axel Schild, Marcus Viernickel, Stefan Vigerske, Dieter Weninger, Carsten Hartmann, Lorenz Richter, Christof Dust and gas emission from cometary nuclei: dynamics in reaction coordinates. ZIB-Report Stanley Schade, Ralf Borndörfer, Matthias Weber (2017). From Metastable to Coherent Jonas T. Witt, Jakob Witzig (2017). The SCIP Schütte, Wei Zhang (2017). Variational the case of comet 67P/Churyumov-Gerasi- 17-09. Breuer, Boris Grimm, Markus Reuther, Thomas Sets – time-discretization schemes. ZIB-Re- Optimization Suite 5.0. ZIB-Report 17-61. characterization of free energy: Theory and menko. ZIB-Report 17-78. (Joint publication: Schlechte, Patrick Siebeneicher (2017). port 17-74. algorithms. ZIB-Report 17-52. Visual Data Analysis, Distributed Algorithms, Jannes Quer, Han Lie (2017). Some connec- Pattern Detection For Large-Scale Railway Ambros Gleixner, Stephen J. Maher, Ben- and Supercomputing) tions between importance sampling and Timetables. ZIB-Report 17-17. Frank Fischer, Thomas Schlechte (2017). jamin Müller, João Pedro Pedroso (2017). Felix Hennings (2017). Benefits and Limitations enhanced sampling methods in molecular Strong Relaxations for the Train Timetabling Exact Methods for Recursive Circle Packing. of Simplified Transient Gas Flow Formulations. Alexander Lange, Robert Schwieger, Julia dynamics. ZIB-Report 17-30. Stanley Schade, Thomas Schlechte, Jakob Problem using Connected Configurations. ZIB-Report 17-07. ZIB-Report 17-39. Plöntzke, Stefan Schäfer, Susanna Röblitz Witzig (2017). Structure-based Decomposition ZIB-Report 17-46. (2017). Follicular competition: the selection Daniel Rehfeldt, Thorsten Koch (2017). Com- for Pattern-Detection for Railway Timetables. Andreas Griewank, Richard Hasenfelder, Benjamin Hiller, Thorsten Koch, Lars Schewe, of dominant follicles as a synergistic effect. bining NP-Hard Reduction Techniques and ZIB-Report 17-40. Lisa Fischer, Sebastian Götschel, Martin Manuel Radons, Lutz Lehmann, Tom Streubel Robert Schwarz, Jonas Schweiger (2017). A ZIB-Report 17-21. Strong Heuristics in an Exact Algorithm for Weiser (2017). Lossy data compression (2017). Integrating Lipschitzian Dynamical System to Evaluate Gas Network Capacities: the Maximum-Weight Connected Subgraph Yuji Shinano (2017). The Ubiquity Generator reduces communication time in hybrid Systems using Piecewise Algorithmic Differ- Concepts and Implementation. ZIB-Report Stephen J. Maher, Tobias Fischer, Tristan Problem. ZIB-Report 17-45. Framework: 7 Years of Progress in Paralleliz- time-parallel integrators. ZIB-Report 17-25. entiation. ZIB-Report 17-44. 17-03. Gally, Gerald Gamrath, Ambros Gleixner, Rob- ing Branch-and-Bound. ZIB-Report 17-60. ert Lion Gottwald, Gregor Hendel, Thorsten Daniel Rehfeldt, Thorsten Koch (2017). Hildegard Franck, Stefan Lohrum, Jannis Boris Grimm, Ralf Borndörfer, Markus Ulrike Homberg, Daniel Baum, Steffen Pro- Koch, Marco E. Lübbecke, Matthias Milten- Generalized preprocessing techniques for Jan Skrzypczak (2017). Weakening Paxos Polojannis (2017). Automatisierte Fernleihe Reuther, Stanley Schade, Thomas Schlechte haska, Jens Günster, Stefanie Krauß-Schüler berger, Benjamin Müller, Marc E. Pfetsch, Steiner tree and maximum-weight connected Consensus Sequences for Commutative im KOBV – Handbuch für Bibliotheken – 5. (2017). A Propagation Approach to Acyclic (2017). Adapting trabecular structures for Christian Puchert, Daniel Rehfeldt, Sebastian subgraph problems. ZIB-Report 17-57. Commands. ZIB-Report 17-64. Auflage. ZIB-Report 17-01. Rolling Stock Rotation Optimization. ZIB-Re- 3-D printing: an image-processing approach Schenker, Robert Schwarz, Felipe Serrano, port 17-24. based on µCT data. ZIB-Report 17-26. Yuji Shinano, Dieter Weninger, Jonas T. Witt, Malte Renken, Amin Ahmadi, Ralf Borndörfer, Tom Streubel, Christian Strohm, Philipp Jakob Witzig (2017). The SCIP Optimization Guvenc Sahin, Thomas Schlechte (2017). Trunschke, Caren Tischendorf (2017). Generic Yvonne Freytag (2017). Optimal Experimental Suite 4.0. ZIB-Report 17-12. Design to Estimate the Time of Death in a Pooja Gupta, Annika Gramatke, Ralf Einspan- Robert Joachimsky, Felix Ambellan, Stefan Demand-Driven Line Planning with Selfish Construction and Efficient Evaluation of Bayesian Context. ZIB-Report 17-14. ier, Christof Schütte, Max von Kleist, Jutta Zachow (2017). Computerassistierte Aus- Routing. ZIB-Report 17-38. Network DAEs and Their Derivatives in the Sharbati (2017). In silicio cytotoxicity assess- wahl und Platzierung von interpositionalen Matthias Miltenberger, Ted Ralphs, Daniel Context of Gas Networks. ZIB-Report 17-41. ment on cultured rat intestinal cells deduced Steffy (2017). Exploring the Numerics of Gerald Gamrath, Timo Berthold, Stefan Heinz, Spacern zur Behandlung früher Gonarthrose. from cellular impedance measurements. ZIB-Report 17-72. Branch-and-Cut for Mixed-Integer Linear Tom Walther, Benjamin Hiller, René Saiten- Michael Winkler (2017). Structure-driven ZIB-Report 17-08. Optimization. ZIB-Report 17-43. fix-and-propagate heuristics for mixed-inte- macher (2017). Polyhedral 3-D Models for ger programming. ZIB-Report 17-56. compressors in gas networks. ZIB-Report 17-66.

