Optimization and Portability of a Fusion OpenACC-based FORTRAN HPC Code from NVIDIA to AMD GPUs

NVIDIA has been the main provider of GPU hardware in HPC systems for over a decade. Most applications that benefit from GPUs have thus been developed and optimized for the NVIDIA software stack. Recent exascale HPC systems are, however, introducing GPUs from other vendors, e.g. with the AMD GPU-based OLCF Frontier system just becoming available. AMD GPUs cannot be directly accessed using the NVIDIA software stack, and require a porting effort by the application developers. This paper provides an overview of our experience porting and optimizing the CGYRO code, a widely-used fusion simulation tool based on FORTRAN with OpenACC-based GPU acceleration. While the porting from the NVIDIA compilers was relatively straightforward using the CRAY compilers on the AMD systems, the performance optimization required more fine-tuning. In the optimization effort, we uncovered code sections that had performed well on NVIDIA GPUs, but were unexpectedly slow on AMD GPUs. After AMD-targeted code optimizations, performance on AMD GPUs has increased to meet our expectations. Modest speed improvements were also seen on NVIDIA GPUs, which was an unexpected benefit of this exercise.Comment: 6 pages, 4 figures, 2 tables, To be published in Proceedings of PEARC2

Impurity transport in Alcator C-Mod in the presence of poloidal density variation induced by ion cyclotron resonance heating

Impurity particle transport in an ion cyclotron resonance heated Alcator C-Mod discharge is studied with local gyrokinetic simulations and a theoretical model including the effect of poloidal asymmetries and elongation. In spite of the strong minority temperature anisotropy in the deep core region, the poloidal asymmetries are found to have a negligible effect on the turbulent impurity transport due to low magnetic shear in this region, in agreement with the experimental observations. According to the theoretical model, in outer core regions poloidal asymmetries may contribute to the reduction of the impurity peaking, but uncertainties in atomic physics processes prevent quantitative comparison with experiments.Comment: 32 pages, 12 figure

Expansion rate measurements at moderate pressure of non-neutral electron plasmas in the Electron Diffusion Gauge (EDG) experiment

Measurements of the expansion rate of pure-electron plasmas have been performed on the Electron Diffusion Gauge (EDG) device at background helium gas pressures in the 5 x 10(superscript -8) Torr to 1 x 10(superscript -5) Torr range, where plasma expansion due to electron-neutral collisions dominates over plasma expansion due to trap asymmetries. It is found that the expansion rate, defined as the time rate of change of the particles' mean-square radius, scales approximately linearly with pressure and inversely as the square of the magnetic field strength in this regime, in agreement with classical predictions

Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

Millimeter Mapping at z ∼ 1:Dust-obscured Bulge Building and Disk Growth

A randomly chosen star in today's Universe is most likely to live in a galaxy with a stellar mass between that of the Milky Way and Andromeda. Yet it remains uncertain how the structural evolution of these bulge-disk systems proceeded. Most of the unobscured star formation we observe building Andromdeda progenitors at 0.790% of their star formation is reprocessed by dust and remains unaccounted for. Here we map 500micron dust continuum emission in an Andromeda progenitor at z=1.25 to probe where it is growing through dust-obscured star formation. Combining resolved dust measurements from the NOEMA interferometer with Hubble Space Telescope Halpha maps and multicolor imaging (including new UV data from the HDUV survey), we find a bulge growing by dust-obscured star formation: while the unobscured star formation is centrally suppressed, the dust continuum is centrally concentrated, filling in the ring-like structures evident in the Halpha and UV emission. Reflecting this, the dust emission is more compact than the optical/UV tracers of star formation with r_e(dust)=3.4kpc, r_e(Halpha)/r_e(dust)=1.4, and r_e(UV)/r_e(dust)=1.8. Crucially, however, the bulge and disk of this galaxy are building simultaneously; although the dust emission is more compact than the rest-optical emission (r_e(optical)/r_e(dust)=1.4), it is somewhat less compact than the stellar mass (r_e(M_*)/r_e(dust)=0.9). Taking the 500micron emission as a tracer of star formation, the expected structural evolution of this galaxy can be accounted for by star formation: it will grow in size by Delta(r_e)/Delta(M_*)~0.3 and central surface density by Delta(Sigma_cen)/Delta(M_*)~0.9. Finally, our observations are consistent with a picture in which merging and disk instabilities drive gas to the center of galaxies, boosting global star formation rates above the main sequence and building bulges.Comment: Submitted to ApJ, key new result of paper shown in Fig.

