April 8, 1984

Abstract. Distributed Hash Tables (DHTs) enable fully distributed Peer-to-Peer network construction and maintenance with name-driven routing. There exist very few DHT approaches that consider heterogeneity of nodes inside the construction process or properly serve data of different load. To our best knowledge, there is no construction which smoothly addresses both these issues. We propose a Peer-to-Peer construction that explicitly uses heterogeneity to simplify the routing and maintenance process even in the presence of an adaptive adversary. Using a hypercube and cube connected cycles networks as a backbone, we show how to cope with two types of heterogeneity: one for nodes and one for data

GekkoFS: A temporary distributed file system for HPC applications

We present GekkoFS, a temporary, highly-scalable burst buffer file system which has been specifically optimized for new access patterns of data-intensive High-Performance Computing (HPC) applications. The file system provides relaxed POSIX semantics, only offering features which are actually required by most (not all) applications. It is able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes, significantly outperforming the capabilities of general-purpose parallel file systems.The work has been funded by the German Research Foundation (DFG) through the ADA-FS project as part of the Priority Programme 1648. It is also supported by the Spanish Ministry of Science and Innovation (TIN2015–65316), the Generalitat de Catalunya (2014–SGR–1051), as well as the European Union’s Horizon 2020 Research and Innovation Programme (NEXTGenIO, 671951) and the European Comission’s BigStorage project (H2020-MSCA-ITN-2014-642963). This research was conducted using the supercomputer MOGON II and services offered by the Johannes Gutenberg University Mainz.Peer ReviewedPostprint (author's final draft

Quantum Circuit Compiler for a Shuttling-Based Trapped-Ion Quantum Computer

The increasing capabilities of quantum computing hardware and the challenge of realizing deep quantum circuits require fully automated and efficient tools for compiling quantum circuits. To express arbitrary circuits in a sequence of native gates specific to the quantum computer architecture, it is necessary to make algorithms portable across the landscape of quantum hardware providers. In this work, we present a compiler capable of transforming and optimizing a quantum circuit targeting a shuttling-based trapped-ion quantum processor. It consists of custom algorithms set on top of the quantum circuit framework Pytket. The performance was evaluated for a wide range of quantum circuits and the results show that the gate counts can be reduced by factors up to 5.1 compared to standard Pytket and up to 2.2 compared to standard Qiskit compilation.Comment: 35 pages, 25 figures, 4 tables, accepted in Quantu

A gearbox model for processing large volumes of data by using pipeline systems encapsulated into virtual containers

Software pipelines enable organizations to chain applications for adding value to contents (e.g., confidentially, reliability, and integrity) before either sharing them with partners or sending them to the cloud. However, the pipeline components add overhead when processing large volumes of data, which can become critical in real-world scenarios. This paper presents a gearbox model for processing large volumes of data by using pipeline systems encapsulated into virtual containers. In this model, the gears represent applications, whereas gearboxes represent software pipelines. This model was implemented as a collaborative system that automatically performs Gear up (by using parallel patterns) and/or Gear down (by using in-memory storage) until all gears produce uniform data processing velocities. This model reduces delays and bottlenecks produced by the heterogeneous performance of applications included in software pipelines. The new container tool has been designed to encapsulate both the collaborative system and the software pipelines into a virtual container and deploy it on IT infrastructures. We conducted case studies to evaluate the performance of when processing medical images and PDF repositories. The incorporation of a capsule to a cloud storage service for pre-processing medical imagery was also studied. The experimental evaluation revealed the feasibility of applying the gearbox model to the deployment of software pipelines in real-world scenarios as it can significantly improve the end-user service experience when pre-processing large-scale data in comparison with state-of-the-art solutions such as Sacbe and Parsl.This work has been partially supported by the “Spanish Ministerio de Economia y Competitividad ” under the project grant TIN2016-79637-P “Towards Unification of HPC and Big Data paradigms”

GekkoFS: A temporary burst buffer file system for HPC applications

Many scientific fields increasingly use high-performance computing (HPC) to process and analyze massive amounts of experimental data while storage systems in today’s HPC environments have to cope with new access patterns. These patterns include many metadata operations, small I/O requests, or randomized file I/O, while general-purpose parallel file systems have been optimized for sequential shared access to large files. Burst buffer file systems create a separate file system that applications can use to store temporary data. They aggregate node-local storage available within the compute nodes or use dedicated SSD clusters and offer a peak bandwidth higher than that of the backend parallel file system without interfering with it. However, burst buffer file systems typically offer many features that a scientific application, running in isolation for a limited amount of time, does not require. We present GekkoFS, a temporary, highly-scalable file system which has been specifically optimized for the aforementioned use cases. GekkoFS provides relaxed POSIX semantics which only offers features which are actually required by most (not all) applications. GekkoFS is, therefore, able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes, significantly outperforming the capabilities of common parallel file systems.Peer ReviewedPostprint (author's final draft

