Cloud benchmarking and performance analysis of an HPC application in Amazon EC2

Cloud computing platforms have been continuously evolving. Features such as the Elastic Fabric Adapter (EFA) in the Amazon Web Services (AWS) platform have brought yet another revolution in the High Performance Computing (HPC) world, further accelerating the convergence of HPC and cloud computing. Other public clouds also support similar features further fueling this change. In this paper, we show how and why the performance of a large-scale computational fluid dynamics (CFD) HPC application on AWS competes very closely with the one on Beskow - a Cray XC40 supercomputer at the PDC Center for High-Performance Computing - in terms of cost-efficiency with strong scaling up to 2304 processes. We perform an extensive set of micro and macro bench- marks in both environments and conduct a comparative analysis. Until as recently as 2020 these benchmarks have notoriously yielded unsatisfactory results for the cloud platforms compared with on-premise infrastructures. Our aim is to access the HPC capabilities of the cloud, and in general to demonstrate how researchers can scale and evaluate the performance of their application in the cloud.ENABL

Restaging role of 18F-FDG-PET/CT in a patient with a Malignant Peripheral Nerve Sheath Tumor (MPNST) caused by neurofibromatosis – case report

Malignant Peripheral Nerve Sheath Tumors (MPNST) are a malignant disease that originates in the cells that cover and protect the peripheral nerves. They are a rare disease, accounting for 6% of soft tissue sarcomas. We present a patient with a malignant peripheral nerve sheath tumor on the left brachium with neurofibromatosis. The patient underwent whole body PET/CT for restaging after total extirpation of a tumor formation originated from n. musculocutaneous in 09.2017, an excision of a recurrent tumor formation in the proximal half of the brachium invading into m. biceps brachii in 12.2017, a performed MRI in 02.2018 - with data for multiple MPSNT in the area between the two previous operations - and subsequent definitive radiotherapy (boost) in the area of the tumor formation and 6 cycles of chemotherapy with Epirubicin. After restaging PET/CT scan of the whole body was performed, progression of the disease was defined - increased in size and activity subpleural lesion in the lower lobe of the right lung

A new class of sum rules for products of Bessel functions

In this paper we derive a new class of sum rules for products of the Bessel functions of first kind. Using standard algebraic manipulations we extend some of the well known properties of $J_n$. Some physical applications of the results are also discussed. A comparison with the Newberger[J. Math. Phys. \textbf{23} (1982) 1278] sum rules is performed on a typical example.Comment: Published in Journal of Mathematical Physics, 9 pages, no picture

Portable simulation framework for diffusion MRI

The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the Bloch-Torrey equation by finite elements is a more recently developed approach for this purpose, in contrast to random walk simulations, which has a longer history. While finite element discretization is more difficult to implement than random walk simulations, the approach benefits from a long history of theoretical and numerical developments by the mathematical and engineering communities. In particular, software packages for the automated solutions of partial differential equations using finite element discretization, such as FEniCS, are undergoing active support and development. However, because diffusion MRI simulation is a relatively new application area, there is still a gap between the simulation needs of the MRI community and the available tools provided by finite element software packages. In this paper, we address two potential difficulties in using FEniCS for diffusion MRI simulation. First, we simplified software installation by the use of FEniCS containers that are completely portable across multiple platforms. Second, we provide a portable simulation framework based on Python and whose code is open source. This simulation framework can be seamlessly integrated with cloud computing resources such as Google Colaboratory notebooks working on a web browser or with Google Cloud Platform with MPI parallelization. We show examples illustrating the accuracy, the computational times, and parallel computing capabilities. The framework contributes to reproducible science and open-source software in computational diffusion MRI with the hope that it will help to speed up method developments and stimulate research collaborations.La Caixa 201

Monitoring the effect of therapy on a patient with a neuroendocrine tumor of the pancreas with PET/CT, 68Ga-DOTATATE - case report

Neuroendocrine tumors (NET) are a rare diagnosis, often without symptoms or mimicking other different symptoms. Тhey are a heterogeneous group of tumors derived from neuroendocrine cells, most commonly of the gastrointestinal tract, but may originate also from other organs including the pancreas, lungs, ovaries, thyroid, pituitary, and adrenal glands (3). Due to the difficult diagnosis, NET‘s are detected at a late stage in their development, often already locally advanced or metastasized. PET/CT with 68Gallium DOTATATE proved to be an effective imaging method not only for the primary diagnosis of NET and subsequent therapeutic behavior, but also for evaluating the effect of the treatment. (1) We present a case of a positive PET/CT scan, performed with Ga-68 DOTATATE in the topical location of the tail of the pancreas after therapy with Sandostain lar

Coherent effects in the field of elliptically polarized light

In the present communication we report on the investigation of the effect of elliptically polarized laser light exciting the Fg=3 Cs D2 absorption line. Coherent resonances in Cs have been studied, obtained in Hanle configuration by scanning of magnetic field parallel to the light propagation direction. The resonances were investigated depending on the polarization of the irradiating light field. It has been observed that for linear polarization dark resonances in the fluorescence are registered, while for circularly polarized light, bright resonances are obtained, probably due to stray orthogonal magnetic field. For elliptical polarization a narrow peak appears superimposed on a broader dip. Theoretical description has been made, which shows that at elliptical polarization and orthogonal magnetic field in the case of weak light fields, a single peak in the excited state population is observed, while strong fields lead to the splitting of this peak into two peaks. The presence of both weak and strong light fields, probably due to reflection of the light beam on the cell walls, could lead to the experimentally observed fluorescence behaviour

Coherent spectroscopy in Cs for precise magnetic field measurements

Investigation on coherent population trapping and electromagnetic induced absorption effects has been made in Cs vapors. A detailed analysis of degenerate and non-degenerate cases is reported. Possible application to precise magnetic field measurements is discussed and preliminary results described

Temperature dependence of coherent resonances in Na and Cs cells

Temperature dependences of coherent resonances in Na and Cs atoms prepared by two coherent laser frequencies or two polarizations of single frequency laser field are presented. It is shown that the temperature dependence of the amplitude or contrast of the resonances in most cases exhibits a maximum. For both types of coherent resonances, a reason for the contrast reduction at higher temperature is the increased absorption of the laser light along the gas cell due to the optical thickness of the medium. Spin-exchange collisions lead to resonance contrast reduction more effectively in a cell with pure alkali atoms