The KMOS3D Survey: Demographics and Properties of Galactic Outflows at z=0.6-2.7

We present a census of ionized gas outflows in 599 normal galaxies at redshift 0.6 < z < 2.7, mostly based on integral field spectroscopy of H alpha, [N II], and [S II] line emission. The sample fairly homogeneously covers the main sequence of star-forming galaxies with masses 9.0 < log(M-*/M-circle dot) < 11.7, and probes into the regimes of quiescent galaxies and starburst outliers. About one-third exhibits the high-velocity component indicative of outflows, roughly equally split into winds driven by star formation (SF) and active galactic nuclei (AGNs). The incidence of SF-driven winds correlates mainly with SF properties. These outflows have typical velocities of similar to 450 km s(-1), local electron densities of n(e) similar to 380 cm(-3), modest mass loading factors of similar to 0.1-0.2 at all galaxy masses, and energetics compatible with momentum driving by young stellar populations. The SF-driven winds may escape from log(M-*/M-circle dot) less than or similar to 10.3 galaxies, but substantial mass, momentum, and energy in hotter and colder outflow phases seem required to account for low galaxy formation efficiencies in the low-mass regime. Faster AGN-driven outflows (similar to 1000-2000 km s(-1)) are commonly detected above log(M-*/M-circle dot) similar to 10.7, in up to similar to 75% of log(M-*/M-circle dot) greater than or similar to 11.2 galaxies. The incidence, strength, and velocity of AGN-driven winds strongly correlates with stellar mass and central concentration. Their outflowing ionized gas appears denser (n(e) similar to 1000 cm(-3)), and possibly compressed and shock-excited. These winds have comparable mass loading factors as the SF-driven winds but carry similar to 10 (similar to 50) times more momentum (energy). The results confirm our previous findings of high-duty-cycle, energy-driven outflows powered by AGN above the Schechter mass, which may contribute to SF quenching.E.S.W. and J.T.M. acknowledge support by the Australian Research Council Center of Excellence for All Sky Astrophysics in Three Dimensions (ASTRO 3D), through project number CE170100013. D.J.W. and M.F. acknowledge the support of the Deutsche Forschungsgemeinschaft via Project ID 3871/1-1 and 3871/1-2. G.B.B. acknowledges support from the Cosmic Dawn Center, which is funded by the Danish National Research Foundation

The impact of surgical delay on resectability of colorectal cancer: An international prospective cohort study

AIM: The SARS-CoV-2 pandemic has provided a unique opportunity to explore the impact of surgical delays on cancer resectability. This study aimed to compare resectability for colorectal cancer patients undergoing delayed versus non-delayed surgery. METHODS: This was an international prospective cohort study of consecutive colorectal cancer patients with a decision for curative surgery (January-April 2020). Surgical delay was defined as an operation taking place more than 4 weeks after treatment decision, in a patient who did not receive neoadjuvant therapy. A subgroup analysis explored the effects of delay in elective patients only. The impact of longer delays was explored in a sensitivity analysis. The primary outcome was complete resection, defined as curative resection with an R0 margin. RESULTS: Overall, 5453 patients from 304 hospitals in 47 countries were included, of whom 6.6% (358/5453) did not receive their planned operation. Of the 4304 operated patients without neoadjuvant therapy, 40.5% (1744/4304) were delayed beyond 4 weeks. Delayed patients were more likely to be older, men, more comorbid, have higher body mass index and have rectal cancer and early stage disease. Delayed patients had higher unadjusted rates of complete resection (93.7% vs. 91.9%, P = 0.032) and lower rates of emergency surgery (4.5% vs. 22.5%, P < 0.001). After adjustment, delay was not associated with a lower rate of complete resection (OR 1.18, 95% CI 0.90-1.55, P = 0.224), which was consistent in elective patients only (OR 0.94, 95% CI 0.69-1.27, P = 0.672). Longer delays were not associated with poorer outcomes. CONCLUSION: One in 15 colorectal cancer patients did not receive their planned operation during the first wave of COVID-19. Surgical delay did not appear to compromise resectability, raising the hypothesis that any reduction in long-term survival attributable to delays is likely to be due to micro-metastatic disease