Real-Time Optical Coherence Tomography Controlled Microsecond Laser Retinal Microsurgery: First In-vivo Results

Reliable mild photocoagulation and selective retina therapy (SRT) selectively damaging the retinal pigment epithelium (RPE) while sparing the neuroretina, the photoreceptors as well as the choroid are highly demanded. However, due to the inter- and intraindividual variability of RPE and choroidal absorption, optical microsurgery requires reliable real-time laser dosing to prevent unwanted overexposure and extended damage of the neuroretina. In this experiment optical coherence tomography (OCT) was implemented to detect minimal damage, and a laser feedback control algorithm was used for real-time dosing. For the first time in-vivo experiments on rabbits were performed with microsecond laser pulses of varying duration. Pigment rabbit eyes (n=6) were exposed to laser pulses of 4, 8, 12, and 20 μs in duration (wavelength, 532 nm; ramp-mode, maximum 15 pulses; repetition rate, 100 Hz). Therefore, a system with a scanning laser ophthalmoscope and spectral-domain OCT (Heidelberg Engineering) extended with a prototype laser (Meridian Medical) was used. For each laser lesion, the increasing ramp’s end energy was individually controlled in real-time using OCT dosimetry (central wavelength, 870 nm; scan rate, 80 kHz). Within 1 hour after irradiation, retinal changes were assessed with fluorescein angiography (FA), indocyanine green angiography (ICGA), color fundus photography (CFP) and OCT. OCT dosimetry utilizing the control algorithm can interrupt the ramp-mode in real-time for each lesion individually. The preconditioned algorithm enabled treatment with a clearly visible breakdown of the blood-retinal barrier (BRB) according to FA and ICGA imaging and barely visible treatment lesions according to CFP. OCT B-scans through the treated areas provided a first indication of the morphological tissue impact. Preliminary evaluation shows that the algorithm stopped the laser at 4 μs at a ramp end energy of 53 μJ (corresponds to 13/15 pulses), at 8 μs at 68 μJ (5/15 pulses), at 12 μs at 74 μJ (7/15 pulses), and at 20 μs at 100 μJ (1/15 pulses). The novel system with OCT based laser dosing proved to induce minimal visible damage and BRB breakdown in a wide range of pulse durations. The new irradiation scheme and algorithm are being optimized and tested in multiple subjects to further limit unwanted damage and enable pure RPE selective laser microsurgery in real-time. This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually

Short-term follow up after Large-Area RPE Removal by Microsecond Laser followed by hiPS-RPE suspension transplantation in rabbits

Cell therapy is a promising treatment for retinal pigment epithelium (RPE)-associated eye diseases. Herein, microsecond laser irradiation targeting RPE cells was used for large-area RPE removal followed by subretinal injection of human induced pluripotent stem cell derived RPE (hiPS-RPE). 19 immunosuppressed pigmented rabbits (Chinchilla bastard hybrid) underwent a large area RPE removal using an infrared reflectance (IR) confocal scanning laser ophthalmoscope (cSLO) with spectral-domain optical coherence tomography (SD-OCT) system (Heidelberg Engineering ) extended with a prototype laser (modified Merilas 532 shortpulse ophthalmic laser photocoagulator, Meridian Medical) (wavelength, 532 nm; pulse duration, 8 µs), followed by a 25G vitrectomy. Subsequently, a suspension of hiPS-RPE (1000 cells/ µl) was grafted subretinally into the RPE laser lesion under real-time intraoperative OCT imaging (RESCAN 700, Zeiss) by manual injection via a 25/38G cannula connected to a 100µl Hamilton syringe. 5 rabbits served as a control with hiPS-RPE injected subretinally over healthy RPE. The rabbits were followed with in vivo multimodal retinal imaging at baseline after laser and then for 7 days including fluorescein (FA) and indocyanine angiography (ICGA), aw well as SD-OCT (Spectralis ®, Heidelberg Engineering). Baseline imaging of RPE laser wounds showed mild late phase FA/ICGA leakage, with normal outer retinal and choroidal reflectivity on OCT, without signs of coagulation. The size of the RPE wounds was typically 10-12mm2. Real time iOCT showed a directed spread of the bleb retinal detachment (bRD) within the lasered zone, in contrast to a circular spread in controls. Subretinal injection ranged from 5-20µl, with lesser volumes/ larger bRD areas over lasered regions. At 7 days, implanted regions showed FA/ICGA leakage, blockage due to hyperpigmentation was observed mostly at the edges of the lasered zone; OCT showed hyperreflectivity of the outer retina with RPE irregularities. Control implantation sites showed hyperreflectivity in all retinal layers and a variably thickened RPE band suggesting clumping. Microsecond laser irradiation to the RPE seems to accelerate the subretinal integration of hiPS-RPE, when compared to subretinal injection over intact RPE. Future work will address correlation of multimodal imaging and histology. This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually