DD-α\alphaAMG on QPACE 3

We describe our experience porting the Regensburg implementation of the DD-$\alpha$AMG solver from QPACE 2 to QPACE 3. We first review how the code was ported from the first generation Intel Xeon Phi processor (Knights Corner) to its successor (Knights Landing). We then describe the modifications in the communication library necessitated by the switch from InfiniBand to Omni-Path. Finally, we present the performance of the code on a single processor as well as the scaling on many nodes, where in both cases the speedup factor is close to the theoretical expectations.Comment: 12 pages, 6 figures, Proceedings of Lattice 201

MRHS multigrid solver for Wilson-clover fermions

We describe our implementation of a multigrid solver for Wilson-clover fermions, which increases parallelism by solving for multiple right-hand sides (MRHS) simultaneously. The solver is based on Grid and thus runs on all computing architectures supported by the Grid framework. We present detailed benchmarks of the relevant kernels, such as hopping and clover term on the various multigrid levels, intergrid operators, and reductions. The benchmarks were performed on the JUWELS Booster system at J\"ulich Supercomputing Centre, which is based on Nvidia A100 GPUs. For example, solving a $24^3\times128$ lattice on 16 GPUs, the overall speedup obtained solely from MRHS is about 10x.Comment: 8 pages, 14 figures, proceedings of Lattice 202

Direct determinations of the nucleon and pion σ\sigma terms at nearly physical quark masses

We present a high statistics study of the pion and nucleon light and strange quark sigma terms using $N_f=2$ dynamical non-perturbatively improved clover fermions with a range of pion masses down to $m_\pi\sim 150$ MeV and several volumes, $Lm_\pi=3.4$ up to $6.7$, and lattice spacings, $a=0.06-0.08$ fm, enabling a study of finite volume and discretisation effects for $m_\pi\gtrsim 260$ MeV. Systematics are found to be reasonably under control. For the nucleon we obtain $\sigma_{\pi N}=35(6)$ MeV and $\sigma_s=35(12)$ MeV, or equivalently in terms of the quark fractions, $f_{T_u}=0.021(4)$, $f_{T_d}=0.016(4)$ and $f_{T_s}=0.037(13)$, where the errors include estimates of both the systematic and statistical uncertainties. These values, together with perturbative matching in the heavy quark limit, lead to $f_{T_c}=0.075(4)$, $f_{T_b}=0.072(2)$ and $f_{T_t}=0.070(1)$. In addition, through the use of the (inverse) Feynman-Hellmann theorem our results for $\sigma_{\pi N}$ are shown to be consistent with the nucleon masses determined in the analysis. For the pion we implement a method which greatly reduces excited state contamination to the scalar matrix elements from states travelling across the temporal boundary. This enables us to demonstrate the Gell-Mann-Oakes-Renner expectation $\sigma_\pi=m_\pi/2$ over our range of pion masses.Comment: 31 pages, 18 figures, v2, small changes to text and figure

pMR: A high-performance communication library

On many parallel machines, the time LQCD applications spent in communication is a significant contribution to the total wall-clock time, especially in the strong-scaling limit. We present a novel high-performance communication library that can be used as a de facto drop-in replacement for MPI in existing software. Its lightweight nature that avoids some of the unnecessary overhead introduced by MPI allows us to improve the communication performance of applications without any algorithmic or complicated implementation changes. As a first real-world benchmark, we make use of the pMR library in the coarse-grid solve of the Regensburg implementation of the DD-$\alpha$AMG algorithm. On realistic lattices, we see an improvement of a factor 2x in pure communication time and total execution time savings of up to 20%.Comment: 7 pages, 2 figures, Proceedings of Lattice 201

DD-αAMG on QPACE 3

We describe our experience porting the Regensburg implementation of the DD-αAMG solver from QPACE 2 to QPACE 3. We first review how the code was ported from the first generation Intel Xeon Phi processor (Knights Corner) to its successor (Knights Landing). We then describe the modifications in the communication library necessitated by the switch from InfiniBand to Omni-Path. Finally, we present the performance of the code on a single processor as well as the scaling on many nodes, where in both cases the speedup factor is close to the theoretical expectations

