Performance optimization and load-balancing modeling for superparametrization by 3D LES

In order to eliminate climate uncertainty w.r.t. cloud and convection parametrizations, superpramaterization (SP) [1] has emerged as one of the possible ways forward. We have implemented (regional) superparametrization of the ECMWF weather model OpenIFS [2] by cloud-resolving, three-dimensional large-eddy simulations. This setup, described in [3], contains a two-way coupling between a global meteorological model that resolves large-scale dynamics, with many local instances of the Dutch Atmospheric Large Eddy Simulation (DALES) [4], resolving cloud and boundary layer physics. The model is currently prohibitively expensive to run over climate or even seasonal time scales, and a global SP requires the allocation of millions of cores. In this paper, we study the performance and scaling behavior of the LES models and the coupling code and present our implemented optimizations. We mimic the observed load imbalance with a simple performance model and present strategies to improve hardware utilization in order to assess the feasibility of a world-covering superparametrization. We conclude that (quasi-)dynamical load-balancing can significantly reduce the runtime for such large-scale systems with wide variability in LES time-stepping speeds

Representing cloud mesoscale variability in superparameterized climate models

In atmospheric modeling, superparameterization (SP) has gained popularity as a technique to improve cloud and convection representations in large-scale models by coupling them locally to cloud-resolving models. We show how the different representations of cloud water in the local and the global models in SP lead to a suppression of cloud advection and ultimately to a systematic underrepresentation of the cloud amount in the large-scale model. We demonstrate this phenomenon in a regional SP experiment with the global model OpenIFS coupled to the local model Dutch Atmospheric Large Eddy Simulation, as well as in an idealized setup, where the large-scale model is replaced by a simple advection scheme. As a starting point for mitigating the problem of suppressed cloud advection, we propose a scheme where the spatial variability of the local model's total water content is enhanced in order to match the global model's cloud condensate amount. The proposed scheme enhances the cloud condensate amount in the test cases, however a large discrepancy remains, caused by rapid dissipation of the clouds added by the proposed scheme

A Python interface to the Dutch Atmospheric Large-Eddy Simulation

We present a Python interface for the Dutch Atmospheric Large Eddy Simulation (DALES), an existing Fortran code for high-resolution, turbulence-resolving simulation of atmospheric physics. The interface is based on an infrastructure for remote and parallel function calls and makes it possible to use and control the DALES weather simulations from a Python context. The interface is designed within the OMUSE framework, and allows the user to set up and control the simulation, apply perturbations and forcings, collect and analyse data in real time without exposing the user to the details of setting up and running the parallel Fortran DALES code. Another significant possibility is coupling the DALES simulation to other models, for example larger scale numerical weather prediction (NWP) models that can supply realistic lateral boundary conditions. Finally, the Python interface to DALES can serve as an educational tool for exploring weather dynamics, which we demonstrate with an example Jupyter notebook

Gp120 on HIV-1 Virions Lacks O-Linked Carbohydrate

As HIV-1-encoded envelope protein traverses the secretory pathway, it may be modified with N- and O-linked carbohydrate. When the gp120s of HIV-1 NL4-3, HIV-1 YU2, HIV-1 Bal, HIV-1 JRFL, and HIV-1 JRCSF were expressed as secreted proteins, the threonine at consensus position 499 was found to be O-glycosylated. For SIVmac239, the corresponding threonine was also glycosylated when gp120 was recombinantly expressed. Similarly-positioned, highly-conserved threonines in the influenza A virus H1N1 HA1 and H5N1 HA1 envelope proteins were also found to carry O-glycans when expressed as secreted proteins. In all cases, the threonines were modified predominantly with disialylated core 1 glycans, together with related core 1 and core 2 structures. Secreted HIV-1 gp140 was modified to a lesser extent with mainly monosialylated core 1 O-glycans, suggesting that the ectodomain of the gp41 transmembrane component may limit the accessibility of Thr499 to glycosyltransferases. In striking contrast to these findings, gp120 on purified virions of HIV-1 Bal and SIV CP-MAC lacked any detectable O-glycosylation of the C-terminal threonine. Our results indicate the absence of O-linked carbohydrates on Thr499 as it exists on the surface of virions and suggest caution in the interpretation of analyses of post-translational modifications that utilize recombinant forms of envelope protein

