Search

EasyBuild is a community effort to develop a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. As its name suggests, EasyBuild makes software installation easy by automating builds, making previous builds reproducible, resolving dependencies, and retaining logs for traceability. It is also one of the components of the European Environment for Scientific Software Installations (EESSI), a collaboration between different European HPC sites and industry partners, with the common goal to set up a shared repository of scientific software installations that can be used on a variety of operating systems and computer architectures. It can be applied in a full size HPC cluster, a cloud environment, a container or a personal workstation.With the deluge of data in the genomics field (e.g., clinical data) and the concomitant development of new technologies, the number of data analysis software has exploded in recent years. The fields of bioinformatics and cheminformatics follow this same trend with ever more developments to optimize and parallelize analyses. The bioinformatics field is now the main provider of new software in EasyBuild. Developers of those tools are not always professional developers, and they do therefore not always follow best practices when releasing their software. As a result, many tools are complicated to install, making them ideal candidates for porting their installation to EasyBuild so that they become more easily accessible to end users.We propose to introduce users to EasyBuild and EESSI, and to port new software to EasyBuild/EESSI (e.g., the participant’s own or favourite software), thereby making it available and discoverable to the entire EasyBuild community. In parallel we would like to build bridges between EESSI and Galaxy to make the scientific software more accessible to researchers in the domain.

Joint technical report on results of (a) porting and optimisation of at least 8new modules related to those developed in the ESDWs tomassively parallel machines(STFC); and (b) benchmarking and scaling of at least 8 new modules relatedto those developed in the ESDWs on a variety of architectures (Juelich).

Committor analysis is a powerful, but computationally expensive, tool to study reaction mechanisms in complex systems. The committor can also be used to generate initial trajectories for transition path sampling, a less-expensive technique to study reaction mechanisms. The main goal of the project was to facilitate an implementation of committor analysis in the software application OpenPathSampling (http://openpathsampling.org/) that is performance portable across a range of HPC hardware and hosting sites. We do this by the use of hardware-enabled MD engines in OpenPathSampling coupled with a custom library extension to the data analytics framework Dask (https://dask.org/) that allows for the execution of MPI-enabled tasks in a steerable High Throughput Computing workflow. The software developed here is being used to generate initial trajectories to study a conformational change in the main protease of the SARS-CoV-2 virus, which causes COVID-19. This conformational change may regulate the accessibility of the active site of the main protease, and a better understanding of its mechanism could aid drug design.

Joint technical report on results of the porting and optimisation of 8 new E-CAM modules to massively parallel machines and their benchmarking and scaling on a variety of architectures. The development of the modules was done in the context of the E-CAM program of Extended Software DevelopmentWorkshop (ESDW) events.

Joint technical report on results of the porting and optimisationof 8 new E-CAM modules to massively parallel machines and their benchmarking and scaling on a variety ofarchitectures. The development of the modules was done in the context of the E-CAM program of Extended SoftwareDevelopmentWorkshop (ESDW) events.

Committor analysis is a powerful, but computationally expensive, tool to study reaction mechanisms in complex systems. The committor can also be used to generate initial trajectories for transition path sampling, a less-expensive technique to study reaction mechanisms. The main goal of the project was to facilitate an implementation of committor analysis in the software application OpenPathSampling (http://openpathsampling.org/) that is performance portable across a range of HPC hardware and hosting sites. We do this by the use of hardware-enabled MD engines in OpenPathSampling coupled with a custom library extension to the data analytics framework Dask (https://dask.org/) that allows for the execution of MPI-enabled tasks in a steerable High Throughput Computing workflow. The software developed here is being used to generate initial trajectories to study a conformational change in the main protease of the SARS-CoV-2 virus, which causes COVID-19. This conformational change may regulate the accessibility of the active site of the main protease, and a better understanding of its mechanism could aid drug design.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community., The authors would also like to thank the Psi-k network for having partially funded several of the ESL workshops. A.O., E.A., D.L.-D., S.G., E.K., A.A.M., and M.C.P. received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 676531 (Centre of Excellence project E-CAM). The same project has partly funded the extended software development workshops in which most of the ESL coding effort has happened. A.G., S.M., and E.A. acknowledge support from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 824143 (Centre of Excellence project MaX). M.A.L.M. acknowledges partial support from the DFG through Project No. MA-6786/1. D.G.A.S. was supported by the U.S. National Science Foundation (NSF) (Grant No. ACI1547580). M.C.P. acknowledges support from the EPSRC under Grant No. EP/P034616/1. A.A.M. acknowledges support from the Thomas Young Centre under Grant No. TYC-101, the Wannier Developers Group, and all of the authors and contributors of the wannier90 code (see Ref. 115 for a complete list). A.M.E. acknowledges support from CoSeC, the Computational Science Centre for Research Communities, through CCP5: The Computer Simulation of Condensed Phases (EPSRC Grant Nos. EP/M022617/1 and EP/P022308/1). A.G. and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. PGC2018-096955-B-C42). E.A., A.G., and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. FIS2015-64886- C5). Y.P., D.L.-D., and E.A. acknowledge support from the Spanish MINECO and EU Structural Investment Funds (Grant No. RTC2016-5681-7). M.L. acknowledges support from the EPRSC under Grant No. EP/M022668/1. M.L., M.J.T.O., and Y.P. acknowledge support from the EU COST action (Grant No. MP1306). J.M. was supported by the European Regional Development Fund (ERDF), project CEDAMNF (Reg. No. CZ.02.1.01/0.0/0.0/15-003/0000358). V.W.-Z.Y., W.P.H., Y.L., and V.B. acknowledge support from the National Science Foundation under Award No. ACI-1450280 (the ELSI project). V.W.-Z.Y. also acknowledges a MolSSI fellowship (NSF Award No. ACI-1547580). Simune Atomistics S.L. is thanked for allowing A.H.L. and Y.P. to contribute to the ESL, as is Synopsys, Inc., for the partial availability of F.C.

This deliverables outlines E-CAM’s Extended Software DevelopmentWorkshop (ESDW) programme for 2020/2021. In addition, it provides the most recent guidelines for the organisation of these events, including: the scope of training at ESDW events the structure of ESDWs; the timeline for the organization of an ESDW; the capture of lectures at ESDWs; the role of the E-CAM online training infrastructure; the role of E-CAM programmers at ESDW events; the concept of a module in E-CAM and its acceptance criteria. The present document is an updated version of deliverable D5.4 [https://doi.org/10.5281/zenodo.2586966] submitted in March 2019, on the guidelines for content, structure and output for our ESDWs. These guidelines are intended to be a living document which evolves to reflect experience gained in running the ESDWs and thus they are subject to further revision based on the outcomes of each year’s activities, with the present document being the fifth, and last iteration. This updated version of the guidelines, valid from April 2020 to March 2021, will help to ensure that the workshops run consistently across the scientific Work Packages (WPs) and meet the quality standards for E-CAM software. In addition to refining the guidelines for our ESDWs, this deliverable also analyses the profile of the participants to our ESDWs and the results of our satisfaction surveys. Specifically, we will report on the analysis of the participants profile (country of origin, gender, qualification) the satisfaction surveys training needs highlighted by the participants of our ESDWs. When appropriate, output from these surveys has been used to refine the reported guidelines.

This deliverables outlines E-CAM’s Extended Software DevelopmentWorkshop (ESDW) programme for 2020/2021. Inaddition, it provides the most recent guidelines for the organisation of these events, including: the scope of training at ESDW events the structure of ESDWs; the timeline for the organization of an ESDW; the capture of lectures at ESDWs; the role of the E-CAM online training infrastructure; the role of E-CAM programmers at ESDW events; the concept of a module in E-CAM and its acceptance criteria. The present document is an updated version of deliverable D5.4 [https://doi.org/10.5281/zenodo.2586966] submitted in March 2019, on the guidelines forcontent, structure and output for our ESDWs. These guidelines are intended to be a living document which evolves toreflect experience gained in running the ESDWs and thus they are subject to further revision based on the outcomesof each year’s activities, with the present document being the fifth, and last iteration. This updated version of theguidelines, valid from April 2020 to March 2021, will help to ensure that the workshops run consistently across thescientific Work Packages (WPs) and meet the quality standards for E-CAM software. In addition to refining the guidelines for our ESDWs, this deliverable also analyses the profile of the participants toour ESDWs and the results of our satisfaction surveys. Specifically, we will report on the analysis of the participants profile (country of origin, gender, qualification) the satisfaction surveys training needs highlighted by the participants of our ESDWs. When appropriate, output from these surveys has been used to refine the reported guidelines.

Update on "Hardware Developments IV" (Deliverable 7.7: https://doi.org/10.5281/zenodo.3256137)which covers: - Report on hardware developments that will affect the scientific areas of interest to E-CAM and detailed feedback to the project software developers; - discussion of project software needs with hardware and software vendors, completion of survey of what is already available for particular hardware platforms; and, - detailed output from direct face-to-face session between the project endusers, developers and hardware vendors.

Update to E-CAM Software Platform IV that highlights the services that are currently available to E-CAM users and outlines the purpose of each service. These services include: Online software repositories and associated services, A number of project management services to facilitate effective collaboration on software projects and to streamline the creation of associated publications, An online training platform populated with the training content delivered at the project’s Extended Software Development Workshops. Over the lifetime of the project these online services will continue to mature and expand, particularly in the case of online learning as new content is added and the platform is increasingly leveraged by training events.

Update toE-CAM Software Platform IV that highlights the services that are currently available to E-CAM users and outlines the purpose of each service. These services include: Online software repositories and associated services, A number of project management services to facilitate effective collaboration on software projects and to streamline the creation of associated publications, An online training platform populated with the training content delivered at the project’s Extended Software Development Workshops. Over the lifetime of the project these online services will continue to mature and expand, particularly in the case of online learning as new content is added and the platform is increasingly leveraged by training events.

In this report for Deliverable 4.5 of E-CAM, nine software modules in meso– and multi–scale modelling are presented. The modules represented efforts integrated into larger software packages and thus extend their applicability. The first package is DL_MESO_DPD [1, 2] that provides a toolbox to do Dissipative Particle Dynamics (DPD) simulations, routinely used in an industrial context to find out the static and dynamic behaviour of soft-matter systems. The DL_MESO packages has previously (in [3]) been identified as one of the important codes for mesoscale simulations within E-CAM, and the single- and multi-GPU version of DL_MESO_DPD have already been introduced in deliverables D4.2[4] and D4.3[5], respectively, and recently tested up to 4096 GPUs with results presented in D4.4[6]. In the current deliverable, we present the following 4 modules that relate to DL_MESO_DPD’s extension, performance and optimisation onmulti-GPU architectures: • Surface boundary conditions • Many-body DPDmodel on single GPU • Long Integer on DL_MESO_DPD multi-GPU • Load balancing formulti-GPU DL_MESO. The second software package covered in this report is A Load-balancing Library (ALL), which is a dynamic load balancing library that is both efficient and widely applicable. Load-balancing is a complex topic, particularly when considering multi-scale approaches, due to heterogeneity in both computational approaches and target architectures. Therefore, it has has not yet been implemented in a number of important codes of the E-CAM multi-scale community, e.g. DL_MESO, DL_POLY, Espresso, Espresso++, to name a few. Other codes (e.g. LAMMPS) have implemented somewhat simpler schemes, which might however turn out to lack sufficient flexibility to accommodate all important cases. Therefore, the ALL library was created in the context of an Extended Software DevelopmentWorkshop (ESDW) within E-CAM, where code developers of CECAM community codes were invited together with E-CAM postdocs, to work on the implementation of load balancing strategies. The goal of this activity was to increase the scalability of these applications to a larger number of cores on HPC systems, for spatially inhomogeneous systems, and thus to reduce the time-to-solution of the applications. ALL aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the Juelich Supercomputing Centre at Forschungszentrum Juelich. It includes several load-balancing schemes, with additional approaches currently being added. The following list gives an overview about the currently included schemes, which each represent a module presented in this report: • Tensor method • Staggered Grid method • UnstructuredMesh scheme • Voronoi Mesh scheme • Histogram method. A short description is written for each module, followed by a link to the respectiveMerge-Request on theGitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules.

The purpose of the current document is to deliver a joint technical report on results of the initial porting and optimization of 8 new E-CAM modules to massively parallel machines and their benchmarking and scaling on a variety of architectures. The development of the modules was done in the context of the E-CAM program of Extended Software Development Workshop (ESDW) events. The particular list of all relevant applications that were investigated were: for Classical Molecular Dynamics: jobqueue_features, a High Throughput Computing library developed by E-CAM. The associated modules were developed in the context of the ESDW "Intelligent High Throughput Computing for Scientific Applications". for Electronic Structure: The ESL demonstrator which is built from the components of the ESL bundle. The associated modules were developed in the context of an ESDW on scaling electronic structure applications. for Quantum Dynamics: CP2K integration into PaPIM code, and the new Surface Hopping code. The associated modules were developed in the context of an ESDW in Quantum Dynamics. for Meso- and Multi-scale Modelling: DL_MESO_DPD multi-GPU support, and GROMACS implementation of GC-AdResS. The associated modules were developed in relation to an ESDW in Meso and multiscale modeling. For the jobqueue_features HTC library, PaPIM, and GC-AdResS; the modules presented in this deliverable represent the incorporation or use of external, scalable community code (in particular LAMMPS, CP2K and GROMACS) as libraries or test-beds. We have looked at the scalability of these community codes in previous iterations of this deliverable2 and do not repeat this effort here. Since these applications are the computational workhorses, we rather investigate the overhead incurred by their incorporation. The HTC library developed by E-CAM is shown to have very low overhead with the potential for significant time (and CPU) savings for appropriate applications. The CP2K integration in PaPIM has been verified and a scientific use case that takes this combination to extreme scale is under preparation. For the GC-AdResS implementation in GROMACS, we find that the automated load-balancing of GROMACS does not deal well with the adaptive resolution scheme and scalability is quite poor as a result. The incorporation of the scheme into ESPResSo++ is being considered and is likely to benefit from the load balancing library also being developed by E-CAM. For the ESL bundle and demonstrator, we see there is still some improvement to be made to the scalability of the demonstrator, which we hope to be further addressed in the upcoming second part of the relevant ESDW3. We only show here some initial assessments of the ESL demonstrator (which is built on top of the ESL bundle). We find that the Surface Hopping code is quite scalable but suffers from a similar problem to the previous iteration of PaPIM: there is insufficient computational work to keep cores busy and MPI overheads can dominate as a result. A significant success story has been the multi-GPU developments undertaken for DL_MESO_DPD. This has been shown to be scalable out to 2048 Tesla P100 GPUs, which is equivalent to almost 10 Petaflops of raw double precision compute performance.

In the particular use case for the mini-project described here, E-CAM is interested in the challenge of bridging timescales. To study molecular dynamics with atomistic detail, timesteps must be used on the order of a femto-second. Many problems in biological chemistry, materials science, and other elds involve events that only spontaneously occur after a millisecond or longer (for example, biomolecular conformational changes, or nucleation processes). That means that around 1012 time steps would be needed to see a single millisecond-scale event. This is the problem of ,,rare events" in theoretical and computational chemistry. Modern supercomputers are beginning to make it possible to obtain trajectories long enough to observe some of these processes, but to fully characterize a transition with proper statistics, many examples are needed. In order to obtain many examples the same application must be run many thousands of times with varying inputs. To manage this kind of computation, task scheduling library is needed. The main elements of the mentioned scheduling library are: task de nition, a task scheduling (handled in Python) and task execution (facilitated by the MPI layer). While traditionally an HTC workload is looked down upon in the HPC space, the scienti c use case for extreme-scale resources exists and algorithms that require a coordinated approach make ecient libraries that implement this approach increasingly important in the HPC space. The 5 Peta op booster technology of JURECA is an interesting concept with respect to this approach since the ooading approach of heavy computation marries perfectly to the concept outlined here.

