Search

MANA-2.0 is a scalable, future-proof design for transparent checkpointing of MPI-based computations. Its network transparency ("network-agnostic") feature ensures that MANA-2.0 will provide a viable, efficient mechanism for transparently checkpointing MPI applications on current and future supercomputers. MANA-2.0 is an enhancement of previous work, the original MANA, which interposes MPI calls, and is a work in progress intended for production deployment. MANA-2.0 implements a series of new algorithms and features that improve MANA's scalability and reliability, enabling transparent checkpoint-restart over thousands of MPI processes. MANA-2.0 is being tested on today's Cori supercomputer at NERSC using Cray MPICH library over the Cray GNI network, but it is designed to work over any standard MPI running over an arbitrary network. Two widely-used HPC applications were selected to demonstrate the enhanced features of MANA-2.0: GROMACS, a molecular dynamics simulation code with frequent point-to-point communication, and VASP, a materials science code with frequent MPI collective communication. Perhaps the most important lesson to be learned from MANA-2.0 is a series of algorithms and data structures for library-based transformations that enable MPI-based computations over MANA-2.0 to reliably survive the checkpoint-restart transition.

This paper describes the development and validation of a Monte Carlo (MC) dose computing module dedicated to organ dose calculations of patients undergoing nuclear medicine (NM) internal radiation exposures involving 18F-FDG PET/CT examination. This new module extends the more-than-10-years-long ARCHER project that developed a GPU-accelerated MC dose engine by adding dedicated NM source-definition features. To validate the code, we compared dose distributions from the 0.511-MeV point photon source calculated for a water phantom as well as a patient PET/CT phantom against a well-tested MC code, GATE. The water-phantom results show excellent agreement, suggesting that the radiation physics module in the new NM code is adequate. To demonstrate the clinical utility and advantage of ARCHER-NM, one set of PET/CT data for an adult male NM patient is calculated using the new code. Radiosensitive organs in the CT dataset are segmented using a CNN-based tool called DeepViewer. The PET image intensity maps are converted to radioactivity distributions to allow for MC radiation transport dose calculations at the voxel level. The dose rate maps and corresponding statistical uncertainties were calculated for the duration of PET image acquisition. The dose rate results of the 18F-FDG PET imaging patient show that ARCHER-NM's results agree very well with those of the GATE within 0.58% to 4.11%. Most impressively, ARCHER-NM obtains such results in less than 0.5 minutes while it takes GATE as much as 376 minutes. This is the first study presenting GPU-accelerated patient-specific MC internal radiation dose rate calculations for clinically realistic 18F-FDG PET/CT imaging cases involving auto-segmentation of whole-body PET/CT images. This study suggests that modern computing tools -- ARCHER-NM and DeepViewer -- are accurate and fast enough for routine internal dosimetry in NM clinics., Comment: 17 pages, 5 figures, 1 table

There is a significant expansion in both volume and range of applications along with the concomitant increase in the variety of data sources. These ever-expanding trends have highlighted the necessity for more versatile analysis tools that offer greater opportunities for algorithmic developments and computationally faster operations than the standard flat-view matrix approach. Tensors, or multi-way arrays, provide such an algebraic framework which is naturally suited to data of such large volume, diversity, and veracity. Indeed, the associated tensor decompositions have demonstrated their potential in breaking the Curse of Dimensionality associated with traditional matrix methods, where a necessary exponential increase in data volume leads to adverse or even intractable consequences on computational complexity. A key tool underpinning multi-linear manipulation of tensors and tensor networks is the standard Tensor Contraction Product (TCP). However, depending on the dimensionality of the underlying tensors, the TCP also comes at the price of high computational complexity in tensor manipulation. In this work, we resort to diagrammatic tensor network manipulation to calculate such products in an efficient and computationally tractable manner, by making use of Tensor Train decomposition (TTD). This has rendered the underlying concepts easy to perceive, thereby enhancing intuition of the associated underlying operations, while preserving mathematical rigour. In addition to bypassing the cumbersome mathematical multi-linear expressions, the proposed Tensor Train Contraction Product model is shown to accelerate significantly the underlying computational operations, as it is independent of tensor order and linear in the tensor dimension, as opposed to performing the full computations through the standard approach (exponential in tensor order).

Given a directed graph $G = (V, E)$, the $k$-path partition problem is to find a minimum collection of vertex-disjoint directed paths each of order at most $k$ to cover all the vertices of $V$. The problem has various applications in facility location, network monitoring, transportation and others. Its special case on undirected graphs has received much attention recently, but the general directed version is seemingly untouched in the literature. We present the first $k/2$-approximation algorithm, for any $k \ge 3$, based on a novel concept of augmenting path to minimize the number of singletons in the partition. When $k \ge 7$, we present an improved $(k+2)/3$-approximation algorithm based on the maximum path-cycle cover followed by a careful $2$-cycle elimination process. When $k = 3$, we define the second novel kind of augmenting paths and propose an improved $13/9$-approximation algorithm., Comment: Extended abstract to appear in FAW 2021

Electric fields can spontaneously decay via the Schwinger effect, the nucleation of a charged particle-anti particle pair separated by a critical distance $d$. What happens if the available distance is smaller than $d$? Previous work on this question has produced contradictory results. Here, we study the quantum evolution of electric fields when the field points in a compact direction with circumference $L < d$ using the massive Schwinger model, quantum electrodynamics in one space dimension with massive charged fermions. We uncover a new and previously unknown set of instantons that result in novel physics that disagrees with all previous estimates. In parameter regimes where the field value can be well-defined in the quantum theory, generic initial fields $E$ are in fact stable and do not decay, while initial values that are quantized in half-integer units of the charge $E = (k/2) g$ with $k\in \mathbb Z$ oscillate in time from $+(k/2) g$ to $-(k/2) g$, with exponentially small probability of ever taking any other value. We verify our results with four distinct techniques: numerically by measuring the decay directly in Lorentzian time on the lattice, numerically using the spectrum of the Hamiltonian, numerically and semi-analytically using the bosonized description of the Schwinger model, and analytically via our instanton estimate., Comment: 45+22 pages, 21 figures and 7 tables; v2: typos corrected, references added; v3: matches the version published in JHEP