The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’)

Facilitate SIMD-Code-Generation in the Polyhedral Model by Hardware-aware Automatic Code-Transformation

Although Single Instruction Multiple Data (SIMD) units are available in general purpose processors already since the 1990s, state-of-the-art compilers are often still not capable to fully exploit them, i.e., they may miss to achieve the best possible performance. We present a new hardware-aware and adaptive loop tiling approach that is based on polyhedral transformations and explicitly dedicated to improve on auto-vectorization. It is an extension to the tiling algorithm implemented within the PluTo framework. In its default setting, PluTo uses static tile sizes and is already capable to enable the use of SIMD units but not primarily targeted to optimize it. We experimented with different tile sizes and found a strong relationship between their choice, cache size parameters and performance. Based on this, we designed an adaptive procedure that specifically tiles vectorizable loops with dynamically calculated sizes. The blocking is automatically fitted to the amount of data read in loop iterations, the available SIMD units and the cache sizes. The adaptive parts are built upon straightforward calculations that are experimentally verified and evaluated. Our results show significant improvements in the number of instructions vectorized, cache miss rates and, finally, running times

Facilitate SIMD-Code-Generation in the Polyhedral Model by Hardware-aware Automatic Code-Transformation

Although Single Instruction Multiple Data (SIMD) units are available in general purpose processors already since the 1990s, state-of-the-art compilers are often still not capable to fully exploit them, i.e., they may miss to achieve the best possible performance. We present a new hardware-aware and adaptive loop tiling approach that is based on polyhedral transformations and explicitly dedicated to improve on auto-vectorization. It is an extension to the tiling algorithm implemented within the PluTo framework. In its default setting, PluTo uses static tile sizes and is already capable to enable the use of SIMD units but not primarily targeted to optimize it. We experimented with different tile sizes and found a strong relationship between their choice, cache size parameters and performance. Based on this, we designed an adaptive procedure that specifically tiles vectorizable loops with dynamically calculated sizes. The blocking is automatically fitted to the amount of data read in loop iterations, the available SIMD units and the cache sizes. The adaptive parts are built upon straightforward calculations that are experimentally verified and evaluated. Our results show significant improvements in the number of instructions vectorized, cache miss rates and, finally, running times

Pure functions in C: A small keyword for automatic parallelization

© 2017 IEEE. The need for parallel task execution has been steadily growing in recent years since manufacturers mainly improve processor performance by scaling the number of installed cores instead of the frequency of processors. To make use of this potential, an essential technique to increase the parallelism of a program is to parallelize loops. However, a main restriction of available tools for automatic loop parallelization is that the loops often have to be 'polyhedral' and that it is, e.g., not allowed to call functions from within the loops.In this paper, we present a seemingly simple extension to the C programming language which marks functions without side-effects. These functions can then basically be ignored when checking the parallelization opportunities for polyhedral loops. We extended the GCC compiler toolchain accordingly and evaluated several real-world applications showing that our extension helps to identify additional parallelization chances and, thus, to significantly enhance the performance of applications

Impact of the Scheduling Strategy in Heterogeneous Systems That Provide Co-Scheduling

ABSTRACT In recent years, the number of processing units per compute node has been increasing. In order to utilize all or most of the available resources of a high-performance computing cluster, at least some of its nodes will have to be shared by several applications at the same time. Yet, even if jobs are co-scheduled on a node, it can happen that high performance resources remain idle, although there are jobs that could make use of them (e. g. if the resource was temporarily blocked when the job was started). Heterogeneous schedulers, which schedule tasks for different devices, can bind jobs to resources in a way that can significantly reduce the idle time. Typically, those schedulers make their decisions based on a static strategy. In this paper, we investigate the impact if a heterogeneous scheduler allows modifications of the strategies at runtime. For a set of applications, we determine the makespan and show how it is influenced by four different scheduling strategies. A well-chosen strategy can result in a speedup of more the 2.5 in comparison to other strategies