Update to E-CAM Software Platform III that highlights the services that are currently available to E-CAM users and outlines the purpose of each service. These services include: • Online software repositories and associated services, • A number of project management services to facilitate effective collaboration on software projects and to streamline the creation of associated publications, • An online training platform populated with the training content delivered at the project’s Extended Software Development Workshops. Over the lifetime of the project these online services will continue to mature and expand, particularly in the case of online learning as new content is added and the platform is increasingly leveraged by training events.

Update to E-CAM Software Platform III that highlights the services that are currently available to E-CAM users and outlines the purpose of each service. These services include: • Online software repositories and associated services, • A number of project management services to facilitate effective collaboration on software projects and to streamline the creation of associated publications, • An online training platform populated with the training content delivered at the project’s Extended Software Development Workshops. Over the lifetime of the project these online services will continue to mature and expand, particularly in the case of online learning as new content is added and the platform is increasingly leveraged by training events.

Joint technical report on results of (a) porting and optimisation of at least 8 new modules related to those developed in the Extended Software Development Workshops (ESDWs) to massively parallel machines; and (b) benchmarking and scaling of at least 8 new modules related to those developed in the ESDWs on a variety of architectures.

6 software modules delivered to the E-CAM repository in the area of quantum dynamics based on user requests and their documentation.

6 software modules delivered to the E-CAM repository in the area of quantum dynamics based on user requests and their documentation.

Joint technical report on results of (a) porting and optimisation of at least 8 new modules related to those developed in the Extended Software Development Workshops (ESDWs) to massively parallel machines; and (b) benchmarking and scaling of at least 8 new modules related to those developed in the ESDWs on a variety of architectures.

Update on E-CAM software tools and platforms jointly by CH and Juelich which includes: - the E-CAM library of software modules and interfaces; - end users portal (to access E-CAM’s resources, make requests for software developments, register for events); - web infrastructure for teaching tools.

Update on E-CAM software tools and platforms jointly by CH and Juelich which includes: - the E-CAM library of software modules and interfaces; - end users portal (to access E-CAM’s resources, make requests for software developments, register for events); - web infrastructure for teaching tools.

Update on "Hardware Developments I" (Deliverable 7.1: https://doi.org/10.5281/zenodo.929533) which covers: - Report on hardware developments that will affect the scientific areas of interest to E-CAM and detailed feedback to the project software developers; - discussion of project software needs with hardware and software vendors, completion of survey of what is already available for particular hardware platforms; and, - detailed output from direct face-to-face session between the project endusers, developers and hardware vendors.

Update on "Hardware Developments I" (Deliverable 7.1: https://doi.org/10.5281/zenodo.929533) which covers: - Report on hardware developments that will affect the scientific areas of interest to E-CAM and detailed feedback to the project software developers; - discussion of project software needs with hardware and software vendors, completion of survey of what is already available for particular hardware platforms; and, - detailed output from direct face-to-face session between the project endusers, developers and hardware vendors.

Update on E-CAM software tools and platforms which includes: - the E-CAM library of software modules and interfaces; - end users portal (to access E-CAM’s resources, make requests for software developments, register for events); - web infrastructure for teaching tools.

Update on E-CAM software tools and platforms which includes: - the E-CAM library of software modules and interfaces; - end users portal (to access E-CAM’s resources, make requests for software developments, register for events); - web infrastructure for teaching tools.

The purpose of the current document is to deliver a joint technical report on results of the initial porting and optimisation of 8 new E-CAM modules to massively parallel machines and their benchmarking and scaling on a variety of architectures.

Review of actual hardware and software solutions and recommendations to software vendors