arXiv subjects

Stefano Markidis

Publications and source records attributed to Stefano Markidis.

At least 127 records · Page 7Linked to original sources

arXiv2017

Preparing HPC Applications for the Exascale Era: A Decoupling Strategy

Production-quality parallel applications are often a mixture of diverse operations, such as computation- and communication-intensive, regular and irregular, tightly coupled and loosely linked operations. In conventional construction of parallel applications, each process performs all the operations, which might result inefficient and seriously limit scalability, especially at large scale. We propose a decoupling strategy to improve the scalability of applications running on large-scale systems. Our strategy separates application operations onto groups of processes and enables a dataflow processing paradigm among the groups. This mechanism is effective in reducing the impact of load imbalance and increases the parallel efficiency by pipelining multiple operations. We provide a proof-of-concept implementation using MPI, the de-facto programming system on current supercomputers. We demonstrate the effectiveness of this strategy by decoupling the reduce, particle communication, halo exchange and I/O operations in a set of scientific and data-analytics applications. A performance evaluation on 8,192 processes of a Cray XC40 supercomputer shows that the proposed approach can achieve up to 4x performance improvement.

cs.DC↗

arXiv2017

MPI Streams for HPC Applications

Data streams are a sequence of data flowing between source and destination processes. Streaming is widely used for signal, image and video processing for its efficiency in pipelining and effectiveness in reducing demand for memory. The goal of this work is to extend the use of data streams to support both conventional scientific applications and emerging data analytic applications running on HPC platforms. We introduce an extension called MPIStream to the de-facto programming standard on HPC, MPI. MPIStream supports data streams either within a single application or among multiple applications. We present three use cases using MPI streams in HPC applications together with their parallel performance. We show the convenience of using MPI streams to support the needs from both traditional HPC and emerging data analytics applications running on supercomputers.

cs.DC↗

arXiv2017

Extending Message Passing Interface Windows to Storage

This work presents an extension to MPI supporting the one-sided communication model and window allocations in storage. Our design transparently integrates with the current MPI implementations, enabling applications to target MPI windows in storage, memory or both simultaneously, without major modifications. Initial performance results demonstrate that the presented MPI window extension could potentially be helpful for a wide-range of use-cases and with low-overhead.

cs.DC↗

arXiv2017

Exploring Application Performance on Emerging Hybrid-Memory Supercomputers

Next-generation supercomputers will feature more hierarchical and heterogeneous memory systems with different memory technologies working side-by-side. A critical question is whether at large scale existing HPC applications and emerging data-analytics workloads will have performance improvement or degradation on these systems. We propose a systematic and fair methodology to identify the trend of application performance on emerging hybrid-memory systems. We model the memory system of next-generation supercomputers as a combination of "fast" and "slow" memories. We then analyze performance and dynamic execution characteristics of a variety of workloads, from traditional scientific applications to emerging data analytics to compare traditional and hybrid-memory systems. Our results show that data analytics applications can clearly benefit from the new system design, especially at large scale. Moreover, hybrid-memory systems do not penalize traditional scientific applications, which may also show performance improvement.

cs.DC↗

arXiv2017

Idle Period Propagation in Message-Passing Applications

Idle periods on different processes of Message Passing applications are unavoidable. While the origin of idle periods on a single process is well understood as the effect of system and architectural random delays, yet it is unclear how these idle periods propagate from one process to another. It is important to understand idle period propagation in Message Passing applications as it allows application developers to design communication patterns avoiding idle period propagation and the consequent performance degradation in their applications. To understand idle period propagation, we introduce a methodology to trace idle periods when a process is waiting for data from a remote delayed process in MPI applications. We apply this technique in an MPI application that solves the heat equation to study idle period propagation on three different systems. We confirm that idle periods move between processes in the form of waves and that there are different stages in idle period propagation. Our methodology enables us to identify a self-synchronization phenomenon that occurs on two systems where some processes run slower than the other processes.

cs.DC↗

arXiv2017

Exploring the Performance Benefit of Hybrid Memory System on HPC Environments

Hardware accelerators have become a de-facto standard to achieve high performance on current supercomputers and there are indications that this trend will increase in the future. Modern accelerators feature high-bandwidth memory next to the computing cores. For example, the Intel Knights Landing (KNL) processor is equipped with 16 GB of high-bandwidth memory (HBM) that works together with conventional DRAM memory. Theoretically, HBM can provide 5x higher bandwidth than conventional DRAM. However, many factors impact the effective performance achieved by applications, including the application memory access pattern, the problem size, the threading level and the actual memory configuration. In this paper, we analyze the Intel KNL system and quantify the impact of the most important factors on the application performance by using a set of applications that are representative of scientific and data-analytics workloads. Our results show that applications with regular memory access benefit from MCDRAM, achieving up to 3x performance when compared to the performance obtained using only DRAM. On the contrary, applications with random memory access pattern are latency-bound and may suffer from performance degradation when using only MCDRAM. For those applications, the use of additional hardware threads may help hide latency and achieve higher aggregated bandwidth when using HBM.

cs.DC↗

arXiv2017

Global three-dimensional simulation of Earth's dayside reconnection using a two-way coupled magnetohydrodynamics with embedded particle-in-cell model: initial results

We perform a three-dimensional (3D) global simulation of Earth's magnetosphere with kinetic reconnection physics to study the flux transfer events (FTEs) and dayside magnetic reconnection with the recently developed magnetohydrodynamics with embedded particle-in-cell model (MHD-EPIC). During the one-hour long simulation, the FTEs are generated quasi-periodically near the subsolar point and move toward the poles. We find the magnetic field signature of FTEs at their early formation stage is similar to a `crater FTE', which is characterized by a magnetic field strength dip at the FTE center. After the FTE core field grows to a significant value, it becomes an FTE with typical flux rope structure. When an FTE moves across the cusp, reconnection between the FTE field lines and the cusp field lines can dissipate the FTE. The kinetic features are also captured by our model. A crescent electron phase space distribution is found near the reconnection site. A similar distribution is found for ions at the location where the Larmor electric field appears. The lower hybrid drift instability (LHDI) along the current sheet direction also arises at the interface of magnetosheath and magnetosphere plasma. The LHDI electric field is about 8 mV/m and its dominant wavelength relative to the electron gyroradius agrees reasonably with MMS observations.

physics.space-ph↗

arXiv2016

On the ions acceleration via collisionless magnetic reconnection in laboratory plasmas

This work presents an analysis of the ion outflow from magnetic reconnection throughout fully kinetic simulations with typical laboratory plasmas values. A symmetric initial configuration for the density and magnetic field is considered across the current sheet. After analyzing the behavior of a set of nine simulations with a reduced mass ratio and with a permuted value of three initial electron temperature and magnetic field intensity, the best ion acceleration scenario is further studied with a realistic mass ratio in terms of the ion dynamics and energy budget. Interestingly, a series of shock waves structures are observed in the outflow, resembling the shock discontinuities found in recent magnetohydrodynamic (MHD) simulations. An analysis of the ion outflow at several distances from the reconnection point is presented, in light of possible laboratory applications. The analysis suggests that magnetic reconnection could be used as a tool for plasma acceleration, with applications ranging from electric propulsion to production of ion thermal beams.

physics.plasm-ph↗

arXiv2016

On the Electron Agyrotropy during Rapid Asymmetric Magnetic Island Coalescence in Presence of a Guide Field

We present an analysis of the properties of the electron velocity distribution during island coalescence in asymmetric reconnection with and without guide field. In a previous study, three main domains were identified, in the case without guide field, as X-, D- and M-regions featuring different reconnection evolutions {Cazzola et al. 2015). These regions are also identified here in the case with guide field. We study the departure from isotropic and gyrotropic behavior by means of different robust detection algorithms proposed in the literature. While in the case without guide field these metrics show an overall agreement, when the guide field is present a discrepancy in the agyrotropy within some relevant regions is observed, such as at the separatrices and inside magnetic islands. Moreover, in light of the new observations from the Multiscale MagnetoSpheric mission, an analysis of the electron velocity phase-space in these domains is presented.

physics.space-ph↗

arXiv2016

Energy exchanges in reconnection outflows

Reconnection outflows are highly energetic directed flows that interact with the ambient plasma or with flows from other reconnection regions. Under these conditions the flow becomes highly unstable and chaotic, as any flow jets interacting with a medium. We report here massively parallel simulations of the two cases of interaction between outflow jets and between a single outflow with an ambient plasma. We find in both case the development of a chaotic magnetic field, subject to secondary reconnection events that further complicate the topology of the field lines. The focus of the present analysis is on the energy balance. We compute each energy channel (electromagnetic, bulk, thermal, for each species) and find where the most energy is exchanged and in what form. The main finding is that the largest energy exchange is not at the reconnection site proper but in the regions where the outflowing jets are destabilized.