Beam-Based Reconstruction of the Shielded Quench-Heater Fields for the LHC Main Dipoles

Small orbit oscillations of the circulating particle beams have been observed immediately following quenches in the LHC’s superconducting main dipole magnets. Magnetic fields generated during the discharge into the quench heaters were identified as the cause. Since the resulting, shielded field inside the beam screen cannot be measured in-situ, the time evolution of the field has to be reconstructed from the measured beam excursions. In this paper, the field-reconstruction method using rotation in normalized phase space and the optimized fitting algorithm are described. The resulting rise times and magnetic field levels are presented for quench events that occurred during regular operation as well as for dedicated beam experiments. Finally, different approaches to model the shielding behavior of the beam screen are discussed

Insights on Zn deficiency and Zn excess effects on the Root Apical Meristem in Arabidopsis

Zinc, an essential cofactor to many enzymes, is an important micronutrient in plants. Crop culture on Zn deficient soils, which are widespread worldwide, is limiting productivity and quality and is considered as a concern for human nutrition. In contrast, with industrialisation, soils were contaminated in large areas with toxic metal concentrations including Zn. To address both issues of Zn deficiency and Zn excess, it is required to better understand the responses to variation in Zn supply in plants, which will enable the design of efficient biofortification or phytoremediation strategies, respectively. Root growth is regulated at the root apex, where mitosis, as well as cell elongation and differentiation occur. Zn deficiency and excess are known to have an effect on root growth, for instance by affecting auxin production and Reactive Oxygen species (ROS) levels in the Root Apical Meristem (RAM). However, a detailed investigation on the delicately balanced regulation of the root meristematic activity by Zn is still missing. In this study, root responses to Zn deficiency and Zn excess were examined in Arabidopsis. We re-assessed RAM activity upon both Zn deficiency and Zn excess and observed distinct effects of both treatments on cell elongation and differentiation, as well as on the cell cycle itself. To better pinpoint which specific processes are affected by altered Zn nutrition, RNA-Seq datasets were generated for root tips versus differentiated roots comparing normal Zn supply to Zn excess or Zn deficiency. We observed root tip specific responses and identified potential candidate genes (e.g. transporters, hormonal response, cell-wall) for involved in these responses Zn supply imbalance. Furthermore, linking the RNA-Seq datasets with Zn localization in root tissues by Laser Ablation-ICP-MS experiments and publicly available single-cell transcriptional maps provided a detailed assessment of the RAM response to Zn supply.Mechanisms of plant Growth adaptation to extreme environment (MechaGro

LHC MD 3205: Beam Screen Shielding from QH Discharge at 70 K

This note summarises the results of LHC Machine Development (MD) 3205, performed on October 31st 2018. During the MD, the quench heaters of the magnet MB.C28L5 were fired while three nominal bunches were circulating in each of the two rings. The resulting vertical kicks on the beams were reconstructed based on the measured beam positions at the ADT ObsBox. Fast rise times of around 100 µs were observed. The first test was performed during the ramp at a beam energy of 3.46 TeV, and the second test at top energy (6.5 TeV). For both tests, the beam screen in the cell 28L5 had been warmed up to approximately 70 K

Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints

Metabolomics data is typically scaled to a common reference like a constant volume of body fluid, a constant creatinine level, or a constant area under the spectrum. Such scaling of the data, however, may affect the selection of biomarkers and the biological interpretation of results in unforeseen ways. Here, we studied how both the outcome of hypothesis tests for differential metabolite concentration and the screening for multivariate metabolite signatures are affected by the choice of scale. To overcome this problem for metabolite signatures and to establish a scale-invariant biomarker discovery algorithm, we extended linear zero-sum regression to the logistic regression framework and showed in two applications to ¹H NMR-based metabolomics data how this approach overcomes the scaling problem. Logistic zero-sum regression is available as an R package as well as a high-performance computing implementation that can be downloaded at https://github.com/rehbergT/zeroSum