Original Article

The pancreas taken from the frog (Rana nigromaculata) was fixed in 1% OsO_4 and sliced into ultrathin sections for electron microscopic studies. The following observations were made: 1. A great \u27number of minute granules found in the cytoplasm of a pancreatic cell were called the microsomes, which were divided into two types, the C-microsome and S-microsome. 2. Electron microsopic studies of the ergastoplasm showed that it is composed of the microsome granules and A-substance. The microsomes were seen embedded in the A-substance which was either filamentous or membranous. The membranous structure, which was called the Am-membrane, was seen to form a sac, with a cavity of varying sizes, or to form a lamella. 3. The Am-membrane has close similarity to α-cytomembrane of Sjostrand, except that the latter is rough-surfaced. It was deduced that the Am-membrane, which is smooth-surfaced, might turn into the rough-surfaced α-cytomembrane. 4. There was the Golgi apparatus in the supranuclear region of a pancreatic cell. It consisted of the Golgi membrane, Golgi vacuole and. Golgi vesicle. 5. The mitochondria of a pancreatic cell appeared like long filaments, and some of them were seen to ramify. 6. The membrane of mitochondria, i. e. the limiting membrane, consisted of the Ammembrane. The mitochondria contained a lot of A-substances, as well as the C-microsomes and S-microsomes. When the mitochondria came into being, there appeared inside them chains of granules, which appeared like strips of beads, as the outgrowths of the A-substance and the microsome granules attached to the Am-membrane. They are the so-called cristae mitochondriales. 7. The secretory granules originate in the microsomes. They came into being when the microsomes gradually thickened and grew in size as various substances became adhered to them. Some of the secretory granules were covered with a membrane and appeared like what they have called the intracisternal granule of Palade.It seemed that this was a phenomenon attendant upon the dissolution and liqutefaction of the secretory granule. 8. Comparative studies were made of the ergastoplasm of the pancreatic cells from the frogs in hibernation, the frogs artificially hungered, the frogs which were given food after a certain period of fasting, the frogs to which pilocarpine was given subcutaneously, and the very young, immature frogs. The studies revealed that the ergastoplasm of the pancreatic cells greatly varied in form with the difference in nutritive condition and with different developmental stages of the cell. The change in form and structure occured as a result of transformation of the microsomes and A-substance. The ergastoplasm, even after it has come into being, might easily be inactivated if nutrition is defective. The ergastoplasm is concerned in the secretory mechanism, which is different from the secretory phenomenon of the secretory granules. It would seem that structurally the mitochondria have no direct relation to this mechanism

OMUSE

The Oceanographic Multi-purpose Software Environment: a package for multi-physics and multi-scale earth science simulations

O-glycosylation status of the similarly positioned conserved Thr of influenza A virus H1N1 Puerto RIco HA1 and of influenza A virus H5N1 Thai HA1.

<p>(A) MALDI-TOF MS of permethylated O-glycans isolated from recombinant HA1 of Influenza A virus H1N1 Puerto Rico (B) MALDI-TOF MS of permethylated O-glycans isolated from recombinant HA1 of Influenza A virus H5N1 Thai (C) Electrospray Nano-LC-MS/MS spectra showing the location and attachment of the major species of O-glycan attached to Thr318 in HA1 of Influenza A virus H1N1 strain Puerto Rico; parent ion [M+2H]²⁺ m/z 895.48. (D) Electrospray Nano-LC-MS/MS spectra showing the location and attachment of the major species of O-glycan attached to Thr318 in HA1 of Influenza A virus H5N1 strain Thai; parent ion [M+2H]²⁺ m/z 895.48.</p