physics.space-ph↗

arXiv2015

Magnetic null points in kinetic simulations of space plasmas

We present a systematic attempt to study magnetic null points and the associated magnetic energy conversion in kinetic Particle-in-Cell simulations of various plasma configurations. We address three-dimensional simulations performed with the semi-implicit kinetic electromagnetic code iPic3D in different setups: variations of a Harris current sheet, dipolar and quadrupolar magnetospheres interacting with the solar wind; and a relaxing turbulent configuration with multiple null points. Spiral nulls are more likely created in space plasmas: in all our simulations except lunar magnetic anomaly and quadrupolar mini-magnetosphere the number of spiral nulls prevails over the number of radial nulls by a factor of 3-9. We show that often magnetic nulls do not indicate the regions of intensive energy dissipation. Energy dissipation events caused by topological bifurcations at radial nulls are rather rare and short-lived. The so-called X-lines formed by the radial nulls in the Harris current sheet and lunar magnetic anomaly simulations are rather stable and do not exhibit any energy dissipation. Energy dissipation is more powerful in the vicinity of spiral nulls enclosed by magnetic flux ropes with strong currents at their axes (their cross-sections resemble 2D magnetic islands). These null lines reminiscent of Z-pinches efficiently dissipate magnetic energy due to secondary instabilities such as the two-stream or kinking instability, accompanied by changes in magnetic topology. Current enhancements accompanied by spiral nulls may signal magnetic energy conversion sites in the observational data.

physics.space-ph↗

arXiv2015

On the electron dynamics during island coalescence in asymmetric magnetic reconnection

We present an analysis of the electron dynamics during rapid island merging in asymmetric magnetic reconnection. We consider a doubly periodic system with two asymmetric transitions. The upper layer is an asymmetric Harris sheet initially perturbed to promote a single reconnection site. The lower layer is a tangential discontinuity that promotes the formation of many X-points, separated by rapidly merging islands. Across both layers the magnetic field and the density have a strong jump, but the pressure is held constant. Our analysis focuses on the consequences of electron energization during island coalescence. We focus first on the parallel and perpendicular components of the electron temperature to establish the presence of possible anisotropies and non-gyrotropies. Thanks to the direct comparison between the two different layers simulated, we can distinguish three main types of behavior characteristic of three different regions of interest. The first type represents the regions where traditional asymmetric reconnections take place without involving island merging. The second type of regions instead show reconnection events between two merging islands. Finally, the third regions identifies the regions between two diverging island and where typical signature of reconnection is not observed. Electrons in these latter regions additionally show a flat-top distribution resulting from the saturation of a two-stream instability generated by the two interacting electron beams from the two nearest reconnection points. Finally, the analysis of agyrotropy shows the presence of a distinct double structure laying all over the lower side facing the higher magnetic field region. The distinguishing features found for the three types of regions investigated provide clear indicators to the recently launched MMS NASA mission for investigating magnetopause reconnection involving multiple islands.

physics.space-ph↗

arXiv2015

Role of Z-pinches in magnetic reconnection in space plasmas

A widely accepted scenario of magnetic reconnection in collisionless space plasmas is the breakage of magnetic field lines in X-points. In laboratory, reconnection is commonly studied in pinches, current channels embedded into twisted magnetic fields. No model of magnetic reconnection in space plasmas considers both null-points and pinches as peers. We have performed a particle-in-cell simulation of magnetic reconnection in a three-dimensional configuration where null-points are present initially, and Z-pinches are formed during the simulation along the lines of spiral null-points. The non-spiral null-points are more stable than spiral ones, and no substantial energy dissipation is associated with them. On the contrary, turbulent magnetic reconnection in the pinches causes the magnetic energy to decay at a rate of ~1.5% per ion gyro period. Dissipation in similar structures is a likely scenario in space plasmas with large fraction of spiral null-points.

physics.space-ph↗

arXiv2015

Energy dissipation in magnetic null points at kinetic scales

We use kinetic particle-in-cell and magnetohydrodynamic simulations supported by an observational dataset to investigate magnetic reconnection in clusters of null points in space plasma. The magnetic configuration under investigation is driven by fast adiabatic flux rope compression that dissipates almost half of the initial magnetic field energy. In this phase powerful currents are excited producing secondary instabilities, and the system is brought into a state of `intermittent turbulence' within a few ion gyro-periods. Reconnection events are distributed all over the simulation domain and energy dissipation is rather volume-filling. Numerous spiral null points interconnected via their spines form null lines embedded into magnetic flux ropes; null point pairs demonstrate the signatures of torsional spine reconnection. However, energy dissipation mainly happens in the shear layers formed by adjacent flux ropes with oppositely directed currents. In these regions radial null pairs are spontaneously emerging and vanishing, associated with electron streams and small-scale current sheets. The number of spiral nulls in the simulation outweighs the number of radial nulls by a factor of 5\---10, in accordance with Cluster observations in the Earth's magnetosheath. Twisted magnetic fields with embedded spiral null points might indicate the regions of major energy dissipation for future space missions such as Magnetospheric Multiscale Mission (MMS).