94 2017 Annual Report Zuse Institute Berlin 95 ZIB Publications

Marcus Weber, Konstantin Fackeldey, Chris- Stefanie Winkelmann, Christof Schütte (2017). Wei Zhang, Christof Schütte (2017). Reliable tof Schütte (2017). Set-free Markov State Hybrid Models for Chemical Reaction Net- approximation of long relaxation timescales in Building. ZIB-Report 17-10. works: Multiscale Theory and Application to molecular dynamics. ZIB-Report 17-19. Gene Regulatory Systems. ZIB-Report 17-29. Marcus Weber (2017). Eigenvalues of non-re- Yulia Zhukova, Christian Hiepen, Petra Knaus, versible Markov chains – A case study. ZIB-Re- Jakob Witzig (2017). Conflict-Driven Diving Marc Osterland, Steffen Prohaska, John W. C. port 17-13. for Mixed-Integer Programming. ZIB-Report Dunlop, Peter Fratzl, Ekaterina V. Skorb (2017). 17-69. The role of titanium surface nanotopography *Martin Weiser, Bodo Erdmann, Sebastian on preosteoblast morphology, adhesion, and Schenkl, Holger Muggenthaler, Michael Thomas Wolf, Chimaobi Amadi (2017). Ratio- migration. ZIB-Report 17-06. Hubig, Gita Mall, Stefan Zachow (2017). Uncer- nal Solutions of Underdetermined Polynomial tainty in Temperature-Based Determination Equations. ZIB-Report 17-33. *Open Access als strategische Leitlinie des of Time of Death. ZIB-Report 17-18. (Joint KOBV. ZIB-Report 17-54. (Joint publication: publication: Numerical Mathematics, Visual Mathematical Optimization, Scientific Infor- Data Analysis) mation)

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98 2017 Annual Report Zuse Institute Berlin 99 References

DUSTING OFF COMETARY SURFACES

[1] T. Kramer, M. Noack, D. Baum, H.-C. Hege, E.J. Heller. Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko. Advances in Physics X, 3, 1404436 (2018). http://dx.doi.org/10.1080/23746149.2017.140 4436.

[2] T. Kramer, M. Noack. On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/ Churyumov-Gerasimenko. The Astrophysical Journal Letters, 823, L11 (2016). https://doi. org/10.3847/2041-8205/823/1/L11.

[3] T. Kramer, M. Läuter, M. Rubin, K. Alt- wegg. Seasonal changes of the volatile density in the coma and on the surface of comet 67P/ Churyumov-Gerasimenko. Monthly Notices of the Royal Astronomical Society, 469, S20–S28 (2017). https://doi.org/10.1093/mnras/stx866.

[4] J.B. Vincent, M.F. A’Hearn et al. Summer fireworks on comet 67P. Monthly Notices of the Royal Astronomical Society, 462, S184– S194 (2016). https://doi.org/10.1093/mnras/ stw2409.

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