Evaluation of Directive-Based GPU Programming Models on a Block Eigensolver with Consideration of Large Sparse Matrices

Achieving high performance and performance portability for large-scale scientific applications is a major challenge on heterogeneous computing systems such as many-core CPUs and accelerators like GPUs. In this work, we implement a widely used block eigensolver, Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG), using two popular directive based programming models (OpenMP and OpenACC) for GPU-accelerated systems. Our work differs from existing work in that it adopts a holistic approach that optimizes the full solver performance rather than narrowing the problem into small kernels (e.g., SpMM, SpMV). Our LOPBCG GPU implementation achieves a 2.8$${\times }$$–4.3$${\times }$$ speedup over an optimized CPU implementation when tested with four different input matrices. The evaluated configuration compared one Skylake CPU to one Skylake CPU and one NVIDIA V100 GPU. Our OpenMP and OpenACC LOBPCG GPU implementations gave nearly identical performance. We also consider how to create an efficient LOBPCG solver that can solve problems larger than GPU memory capacity. To this end, we create microbenchmarks representing the two dominant kernels (inner product and SpMM kernel) in LOBPCG and then evaluate performance when using two different programming approaches: tiling the kernels, and using Unified Memory with the original kernels. Our tiled SpMM implementation achieves a 2.9$${\times }$$ and 48.2$${\times }$$ speedup over the Unified Memory implementation on supercomputers with PCIe Gen3 and NVLink 2.0 CPU to GPU interconnects, respectively

GPU-Accelerated 3D Mesh Deformation for Optimization Based on the Finite Element Method

This paper discusses a strategy for speeding up the mesh deformation process in the design-by-optimization of high-frequency components involving electromagnetic field simulations using the 3D finite element method (FEM). The mesh deformation is assumed to be described by a linear elasticity model of a rigid body; therefore, each time the shape of the device is changed, an auxiliary elasticity finite-element problem must be solved. In order to accomplish this in a very short time numerical integration and the solution of the resulting system of equations are performed using a graphics processing unit (GPU). The performance of the proposed algorithm is illustrated are verified using a complex example involving 3D FEM analysis of a dielectric-resonator filter

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Effect of short-lasting undernutrition of gilts during peri-conceptional period on biochemical and haematological parameters in blood plasma during peri-implantation period

In gilts, the period of early pregnancy occurring from the time of fertilization to the beginning of implantation is sensitive to any environmental disruptions, including an unbalanced diet of a future mother. Previously, we found that due to the undernutrition in gilts during this period, the endocrine intrauterine microenvironment and DNA methylation in the uterus have been changed. These distortions may diminish the success of pregnancy. In this study we focused on the influence of a restricted diet used in gilts during the first days of pregnancy on their biochemical and haematological parameters in peripheral blood. The applied restrictive diet vs. normal diet covered only 70% of the nutritional demands of early pregnant gilts. Normal (n = 4 gilts) or restrictive (n = 5 gilts) diets were used from the day of the first signs of the estrus until day 9 of pregnancy and biochemical and haematological parameters in blood plasma were determined during peri-implantation period, e.g. on days 15 to16 of pregnancy. In restrictive vs. normal fed gilts significantly lower plasma phosphorus, calcium and total cholesterol as well as the tendency to increasing concentrations of triglicerydes and asparate aminotranserase were found. Haematological parameters did not differ between the studied gilts. Thus, it seems that the availability of nutritional factors became suboptimal in restrictively fed early pregnant gilts. Even short-lasting undernutrition of females during the peri-conceptional period may cause a disruption of biochemical homeostasis during the peri-implantation period and probably affect the success of pregnancy

Fourier-Transform MS and Closed-Path Multireflection Time-of-Flight MS Using an Electrostatic Linear Ion Trap

An electrostatic linear ion trap (ELIT) has been configured to allow for the simultaneous acquisition of mass spectra via Fourier transform (FT) techniques (frequency measurement) and via time-of-flight (TOF; time measurement). In the former case, the time-domain image charge derived from a pick-up electrode in the field-free region of the ELIT is converted to frequency-domain data via Fourier transformation (i.e., FT-ELIT MS). In the latter case, the time difference between ion injection into the ELIT and ion detection after release from the ELIT using a microchannel plate (MCP) enables the acquisition of multireflection time-of-flight mass spectra (MR-TOF MS). The ELIT geometry facilitates the acquisition of both types of data simultaneously because the detection schemes are independent and do not preclude one another. The two MS approaches exhibit a degree of complementarity. Resolution increases much faster with time with the MR-TOF approach, for example, but the closed-path nature of executing MR-TOF in an ELIT limits both the <i>m</i>/<i>z</i> range and the peak capacity. For this reason, the FT-ELIT MS approach is most appropriate for wide <i>m</i>/<i>z</i> range applications, whereas MR-TOF MS can provide advantages in a “zoom-in” mode in which moderate resolution (<i>M</i>/Δ<i>M</i>_fwhm ≈ 10000) at short analysis times (10 ms) is desirable