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Software

Software

Please find further information and user's documentation by following the links below:

 

DfAnalyzer framework

DfAnalyzer framework is an instantiation of ARMFUL architecture that can be coupled to existing Scientific Workflow Management Systems (SWMS) and scientific applications. DfAnalyzer keeps all the parallel execution control at the code of the SWMS or the scientific application. It is only recommended to couple Provenance Gatherer to existing SWMS without provenance data management. If the SWMS manages provenance data, it is recommended to extend the provenance support of the SWMS with the purpose of managing raw data from files.

d-Chiron

d-Chiron is a Scientific Workflow Management System with parallel capabilities that manages complex data-intensive workflows and registers data provenance at runtine to enable user steering and human-in-the-loop. d-Chiron utilizes MySQL Cluster as its core in-memory distributed data structure used for managing execution, provenance, and domain dataflow data.

Download  The HPC4E Seismic Test Suite

 

Download  The HPC4E Seismic Test Suite

 

 

MaPHyS

MaPHyS (Massively Parallel Hybrid Solver) is a software package whose prototype was initially developed in the framework of the PhD thesis of Azzam Haidar (CERFACS) and further consolidated thanks to the ANR-CIS Solstice funding. This parallel linear solver couples direct and iterative approaches. The underlying idea is to apply to general unstructured linear systems domain decomposition ideas developed for the solution of linear systems arising from PDEs

PaStiX

PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. Numerical algorithms are implemented in single or double precision (real or complex) using LLt, LDLt and LU with static pivoting (for non symmetric matrices having a symmetric pattern). This solver provides also an adaptive blockwise iLU(k) factorization that can be used as a parallel preconditioner using approximated supernodes to build a coarser block structure of the incomplete factors.

Download  The HPC4E Seismic Test Suite

 

Download  The HPC4E Seismic Test Suite

 

 

BOAST

BOAST is a code generator that allows powerful meta-programming of computing kernels with optimizations.

3D acoustic wave simulation

Open source hybrid MPI/OpenMP finite difference code for 3D acoustic wave equation.

Download  The HPC4E Seismic Test Suite

 

Download  The HPC4E Seismic Test Suite

 

libMesh

libMesh is an open-source finite-element library that supports parallel adaptive mesh refinement and has been used in several multi-physics applications. As an application built upon the libMesh library, libMesh-sedimentation simulates turbidity currents typically found in geological processes. The sediment transported due to fluid motion is described by a Eulerian framework in which the mathematical models result from the incompressible Navier-Stokes equations (fluid) combined with an advection-dominated transport equation (sediment concentration). 

ALYA

The Alya System is a Computational Mechanics code capable of solving different physics, each one with its own modelization characteristics, in a coupled way. Among the problems it solves are: convection-diffusion reactions, incompressible flows, compressible flows, turbulence, bi-phasic flows and free surface, excitable media, acoustics, thermal flow, quantum mechanics (DFT) and solid mechanics (large strain). ALYA is written in Fortran 90/95 and parallelized using MPI and OpenMP.

Download   The HPC4E Seismic Test Suite

Download  The HPC4E Seismic Test Suite

StarVZ

StarVZ consists in a performance analysis workflow that combines the power of the R language (and the tidyverse realm) and many auxiliary tools to provide a consistent, flexible, extensible, fast, and versatile framework for the performance analysis of task-based applications that run on top of the StarPU runtime (with its MPI layer for multi-node support). Its goal is to provide a fruitful prototypical environment to conduct performance analysis hypothesis-checking for task-based applications that run on heterogeneous (multi-GPU, multi-core) multi-node HPC platforms. StarVZ has been successfully applied to the performance analysis of a dense cholesky factorization using eight hybrid nodes with 224 cores and 16 GPUs, suggesting changes to the runtime that enable performance gains of up to 13% in total makespan. The source code of this framework is released under the GPLv3 license.

FWI mock-up

Full Waveform Inversion (FWI) tool, is a geophysical imaging system that is at the center of the geophysical exploration. Its intent is to produce models of the Earth internals for exploration porpoises. FWI mock-up, is oriented towards providing a system that behaves like an actual FWI system in terms of HPC resources consumption. However, the results from the mock-up are not valid from the geophysical imaging point of view. FWI mock-up main aim is to enable the scientific community to test new programming models, parallel paradigms or hardware architectures at a low cost. Without needing to modify a real FWI system, without associated investment in the man power needed to port or optimize a production code for doing a performance evaluation.

Download   The HPC4E Seismic Test Suite

Download   The HPC4E Seismic Test Suite

SAVIME

SAVIME (Simulation Analysis and Visualization In MEmory) is a DBMS-like system that stores data in the format of typed multidiomensional arrays. It is desgined to help querying and vizualize numerical simulation data. However, it can also be used as an analytical in-memory array database management system. SAVIME is at early development stages, and supports only a handful of operations. But it is already able to perform many tasks, even for large datasets in memory.

AGIOS / TWINS

AGIOS is an I/O scheduling tool that can be used by I/O services to manage incoming I/O requests at files level. AGIOS aims at being generic, non-invasive, and easy to use. Moreover, it offers five scheduling algorithm options, covering multiple advantages and drawbacks: aIOLi, MLF, SJF, TO, TO-agg and TWINS.

Download   The HPC4E Seismic Test Suite

Download   The HPC4E Seismic Test Suite

 

 

Software used in the context of HPC4E

Cantera

HPC for Energy project also uses Cantera, a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. Cantera provides types (or classes) of objects representing phases of matter, interfaces between these phases, reaction managers, time-dependent reactor networks, and steady one-dimensional reacting flows. Cantera is currently used for applications including combustion, detonations, electrochemical energy conversion and storage, fuel cells, batteries, aqueous electrolyte solutions, plasmas, and thin film deposition. Please, feel free to download Cantera software tools by following this link.

 

SimGrid

SimGrid is a simulation toolkit allowing to study the behavior of large-scale distributed systems such as Grids, Clouds, HPC or P2P systems. In the context of the HPC4E project it is used to evaluate the performance at scale of MPI applications and to optimize their deployment. Please, feel free to download SimGrid toolkit by following this link.

 

DMTCP

DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc. It is robust and widely used (on Sourceforge since 2007). Among the applications supported by DMTCP are MPI (various implementations), OpenMP, MATLAB, Python, Perl, R, and many programming languages and shell scripting languages. With the use of TightVNC, it can also checkpoint and restart X-Window applications. The OpenGL library for 3D graphics is supported through a special plugin. It also has strong support for HPC (High Performance Computing) environments, including MPI, SLURM, InfiniBand, and other components. DMTCP supports the commonly used OFED API for InfiniBand, as well as its integration with various implementations of MPI, and resource managers (e.g., SLURM). Follow this link to dowload it.

 

Slurm

The Slurm Workload Manager (formerly known as Simple Linux Utility for Resource Management or SLURM), or Slurm, is a free and open-source job scheduler for Linux and Unix-like kernels, used by many of the world's supercomputers and computer clusters. It provides three key functions. First, it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job such as MPI) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending jobs. Slurm is the workload manager on about 60% of the TOP500 supercomputers, including Tianhe-2 that, until 2016, was the world's fastest computer. Slurm uses a best fit algorithm based on Hilbert curve scheduling or fat tree network topology in order to optimize locality of task assignments on parallel computers. Please, feel free to download Slurm following this link.