E-CAM Final Report
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2 Highlights from E-CAM Software Developments • E-CAM software library: During the lifetime of the project we built a library of software with more than 200 contributions in the areas of classical molecular dynamics (WP1), electronic structure (WP2), quantum dynamics (WP3) and meso- and multi-scale modelling (WP4). Many of these have applications in industry and are targeted at solving an industrial problem. E-CAM’s software modules satisfy the E-CAM style guidelines for best-practice programming, documentation and testing. – The community of users is large, and in some of our WPs the majority of contributions to the software were provided by external contributors not funded by the project. This is the case of WP2 and WP3, with 51% and 63% of the total number of E-CAM modules produced from participants to the Extended Software Development Workshops (ESDWs) and from collaborations, respectively. • E-CAM has developed transversal libraries aimed at tackling issues that become increasingly important when running applications at scale, in particular relating to the coordination of an ensemble of petascale calculations, and load balancing: – High Throughput Computing library (jobqueue_features) [1]: the library addresses interactive HTC workloads with HPC characteristics, dynamic task-scheduling leveraging the data analytics framework Dask and providing the ability to run multi-node tasks, and on heterogeneous resources (GPU, KNL, ...). In a prototypical application, the HTC library coupled with the OpenPathSampling code for rare events is being used to study the dynamical transitions of the binding/unbinding reaction of the SARS-CoV-2 main protease. – Load Balancing Library (ALL): ALL provides an easy and portable way to include dynamic load balancing into particle based simulation codes, improving the code scalability and the size of systems that can be simulated. The library has significant applicability in codes from the E-CAM community and beyond, and is already implemented in several codes (including the flagship code HemeLB from CompBioMed CoE [2]). • Multi-GPU version of DL_MESO_DPD [3]: The current multi-GPU version of DL_MESO_DPD scales with an 85% parallel efficiency up to 4096 GPUs. This version of the code also includes the ALL library for load balancing, and the Kokkos library for accelerator performance portability has been investigated. • Electronic structure library(ESL) [4]: The goal of the Electronic Structure Library (ESL) is to develop and maintain a set of common libraries for the electronic structure community. E-CAM has been working closely with the ESL for some years now, and we provided support for this community effort through our ESDWs in WP 2 Electronic Structure, and the access to our experts on code development. • Development of the OPS package: E-CAM has been supporting the development of rare events sampling methods [5] and the OpenPathSampling (OPS) library [6],[7], a Python library to facilitate path sampling simulations. OPS was interfaced with MD codes such as LAMMPS and GROMACS to take advantage of their high scalability. Furthermore, OPS was also integrated with our HTC library to run on the largest HPC sites in Europe. • Development of n2p2, a package that provides ready-to-use software for high-dimensional neural network potentials in computational physics and chemistry. One of the major advantages of n2p2 from the user’s perspective is its integration in LAMMPS, as a user contributed package, which allows one to run massively parallelised molecular dynamics simulations with pre-trained neural network potentials. • Development of PANNA: Properties from Artificial Neural Network Architectures[8], a package to train and validate all-to-all connected network models for Behler–Parrinello and modified-Behler–Parrinello type local atomic environment descriptors and atomic potentials. • In a collaboration with the CoE MaX and the NCCR MARVEL, we have developed a new procedure for automatically generating Maximally-Localised Wannier functions (MLWFs) for high-throughput frameworks[9]. This work can facilitate the development of novel materials.