Expansion Rate Measurements at Moderate Pressure of Nonneutral Electron Plasmas in the Electron Diffusion Gauge (EDG) Experiment

Measurements of the expansion rate of pure-electron plasmas have been performed on the Electron Diffusion Gauge (EDG) device at background helium gas pressures in the 5 x 10(superscript -8) Torr to 1 x 10(superscript -5) Torr range, where plasma expansion due to electron-neutral collisions dominates over plasma expansion due to trap asymmetries. It is found that the expansion rate, defined as the time rate of change of the particles' mean-square radius, scales approximately linearly with pressure and inversely as the square of the magnetic field strength in this regime, in agreement with classical predictions

From Nuclear to Circumgalactic: Zooming in on AGN-driven Outflows at z similar to 2.2 with SINFONI

We use deep adaptive optics assisted integral field spectroscopy from SINFONI on the VLT to study the spatially resolved properties of ionized gas outflows driven by active galactic nuclei (AGNs) in three galaxies at z ~ 2.2-K20-ID5, COS4-11337, and J0901 + 1814. These systems probe AGN feedback from nuclear to circumgalactic scales and provide unique insights into the different mechanisms by which AGN-driven outflows interact with their host galaxies. K20-ID5 and COS4-11337 are compact star-forming galaxies with powerful ~1500 km s−1 AGN-driven outflows that dominate their nuclear Hα emission. The outflows do not appear to have any impact on the instantaneous star formation activity of the host galaxies, but they carry a significant amount of kinetic energy that could heat the halo gas and potentially lead to a reduction in the rate of cold gas accretion onto the galaxies. The outflow from COS4-11337 is propagating directly toward its companion galaxy COS4-11363, at a projected separation of 5.4 kpc. COS4-11363 shows signs of shock excitation and recent truncation of star formation activity, which could plausibly have been induced by the outflow from COS4-11337. J0901 + 1814 is gravitationally lensed, giving us a unique view of a compact (R = 470 +- 70 pc), relatively low-velocity (~650 km s−1) AGN-driven outflow. J0901 + 1814 has a similar AGN luminosity to COS4-11337, suggesting that the difference in outflow properties is not related to the current AGN luminosity and may instead reflect a difference in the evolutionary stage of the outflow and/or the coupling efficiency between the AGN ionizing radiation field and the gas in the nuclear regions

Ionized and Molecular Gas Kinematics in a z=1.4 Star-forming Galaxy

We present deep observations of a z = 1.4 massive, star-forming galaxy (SFG) in molecular and ionized gas at comparable spatial resolution (CO 3–2, NOrthern Extended Millimeter Array (NOEMA); Hα, Large Binocular Telescope (LBT)). The kinematic tracers agree well, indicating that both gas phases are subject to the same gravitational potential and physical processes affecting the gas dynamics. We combine the one-dimensional velocity and velocity dispersion profiles in CO and Hα to forward-model the galaxy in a Bayesian framework, combining a thick exponential disk, a bulge, and a dark matter halo. We determine the dynamical support due to baryons and dark matter, and find a dark matter fraction within one effective radius of ${f}_{\mathrm{DM}}(\leqslant {R}_{e})={0.18}_{-0.04}^{+0.06}$. Our result strengthens the evidence for strong baryon-dominance on galactic scales of massive z ~ 1–3 SFGs recently found based on ionized gas kinematics alone