- An erasure-resilient and compute-efficient coding scheme for storage applications (2013)
- Driven by rapid technological advancements, the amount of data that is created, captured, communicated, and stored worldwide has grown exponentially over the past decades. Along with this development it has become critical for many disciplines of science and business to being able to gather and analyze large amounts of data. The sheer volume of the data often exceeds the capabilities of classical storage systems, with the result that current large-scale storage systems are highly distributed and are comprised of a high number of individual storage components. As with any other electronic device, the reliability of storage hardware is governed by certain probability distributions, which in turn are influenced by the physical processes utilized to store the information. The traditional way to deal with the inherent unreliability of combined storage systems is to replicate the data several times. Another popular approach to achieve failure tolerance is to calculate the block-wise parity in one or more dimensions. With better understanding of the different failure modes of storage components, it has become evident that sophisticated high-level error detection and correction techniques are indispensable for the ever-growing distributed systems. The utilization of powerful cyclic error-correcting codes, however, comes with a high computational penalty, since the required operations over finite fields do not map very well onto current commodity processors. This thesis introduces a versatile coding scheme with fully adjustable fault-tolerance that is tailored specifically to modern processor architectures. To reduce stress on the memory subsystem the conventional table-based algorithm for multiplication over finite fields has been replaced with a polynomial version. This arithmetically intense algorithm is better suited to the wide SIMD units of the currently available general purpose processors, but also displays significant benefits when used with modern many-core accelerator devices (for instance the popular general purpose graphics processing units). A CPU implementation using SSE and a GPU version using CUDA are presented. The performance of the multiplication depends on the distribution of the polynomial coefficients in the finite field elements. This property has been used to create suitable matrices that generate a linear systematic erasure-correcting code which shows a significantly increased multiplication performance for the relevant matrix elements. Several approaches to obtain the optimized generator matrices are elaborated and their implications are discussed. A Monte-Carlo-based construction method allows it to influence the specific shape of the generator matrices and thus to adapt them to special storage and archiving workloads. Extensive benchmarks on CPU and GPU demonstrate the superior performance and the future application scenarios of this novel erasure-resilient coding scheme.
- Refactoring the UrQMD model for many-core architectures (2013)
- Ultrarelativistic Quantum Molecular Dynamics is a physics model to describe the transport, collision, scattering, and decay of nuclear particles. The UrQMD framework has been in use for nearly 20 years since its first development. In this period computing aspects, the design of code, and the efficiency of computation have been minor points of interest. Nowadays an additional issue arises due to the fact that the run time of the framework does not diminish any more with new hardware generations. The current development in computing hardware is mainly focused on parallelism. Especially in scientific applications a high order of parallelisation can be achieved due to the superposition principle. In this thesis it is shown how modern design criteria and algorithm redesign are applied to physics frameworks. The redesign with a special emphasise on many-core architectures allows for significant improvements of the execution speed. The most time consuming part of UrQMD is a newly introduced relativistic hydrodynamic phase. The algorithm used to simulate the hydrodynamic evolution is the SHASTA. As the sequential form of SHASTA is successfully applied in various simulation frameworks for heavy ion collisions its possible parallelisation is analysed. Two different implementations of SHASTA are presented. The first one is an improved sequential implementation. By applying a more concise design and evading unnecessary memory copies, the execution time could be reduced to the half of the FORTRAN version’s execution time. The usage of memory could be reduced by 80% compared to the memory needed in the original version. The second implementation concentrates fully on the usage of many-core architectures and deviates significantly from the classical implementation. Contrary to the sequential implementation, it follows the recalculate instead of memory look-up paradigm. By this means the execution speed could be accelerated up to a factor of 460 on GPUs. Additionally a stability analysis of the UrQMD model is presented. Applying metapro- gramming UrQMD is compiled and executed in a massively parallel setup. The resulting simulation data of all parallel UrQMD instances were hereafter gathered and analysed. Hence UrQMD could be proven of high stability to the uncertainty of experimental data. As a further application of modern programming paradigms a prototypical implementa- tion of the worldline formalism is presented. This formalism allows for a direct calculation of Feynman integrals and constitutes therefore an interesting enhancement for the UrQMD model. Its massively parallel implementation on GPUs is examined.
- On development, feasibility, and limits of highly efficient CPU and GPU programs in several fields (2013)
- With processor clock speeds having stagnated, parallel computing architectures have achieved a breakthrough in recent years. Emerging many-core processors like graphics cards run hundreds of threads in parallel and vector instructions are experiencing a revival. Parallel processors with many independent but simple arithmetical logical units fail executing serial tasks efficiently. However, their sheer parallel processing power makes them predestined for parallel applications while the simple construction of their cores makes them unbeatably power efficient. Unfortunately, old programs cannot profit by simple recompilation. Adaptation often requires rethinking and modifying algorithms to make use of parallel execution. Many applications have some serial subroutines which are very hard to parallelize, hence contemporary compute clusters are often homogeneous, offering fast processors for serial tasks and parallel processors for parallel tasks. In order not to waste the available compute power, highly efficient programs are mandatory. This thesis is about the development of fast algorithms and their implementations on modern CPUs and GPUs, about the maximum achievable efficiency with respect to peak performance and to power consumption respectively, and about feasibility and limits of programs for CPUs, GPUs, and heterogeneous systems. Three totally different applications from distinct fields, which were developed in the extent of this thesis, are presented. The ALICE experiment at the LHC particle collider at CERN studies heavy-ion collisions at high rates of several hundred Hz, while every collision produces thousands of particles, whose trajectories must be reconstructed. For this purpose, ALICE track reconstruction and ALICE track merging have been adapted for GPUs and deployed on 64 GPU-enabled compute-nodes at CERN. After a testing phase, the tracker ran in nonstop operation during 2012 providing full real-time track reconstruction. The tracker employs a multithreaded pipeline as well as asynchronous data transfer to ensure continuous GPU utilization and outperforms the fastest available CPUs by about a factor three. The Linpack benchmark is the standard tool for ranking compute clusters. It solves a dense system of linear equations using primarily matrix multiplication facilitated by a routine called DGEMM. A heterogeneous GPU-enabled version of DGEMM and Linpack has been developed, which can utilize the CAL, CUDA, and OpenCL APIs as backend. Employing this implementation, the LOEWE-CSC cluster ranked place 22 in the November 2010 Top500 list of the fastest supercomputers, and the Sanam cluster achieved the second place in the November 2012 Green500 list of the most power efficient supercomputers. An elaborate lookahead algorithm, a pipeline, and asynchronous data transfer hide the serial CPU-bound tasks of Linpack behind DGEMM execution on the GPU reaching the highest efficiency on GPU-accelerated clusters. Failure erasure codes enable failure tolerant storage of data and real-time failover, ensuring that in case of a hardware defect servers and even complete data centers remain operational. It is an absolute necessity for present-day computer infrastructure. The mathematical theory behind the codes involves matrix-computations in finite fields, which are not natively supported by modern processors and hence computationally very expensive. This thesis presents a novel scheme for fast encoding matrix generation and demonstrates a fast implementation for the encoding itself, which uses exclusively either integer or logical vector instructions. Depending on the scenario, it is always hitting different hard limits of the hardware: either the maximum attainable memory bandwidth, or the peak instruction throughput, or the PCI Express bandwidth limit when GPUs or FPGAs are used. The thesis demonstrates that in most cases with respect to the available peak performance, GPU implementations can be as efficient as their CPU counterparts. With respect to costs or power consumption, they are much more efficient. For this purpose, complex tasks must be split in serial as well as parallel parts and the execution must be pipelined such that the CPU bound tasks are hidden behind GPU execution. Few cases are identified where this is not possible due to PCI Express limitations or not reasonable because practical GPU languages are missing.
