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Tweed.README

Copyright © 2016, 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>

Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without any warranty.

Introduction

TWEED is a system for organizing engineering software. TWEED software applications can be moved freely, as a group, from one computer to another. All software versions can be maintained and all dependencies remain intact. TWEED is the Transferable Working Environment for Engineering Design.

In the domains of computational science and computer-aided engineering it is common to develop workflows to accomplish a task or investigate a process. The workflow comprises a set of software applications and associated data. A problem with many workflows is that they are fragile. Hardware breaks, software licenses expire, data in restricted formats becomes inaccessible. It can be a major task to re-build complex, carefully constructed workflows. The purpose of TWEED is to make it easier to develop sustainable workflows . Using the term sustainable in this context is to say the workflows should be easy to move around and durable over time.

In this model TWEED provides the workflow applications. The user supplies, or generates, the data. Applications are included in TWEED for tasks such as 3D modelling and numerical simulation. Users may choose from applications geared towards manufacturing operations, such as 2D draughting, or instead concentrate efforts on research and development using advanced optimization algorithms, as one example. Tools are included for generating grids for arbitrarily complex shapes and displaying results.

A key feature of TWEED is the separation of the applications from the underlying operating system. TWEED may be installed on any computer running any operating system. This includes laptops and supercomputers and anything in between. All that is needed is disk space for the applications and their libraries (10 GB is recommended).

The separation of the applications from the operating system makes the working environment transferable. This is useful for an engineer moving a workflow that has been developed on one computer to another, possibly different, computer. It is also useful in scaling a development environment, on a small system, to a production environment, on a larger system. The installation of the applications is exactly the same in each case.

Package Managers

A major advantage of using TWEED in preference to the operating system package managers is the relative speed of upgrading packages. Whereas the upgrade cycle of the operating system packages may be in the region of 2--3 years, application upgrades in TWEED may be performed within days. This is especially helpful in the realm of computational science, where new methods are being introduced at a rapid pace.

TWEED automates the compilation and build processes of new package versions and keeps track of dependencies. In comparison to individual installations from source, TWEED keeps the filesystem neat and tidy. It is also easier to maintain, having dedicated commands for upgrading packages and removing unused files.

To make this possible TWEED makes use of modern package management software. Three package managers are used:

  1. GNU Guix
  2. Nix
  3. HashDist

A shared characteristic of these package managers is their ability to install all of the required dependencies of a given package in a unique location, alongside the main operating system. This allows for multiple versions of the same application to be installed and made available simultaneously. On a multi-user system, it is also possible for each user to individually specify their own set of preferred applications.

Applications

TWEED comprises an instruction set and configuration files to install the following applications:

  1. LibreCAD---2D draughting
  2. FreeCAD---3D modelling
  3. Gmsh---grid generation
  4. FEniCS---numerical simulation (finite element)
  5. OpenFOAM---numerical simulation (finite volume)
  6. ParaView---post processing

Directory Structure

The directory structure for a typical TWEED installation is shown in the diagram below. The configuration files are stored in the tweed directory, located in the user's home directory. The three package managers use the directories $HOME/.hashdist, /gnu and /nix respectively to store the application files. GNU Guix uses sub-directories in /var to store log files and database files.

  / (root)
  ├── OS
  ├── var
  │   ├── guix
  │   └── log
  │       └── guix
  │
  ├── $HOME
  │   ├── .hashdist
  │   └── tweed
  │       ├── hashdist
  │       └── hashstack
  │
  ├── gnu
  └── nix

A user may install a subset of the TWEED packages. It is also possible for the user to extend the list of packages, beyond the group offered by TWEED. For details of the installation procedure, please see the file INSTALL.

Data Formats

The applications in TWEED make use of and generate data. Each application defines its own internal data structure, optimised for that application in particular. When there is a need to transfer data from one application to another it is necessary to use a data format that is recognised by both. There are a number of industry standard data formats for this purpose. These are well-established and widely used. In addition, there are specific data formats used by particular applications only. TWEED applications are able to make use of both types of data format. Communication between the applications is possible in a number of ways. A configuration of applications and exchange formats that demonstrates the principle is shown in the diagram below:

connectivities

This configuration forms a template for a typical engineering workflow. It is suitable for a wide range of design and development projects. The Gmsh application is central in this configuration. It provides the pre- and post-processing facilities for computer simulations. Gmsh is capable of generating the geometry for simple meshes itself. For more complex cases the geometry can be defined in FreeCAD and passed on to Gmsh. Finite element models, using the meshes from Gmsh, can be solved with FEniCS. Finite volume models can be solved with OpenFOAM. Result files can be passed back to Gmsh or on to ParaView for post-processing.

In this configuration there are three standard file formats:

  1. DXF - 2D CAD data
  2. STEP - 3D CAD data
  3. XDMF - mesh and result data

and two specific formats:

  1. MSH - Gmsh mesh and result data
  2. FOAM - OpenFOAM mesh and result data

All of the applications in TWEED can read from and write to at least one standard data format. For example, FEniCS can write out result files in xdmf format. These files can subsequently be read in by ParaView.

However, the best method for communication with the Gmsh application is to use the Gmsh-specific msh format. To do this, input/output (i/o) scripts are used to convert the data to and from the numerical solver formats.

In the case of FEniCS, the multi-format utility meshio can be used to convert between xdmf and msh formats. For OpenFOAM, gmshToFoam is available, supplied as one of the mesh conversion utilities. It is also possible to convert OpenFOAM result data to Gmsh msh format. An example script is foam2gmsh.py, available from the ONELAB wiki.

Future

Over time, in the development of TWEED itself, packages may be added to or subtracted from the included group. However, it is an objective that the size of the group will stabilize at a figure that can be reasonably maintained by a single engineer. This figure has not been fixed. Suggestions are welcome!

Infrequently, there may also be change to the list of package managers used by TWEED. An ideal list would contain a single package manager. This is a long-term objective. However, the list may increase or decrease in length temporarily as package management technology evolves and as the availability of applications provided by the different package managers changes.

Paul Garlick

April 2018