Category: Software

A new Graphical User Interface (GUI) on top of these workflow building blocks (and eventually on top of all the building blocks developed in BioExcel) is being developed: biobb web server. This GUI will ease the usage of BioExcel workflows and tools for a big community that is still not familiar with HPC programming, but have a real interest on this topic, which can include pharmaceutical companies (used to work with GUIs) but also entry level users, whose interest is demonstrated in the high number of registered users (~4000) and pipelines run as of today with web server interfaces such as MDWeb. biobb web server will allow users to run a set of chosen, pre-configured workflows built using BioExcel building blocks, such as a structure quality checking, a structure energy minimization, a complete MD setup, or a complete MD simulation (with length restrictions). The GUI will also provide an additional interactivity to our building blocks. A great example is the possibility to run a quality check of a structure, while at the same time a 3D representation of the molecule is shown in the same interface, highlighting the region of the structure of particular interest. This interactivity can be applied also to the set of analyses generated by the workflows.

Workflows will be submitted and treated by a queue manager, which will serve them in an on-demand processing model performed by Virtual Machines automatically deployed in an Open Nebula OneFlow cloud environment. A direct connection to HPC supercomputing infrastructures to submit long molecular dynamics simulations prepared using the portal will be studied.

biobb server will also be the entry point for BioExcel building blocks. The web page will gather all the information on how to obtain, install and run the building blocks and workflows generated by BioExcel: for developers or experts in the field (github, bioconda, biocontainers, VMs/Cloud) for HPC users (environment modules) and for entry level users (Galaxy, KNIME, web server).

Nek5000 is a computational fluid dynamics code that employs the spectral element method, ahigh-order weighted residual technique, for applications in a wide range of fields including fluid flow, thermal convection, conjugate heat transfer, combustion and magnetohydrodynamics. It features state-of-the-art, scalable algorithms that are fast and efficient on platforms ranging from laptops to the world’s fastest computers. Nek5000, which is actively developed and improved for more than 30 years at Argonne National Laboratory (ANL), was extended for the direct numerical simulation of low Mach number reactive flows at the Swiss Federal Institute of Technology Zurich and is been used to investigate gas-phase and catalytic combustion in a number of laboratory-scale setups of fundamental and applied interest including internal combustion engines. Nek5000 won a Gordon Bell prize for its outstanding scalability on high-performance parallel computers and the 2016 R&D 100 Award. It is part of the Center for Efficient Exascale Discretizations (CEED) co-design effort, and its user community involves hundreds of scientists and engineers in academia, laboratories and industry.

AVBP Combustion instabilities and emission prediction. Explosion in confined spaces.

Vistle: software environment that integrates simulations on supercomputers, post- processing and parallel interactive visualization in immersive virtual environments

UQit: Python toolbox for uncertainty quantification

PAAKAT: high-performance computing in-situ analysis tool

TPLS open-source program for simulation of two-phase flows. Flow modelling like oil and gas fl ows in long-distance pipelines or refi nery distillation columns, liquid cooling of micro-electronic devices, carbon capture and cleaning processes, water treatment plants, blood fl ows in arteries, and enzyme interactions.

FEniCS is a collection of software for automated solution of PDEs using FEM. FEniCS is a popular open-source (LGPLv3) computing platform for solving partial differential equations (PDEs). FEniCS enables users to quickly translate scientific models into efficient finite element code. With the high-level Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also powerful capabilities for more experienced programmers. FEniCS runs on a multitude of platforms ranging from laptops to high-performance clusters.

Coda Design process and simulation of full equipped aeroplanes. CFD coupling with computational structural mechanics including elastic effects.

waLBerla is a massively parallel simulation framework. It contains efficient, hardware specific compute kernels to get optimal performance on today’s supercomputing architectures. waLBerla employs a block-structured partitioning of the simulation domain including support for grid refinement. These grid data structures make it easy to integrate various data parallel algorithms like Multigrid, CG, or phasefield models. waLBerla uses the lattice Boltzmann method (LBM), which is an alternative to classical Navier-Stokes solvers for computational fluid dynamics simulations. All of the common LBM collision models are implemented (SRT, TRT, MRT). Additionally, a coupling to the rigid body physics engine pe is available. waLBerla is written in C++, which allows for modular and portable software design without having to make any performance trade-offs.