- On-line reconstruction algorithms for the CBM and ALICE experiments (2013)
- This thesis presents various algorithms which have been developed for on-line event reconstruction in the CBM experiment at GSI, Darmstadt and the ALICE experiment at CERN, Geneve. Despite the fact that the experiments are different — CBM is a fixed target experiment with forward geometry, while ALICE has a typical collider geometry — they share common aspects when reconstruction is concerned. The thesis describes: — general modifications to the Kalman filter method, which allows one to accelerate, to improve, and to simplify existing fit algorithms; — developed algorithms for track fit in CBM and ALICE experiment, including a new method for track extrapolation in non-homogeneous magnetic field. — developed algorithms for primary and secondary vertex fit in the both experiments. In particular, a new method of reconstruction of decayed particles is presented. — developed parallel algorithm for the on-line tracking in the CBM experiment. — developed parallel algorithm for the on-line tracking in High Level Trigger of the ALICE experiment. — the realisation of the track finders on modern hardware, such as SIMD CPU registers and GPU accelerators. All the presented methods have been developed by or with the direct participation of the author.
- Commissioning of the ALICE High-Level Trigger (2012)
- A new era in experimental nuclear physics has begun with the start-up of the Large Hadron Collider at CERN and its dedicated heavy-ion detector system ALICE. Measuring the highest energy density ever produced in nucleus-nucleus collisions, the detector has been designed to study the properties of the created hot and dense medium, assumed to be a Quark-Gluon Plasma. Comprised of 18 high granularity sub-detectors, ALICE delivers data from a few million electronic channels of proton-proton and heavy-ion collisions. The produced data volume can reach up to 26 GByte/s for central Pb–Pb collisions at design luminosity of L = 1027 cm−2 s−1 , challenging not only the data storage, but also the physics analysis. A High-Level Trigger (HLT) has been built and commissioned to reduce that amount of data to a storable value prior to archiving with the means of data filtering and compression without the loss of physics information. Implemented as a large high performance compute cluster, the HLT is able to perform a full reconstruction of all events at the time of data-taking, which allows to trigger, based on the information of a complete event. Rare physics probes, with high transverse momentum, can be identified and selected to enhance the overall physics reach of the experiment. The commissioning of the HLT is at the center of this thesis. Being deeply embedded in the ALICE data path and, therefore, interfacing all other ALICE subsystems, this commissioning imposed not only a major challenge, but also a massive coordination effort, which was completed with the first proton-proton collisions reconstructed by the HLT. Furthermore, this thesis is completed with the study and implementation of on-line high transverse momentum triggers.
- Conceptual design of an ALICE Tier-2 centre integrated into a multi-purpose computing facility (2012)
- This thesis discusses the issues and challenges associated with the design and operation of a data analysis facility for a high-energy physics experiment at a multi-purpose computing centre. At the spotlight is a Tier-2 centre of the distributed computing model of the ALICE experiment at the Large Hadron Collider at CERN in Geneva, Switzerland. The design steps, examined in the thesis, include analysis and optimization of the I/O access patterns of the user workload, integration of the storage resources, and development of the techniques for effective system administration and operation of the facility in a shared computing environment. A number of I/O access performance issues on multiple levels of the I/O subsystem, introduced by utilization of hard disks for data storage, have been addressed by the means of exhaustive benchmarking and thorough analysis of the I/O of the user applications in the ALICE software framework. Defining the set of requirements to the storage system, describing the potential performance bottlenecks and single points of failure and examining possible ways to avoid them allows one to develop guidelines for selecting the way how to integrate the storage resources. The solution, how to preserve a specific software stack for the experiment in a shared environment, is presented along with its effects on the user workload performance. The proposal for a flexible model to deploy and operate the ALICE Tier-2 infrastructure and applications in a virtual environment through adoption of the cloud computing technology and the 'Infrastructure as Code' concept completes the thesis. Scientific software applications can be efficiently computed in a virtual environment, and there is an urgent need to adapt the infrastructure for effective usage of cloud resources.