Non-equilibrium molecular dynamics study of an amphiphilic model system

Diese Doktorarbeit untersucht das Verhalten von komplexenFluidenunter Scherung, insbesondere den Einfluss von Scherflüssenauf dieStrukturbildung.Dazu wird ein Modell dieser entworfen, welches imRahmen von Molekulardynamiksimulationen verwendet wird.Zunächst werden Gleichgewichtseigenschaften dieses Modellsuntersucht. Hierbei wird unter anderem die Lage desOrdnungs--Unordnungsübergangs von derisotropen zur lamellaren Phase der Dimere bestimmt.Der Einfluss von Scherflüssen auf diese lamellare Phase wirdnununtersucht und mit analytischen Theorien verglichen. Die Scherung einer parallelen lamellaren Phase ruft eineNeuausrichtung des Direktors in Flussrichtung hervor.Das verursacht eine Verminderung der Schichtdicke mitsteigender Scherrateund führt oberhalb eines Schwellwertes zu Ondulationen.Ein vergleichbares Verhalten wird auch in lamellarenSystemengefunden, an denen in Richtung des Direktors gezogen wird.Allerdings wird festgestellt, dass die Art der Bifurkationenin beidenFällen unterschiedlich ist.Unter Scherung wird ein Übergang von Lamellen parallelerAusrichtung zu senkrechter gefunden.Dabei wird beoachtet, dass die Scherspannung in senkrechterOrientierungniedriger als in der parallelen ist.Dies führt unter bestimmten Bedingungen zum Auftreten vonScherbändern, was auch in Simulationen beobachtet wird. Es ist gelungen mit einem einfachen Modell viele Apsekte desVerhalten vonkomplexen Fluiden wiederzugeben. Die Strukturbildung hängt offensichtlich nurbedingt von lokalen Eigenschaften der Moleküle ab.This thesis is concerned with the behavior of complex fluidsunder shear flows, especially the influence on structureformation.A model of such fluid is developed, which is later used inthe scopeof molecular dynamics (MD) simulations.First equilibrium properties of model are investigated.Then order--disorder transition of a dimer--melt is locatedandinfluence of shear on the lamellar phase is studied.Results are compared to appropriate analytical theories. Shear on parallel oriented lamellae causes a flow alignmentof the director.This alignment leads to a shrinkage in the layer thicknessand above a certain threshold to undulation of the layers.A similar behavior is also found in dilatation simulationsbut thebifurcation at the onset is here different.A transition from a parallel to a perpendicular orientationis alsofound. The shear stress of the perpendicular oriented sampleis lowerthan the shear stress found in the parallel orientation atsame strain rates. This may lead to shear bands which are observed as acoexistence of isotropic and perpendicular regionsexhibitingdifferent local strain rates.This thesis succeeds in describing the essential physics ofspecialcomplex fluids under shear flow with a simple andcomputationalefficient model

The LAMA Approach for Writing Portable Applications on Heterogenous Architectures

Ensuring longevity and maintainability of modern software applications is mandatory for a proper return on investment. Since the hardware landscape is changing rapidly and will continue to do so, it is imperative to take on those topics also in the HPC (High Performance Computing, uses parallel processing for running advanced application programs efficiently.) domain where applications traditionally have a long live-span. For recent years, we have observed a trend towards more and more heterogeneous systems in computing. Realizing the performance promises of the hardware vendors is a huge challenge to the software developer. Portability is the second challenge to be met in this context. In this paper we present our library LAMA (Library for Accelerated Math Applications). LAMA is a framework for developing hardware-independent, high performance code for heterogeneous computing systems. We created this library to address both challenges successfully in the realm of linear algebra and numerical mathematics. We introduce our solutions to heterogeneous memory and kernel management as well as our solutions to task parallelism. In the end we do performance and scalability benchmarks drawing a comparison to PETSc (Portable, Extensible Toolkit for Scientific Computation, open-source project developed at the Argonne National Laboratory.) for the example of a CG (Conjugate Gradient method, an algorithm for the numerical solution of particular systems of linear equations) solver

Method and computer program for determining a placement of at least one circuit for a reconfigurable logic device

Embodiments relate to a method and computer program for determining a placement of at least one circuit for a reconfigurable logic device. The method comprises obtaining (110) information related to the at least one circuit. The at least one circuit comprises a plurality of blocks and a plurality of connections between the plurality of blocks. The plurality of blocks comprise a plurality of logic blocks. The method further comprises calculating (120) a circuit graph based on the information related to the at least one circuit. The circuit graph comprises a plurality of nodes and a plurality of edges. The plurality of nodes represent at least a subset of the plurality of blocks of the at least one circuit and wherein the plurality of edges represent at least a subset of the plurality of connections between the plurality of blocks of the at least one circuit. The method further comprises determining (130) a force-directed layout of the circuit graph. The force-directed layout is based on attractive forces based on the plurality of connections between the plurality of blocks and based on repulsive forces between the plurality of blocks. The method further comprises determining (140) a placement of the plurality of logic blocks onto a plurality of available logic cells of the reconfigurable logic device based on the force-directed layout of the circuit graph

A Data Management System for UNICORE 6

Data produced in scientic and industrial applications is growing exponentially but most resource middleware systems lack of appropriate support for data and metadata management. In particular easy and intuitive retrieval of data for later use is a serious problem. In this context the paper proposes a pragmatic approach for data management of distributed data with focus on appropriate means for data organization improving data retrieval. The paper presents the key concepts and architecture of a dedicated data management system for sharing data located on heterogeneous storage resources. The dierent specics of storage systems such as data object names, data locations, and data access methods are abstracted to allow transparent data access. Moreover, the system provides means for data structuring and organization by supporting custom data models and annotation of individual metadata on data objects. Current development status of the system is illustrated by presenting an integration with the UNICORE Rich Client which has been validated in the context of the AeroGrid project