Abstract: Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, standalone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming language and takes advantage of modern object-oriented technologies. In addition, PenRed offers the capability to read and process DICOM images as well as to construct and simulate image-based voxelized geometries, so as to facilitate its usage in medical applications. Our framework has been successfully verified against the original PENELOPE Fortran code. Furthermore, the implemented parallelism has been tested showing a significant improvement in the simulation time without any loss in precision of results. Program summary Program title: PenRed: Parallel Engine for Radiation Energy Deposition. CPC Library link to program files: https://doi .org /10 .17632/rkw6tvtngy.1 Licensing provision: GNU Affero General Public License (AGPL). Programming language: C++ standard 2011. Nature of problem: Monte Carlo simulations usually require a huge amount of computation time to achieve low statistical uncertainties. In addition, many applications necessitate particular characteristics or the extraction of specific quantities from the simulation. However, most available Monte Carlo codes do not provide an efficient parallel and truly modular structure which allows users to easily customise their code to suit their needs without an in-depth knowledge of the code system. Solution method: PenRed is a fully parallel, modular and customizable framework for Monte Carlo simulations of the passage of radiation through matter. It is based on the PENELOPE [1] code system, from which inherits its unique physics models and tracking algorithms for charged particles. PenRed has been coded in C++ following an object-oriented programming paradigm restricted to the C++11 standard. Our engine implements parallelism via a double approach: on the one hand, by using standard C++ threads for shared memory, improving the access and usage of the memory, and, on the other hand, via the MPI standard for distributed memory infrastructures. Notice that both kinds of parallelism can be combined together in the same simulation. Moreover, both threads and MPI processes, can be balanced using the builtin load balance system (RUPER-LB [30]) to maximise the performance on heterogeneous infrastructures. In addition, PenRed provides a modular structure with methods designed to easily extend its functionality. Thus, users can create their own independent modules to adapt our engine to their needs without changing the original modules. Furthermore, user extensions will take advantage of the builtin parallelism without any extra effort or knowledge of parallel programming. Additional comments including restrictions and unusual features: PenRed has been compiled in linux systems withg++ of GCC versions 4.8.5, 7.3.1, 8.3.1 and 9; clang version 3.4.2 and intel C++ compiler (icc) version 19.0.5.281. Since it is a C++11-standard compliant code, PenRed should be able to compile with any compiler with C++11 support. In addition, if the code is compiled without MPI support, it does not require any non standard library. To enable MPI capabilities, the user needs to install whatever available MPI implementation, such as openMPI [24] or mpich [25], which can be found in the repositories of any linux distribution. Finally, to provide DICOM processing support, PenRed can be optionally compiled using the dicom toolkit (dcmtk) [32] library. Thus, PenRed has only two optional dependencies, an MPI implementation and the dcmtk library.

Abstract: This paper describes CosmoGattice, a modern package for lattice simulations of the dynamics of interacting scalar and gauge fields in an expanding universe. CosmoGattice incorporates a series of features that makes it very versatile and powerful: i) it is written in C++ fully exploiting the object oriented programming paradigm, with a modular structure and a clear separation between the physics and the technical details, ii) it is MPI-based and uses a discrete Fourier transform parallelized in multiple spatial dimensions, which makes it specially appropriate for probing scenarios with well -separated scales, running very high resolution simulations, or simply very long ones, iii) it introduces its own symbolic language, defining field variables and operations over them, so that one can introduce differential equations and operators in a manner as close as possible to the continuum, iv) it includes a library of numerical algorithms, ranging from O(delta t(2)) to O(delta t(10)) methods, suitable for simulating global and gauge theories in an expanding grid, including the case of 'self-consistent' expansion sourced by the fields themselves. Relevant observables are provided for each algorithm (e.g. energy densities, field spectra, lattice snapshots) and we note that, remarkably, all our algorithms for gauge theories (Abelian or non-Abelian) always respect the Gauss constraint to machine precision. Program summary Program Title:: CosmoGattice CPC Library link to program files: https://doi .org /10 .17632 /44vr5xssc6 .1 Developer's repository link: http://github .com /cosmolattice /cosmolattice Licensing provisions: MIT Programming language: C++, MPI Nature of problem: The phenomenology of high energy physics in the early universe is typically characterized by non-linear dynamics, which cannot be captured accurately with analytical techniques. In order to fully understand the non-linearities developed in a given scenario, one needs to carry out lattice simulations. A number of public packages for lattice simulations have appeared over the years, but most of them are only capable of simulating scalar fields. However, realistic models of particle physics do contain other kind of field species, such as (Abelian or non-Abelian) gauge fields, whose non-linear dynamics can also play a relevant role in the early universe. Tensor modes representing gravitational waves are also naturally expected in many scenarios. Solution method: CosmoGattice represents a modern code for lattice simulations of scalar-gauge field theories in an expanding universe. It allows for the simulation of the evolution of interacting (singlet) scalar fields, charged scalar fields under U(1) and/or SU(2) gauge groups, and the corresponding associated Abelian and/or non-Abelian gauge fields. From version 1.1 onward, CosmoGattice also allows to simulate the production of gravitational waves. Simulations can be done either in a flat space-time background, or in a homogeneous and isotropic (spatially flat) expanding FLRW background. CosmoGattice provides symplectic integrators, with accuracy ranging from O (delta t(2)) up to O(delta t(10)), to simuate the non-linear dynamics of the appropriate fields in comoving three-dimensional lattices. The code is parallelized with MPI, and uses a discrete Fourier Transform parallelized in multiple spatial dimensions, which makes it a very powerful code for probing physical problems with well-separated scales. Moreover, the code has been designed as a `platform' to implement any system of dynamical equations suitable for discretization on a lattice.

Abstract: The KM3NeT Collaboration is building and operating two deep sea neutrino telescopes at the bottom of the Mediterranean Sea. The telescopes consist of latices of photomultiplier tubes housed in pressure-resistant glass spheres, called digital optical modules and arranged in vertical detection units. The two main scientific goals are the determination of the neutrino mass ordering and the discovery and observation of high-energy neutrino sources in the Universe. Neutrinos are detected via the Cherenkov light, which is induced by charged particles originated in neutrino interactions. The photomultiplier tubes convert the Cherenkov light into electrical signals that are acquired and timestamped by the acquisition electronics. Each optical module houses the acquisition electronics for collecting and timestamping the photomultiplier signals with one nanosecond accuracy. Once finished, the two telescopes will have installed more than six thousand optical acquisition nodes, completing one of the more complex networks in the world in terms of operation and synchronization. The embedded software running in the acquisition nodes has been designed to provide a framework that will operate with different hardware versions and functionalities. The hardware will not be accessible once in operation, which complicates the embedded software architecture. The embedded software provides a set of tools to facilitate remote manageability of the deployed hardware, including safe reconfiguration of the firmware. This paper presents the architecture and the techniques, methods and implementation of the embedded software running in the acquisition nodes of the KM3NeT neutrino telescopes. Program summary Program title: Embedded software for the KM3NeT CLB CPC Library link to program files: https://doi.org/10.17632/s847hpsns4.1 Licensing provisions: GNU General Public License 3 Programming language: C Nature of problem: The challenge for the embedded software in the KM3NeT neutrino telescope lies in orchestrating the Digital Optical Modules (DOMs) to achieve the synchronized data acquisition of the incoming optical signals. The DOMs are the crucial component responsible for capturing neutrino interactions deep underwater. The embedded software must configure and precisely time the operation of each DOM. Any deviation or timing mismatch could compromise data integrity, undermining the scientific value of the experiment. Therefore, the embedded software plays a critical role in coordinating, synchronizing, and operating these modules, ensuring they work in unison to capture and process neutrino signals accurately, ultimately advancing our understanding of fundamental particles in the Universe. Solution method: The embedded software on the DOMs provides a solution based on a C-based bare-metal application, operating without a real-time embedded OS. It is loaded into the RAM during FPGA configuration, consuming less than 256 kB of RAM. The software architecture comprises two layers: system software and application. The former offers OS-like features, including a multitasking scheduler, firmware updates, peripheral drivers, a UDP-based network stack, and error handling utilities. The application layer contains a state machine ensuring consistent program states. It is navigated via slow control events, including external inputs and autonomous responses. Subsystems within the application code control specific acquisition electronics components via the associated driver abstractions. Additional comments including restrictions and unusual features: Due to the operation conditions of the neutrino telescope, where access is restricted, the embedded software implements a fail-safe procedure to reconfigure the firmware where the embedded software runs.