An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes.Comment: SC17 conference paper, 12 pages, 7 figure

Deconfinement critical point of lattice QCD with Nf=2N_{\rm f}=2 Wilson fermions

The ${\rm SU}(3)$ pure gauge theory exhibits a first-order thermal deconfinement transition due to spontaneous breaking of its global $Z_3$ center symmetry. When heavy dynamical quarks are added, this symmetry is broken explicitly and the transition weakens with decreasing quark mass until it disappears at a critical point. We compute the critical hopping parameter and the associated pion mass for lattice QCD with $N_f=2$ degenerate standard Wilson fermions on $N_\tau\in\{6,8,10\}$ lattices, corresponding to lattice spacings $a=0.12\, {\rm fm}$, $a=0.09\, {\rm fm}$, $a=0.07\, {\rm fm}$, respectively. Significant cut-off effects are observed, with the first-order region growing as the lattice gets finer. While current lattices are still too coarse for a continuum extrapolation, we estimate $m_\pi^c\approx 4 {\rm GeV}$ with a remaining systematic error of $\sim 20\%$. Our results allow to assess the accuracy of the LO and NLO hopping expanded fermion determinant used in the literature for various purposes. We also provide a detailed investigation of the statistics required for this type of calculation, which is useful for similar investigations of the chiral transition.Comment: 12 pages, 6 figures, minor changes to match the version published in PR

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Three-Dimensional Processing-In-Memory-Architectures: A Holistic Tool For Modeling And Simulation

Die gemeinhin als Memory Wall bekannte, sich stetig weitende Leistungslücke zwischen Prozessor- und Speicherarchitekturen erfordert neue Konzepte, um weiterhin eine Skalierung der Rechenleistung zu ermöglichen. Da Speicher als die Beschränkung innerhalb einer Von-Neumann-Architektur identifiziert wurden, widmet sich die Arbeit dieser Problemstellung. Obgleich dreidimensionale Speicher zu einer Linderung der Memory Wall beitragen können, sind diese alleinig für die zukünftige Skalierung ungenügend. Aufgrund höherer Effizienzen stellt die Integration von Rechenkapazität in den Speicher (Processing-In-Memory, PIM) ein vielversprechender Ausweg dar, jedoch existiert ein Mangel an PIM-Simulationsmodellen. Daher wurde ein flexibles Simulationswerkzeug für dreidimensionale Speicherstapel geschaffen, welches zur Modellierung von dreidimensionalen PIM erweitert wurde. Dieses kann Speicherstapel wie etwa Hybrid Memory Cube standardkonform simulieren und bietet zugleich eine hohe Genauigkeit indem auf elementaren Datenpaketen in Kombination mit dem Hardware validierten Simulator BOBSim modelliert wird. Ein eigens entworfener Simulationstaktbaum ermöglicht zugleich eine schnelle Ausführung. Messungen weisen im funktionalen Modus eine 100-fache Beschleunigung auf, wohingegen eine Verdoppelung der Ausführungsgeschwindigkeit mit Taktgenauigkeit erzielt wird. Anhand eines eigens implementierten, binärkompatiblen GPU-Beschleunigers wird die Modellierung einer vollständig dreidimensionalen PIM-Architektur demonstriert. Dabei orientieren sich die maximalen Hardwareressourcen an einem PIM-Beschleuniger aus der Literatur. Evaluiert wird einerseits das GPU-Simulationsmodell eigenständig, andererseits als PIM-Verbund jeweils mit Hilfe einer repräsentativ gewählten, speicherbeschränkten geophysikalischen Bildverarbeitung. Bei alleiniger Betrachtung des GPU-Simulationsmodells weist dieses eine signifikant gesteigerte Simulationsgeschwindigkeit auf, bei gleichzeitiger Abweichung von 6% gegenüber dem Verilator-Modell. Nachfolgend werden innerhalb dieser Arbeit unterschiedliche Konfigurationen des integrierten PIM-Beschleunigers evaluiert. Je nach gewählter Konfiguration kann der genutzte Algorithmus entweder bis zu 140GFLOPS an tatsächlicher Rechenleistung abrufen oder eine maximale Recheneffizienz von synthetisch 30% bzw. real 24,5% erzielen. Letzteres stellt eine Verdopplung des Stands der Technik dar. Eine anknüpfende Diskussion erläutert eingehend die Resultate.The steadily widening performance gap between processor- and memory-architectures - commonly known as the Memory Wall - requires novel concepts to achieve further scaling in processing performance. As memories were identified as the limitation within a Von-Neumann-architecture, this work addresses this constraining issue. Although three-dimensional memories alleviate the effects of the Memory Wall, the sole utilization of such memories would be insufficient. Due to higher efficiencies, the integration of processing capacity into memories (so-called Processing-In-Memory, PIM) depicts a promising alternative. However, a lack of PIM simulation models still remains. As a consequence, a flexible simulation tool for three-dimensional stacked memories was established, which was extended for modeling three-dimensional PIM architectures. This tool can simulate stacked memories such as Hybrid Memory Cube standard-compliant and simultaneously offers high accuracy by modeling on elementary data packets (FLIT) in combination with the hardware validated BOBSim simulator. To this, a specifically designed simulation clock tree enables an rapid simulation execution. A 100x speed up in simulation execution can be measured while utilizing the functional mode, whereas a 2x speed up is achieved during clock-cycle accuracy mode. With the aid of a specifically implemented, binary compatible GPU accelerator and the established tool, the modeling of a holistic three-dimensional PIM architecture is demonstrated within this work. Hardware resources used were constrained by a PIM architecture from literature. A representative, memory-bound, geophysical imaging algorithm was leveraged to evaluate the GPU model as well as the compound PIM simulation model. The sole GPU simulation model depicts a significantly improved simulation performance with a deviation of 6% compared to a Verilator model. Subsequently, various PIM accelerator configurations with the integrated GPU model were evaluated. Depending on the chosen PIM configuration, the utilized algorithm achieves 140GFLOPS of processing performance or a maximum computing efficiency of synthetically 30% or realistically 24.5%. The latter depicts a 2x improvement compared to state-of-the-art. A following discussion showcases the results in depth