astro-ph.EP↗

arXiv2015

Energetics of kinetic reconnection in a three-dimensional null points cluster

We performed three-dimensional Particle-in-Cell simulations of magnetic reconnection with multiple magnetic null points. Magnetic field energy conversion into kinetic energy was about five times higher than in traditional Harris sheet configuration. More than 85% of initial magnetic field energy was transferred to particle energy during 25 reversed ion cyclofrequencies. Magnetic reconnection in the cluster of null points evolved in three phases. During the first phase, ion beams were excited, that then gave part of their energy back to magnetic field in the second phase. In the third phase, magnetic reconnection occurs in many small patches around the current channels formed along the stripes of low magnetic field. Magnetic reconnection in null points presents essentially three-dimensional features, with no two dimensional symmetries or current sheets.

physics.space-ph↗

arXiv2014

Kinetic plasma turbulence during the nonlinear stage of the Kelvin-Helmholtz instability

Using a full kinetic, implicit particle-in-cell code, iPiC3D, we studied the properties of plasma kinetic turbulence, such as would be found at the interface between the solar wind and the Earth magnetosphere at low latitude during northwards periods. In this case, in the presence of a magnetic field B oriented mostly perpendicular to the velocity shear, turbulence is fed by the disruption of a Kelvin-Helmholtz vortex chain via secondary instabilities, vortex pairing and non-linear interactions. We found that the magnetic energy spectral cascade between ion and electron inertial scales, $d_i$ and $d_e$, is in agreement with satellite observations and other previous numerical simulations; however, in our case the spectrum ends with a peak beyond $d_e$ due to the occurrence of the lower hybrid drift instability. The electric energy spectrum is influenced by effects of secondary instabilities: anomalous resistivity, fed by the development of the lower hybrid drift instability, steepens the spectral decay and, depending on the alignment or anti-alignment of B and the shear vorticity, peaks due to ion-Bernstein waves may dominate the spectrum around $d_i$. These waves are generated by counter-streaming flow structures, through flux freezing also responsible for reconnection of the in-plane component of the magnetic field, which then generates electron pressure anisotropy and flattening of the field-aligned component of the electron distribution function.

physics.plasm-ph↗

arXiv2014

Separatrices: the crux of reconnection

Reconnection is one of the key processes in astrophysical and laboratory plasmas: it is the opposite of a dynamo. Looking at energy, a dynamo transforms kinetic energy in magnetic energy while reconnection takes magnetic energy and returns is to its kinetic form. Most plasma processes at their core involve first storing magnetic energy accumulated over time and then releasing it suddenly. We focus here on this release. A key concept in analysing reconnection is that of the separatrix, a surface (line in 2D) that separates the fresh unperturbed plasma embedded in magnetic field lines not yet reconnected with the hotter exhaust embedded in reconnected field lines. In kinetic physics, the separatrices become a layer where many key processes develop. We present here new results relative to the processes at the separatrices that regulate the plasma flow, the energisation of the species, the electromagnetic fields and the instabilities developing at the separatrices.

physics.plasm-ph↗

arXiv2014

Electromagnetic Energy Conversion in Downstream Fronts from 3D Kinetic Reconnection

The electromagnetic energy equation is analyzed term by term in a 3D simulation of kinetic reconnection previously reported by \citet{vapirev2013formation}. The evolution presents the usual 2D-like topological structures caused by an initial perturbation independent of the third dimension. However, downstream of the reconnection site, where the jetting plasma encounters the yet unperturbed pre-existing plasma, a downstream front (DF) is formed and made unstable by the strong density gradient and the unfavorable local acceleration field. The energy exchange between plasma and fields is most intense at the instability, reaching several $pW/m^3$, alternating between load (energy going from fields to particles) and generator (energy going from particles to fields) regions. Energy exchange is instead purely that of a load at the reconnection site itself in a region focused around the x-line and elongated along the separatrix surfaces. Poynting fluxes are generated at all energy exchange regions and travel away from the reconnection site transporting an energy signal of the order of about $\mathbf S \approx 10^{-3} W/m^2$.

physics.plasm-ph↗