BGLgeom library

Course on Advanced programming for scientific computing

Politecnico di Milano (ITALY)

Author : Ilaria Speranza & Mattia Tantardini

Mailto : [email protected], [email protected]

Date : January 2017

---

The project

---

The BGLgeom library project is divided into three parts, each one in its own folder:

• libBGLgeom : Source code for BGLgeom library
• fracture_intersection : First application example
• network_diffusion : Second application example

libBGLgeom

This library wants to expand the Boost Graph Library (BGL) in order to manage geometrical properties needed by graphs for particular applications. For this purpouse, the library provides easy methods to append geometrical properties to a graph, such as coordinates for vertices or different geometries for the edges. It also provides functionalities to compute meshes, geometrical quantities related to the edges and find intersections between linear edges. It can handle both the 2 and the 3 dimensional setting.

fracture_intersection

This example concerns the creation of a graph starting from a raw set of fractures, i.e. lines, in a plane.

network_diffusion

In this example a simple diffusion problem on a graph representing a vascular network is solved.

---

How to build the library

---

Prerequisites

To compile the whole project you need five libraries: the Boost Graph Library, Eigen and the VTK library are required for the whole project, while GetFEM++ and the MANworks library are used only for the network diffusion application. We specify here the requirements for the first three libraries; for the last two, see the README file in the network_diffusion folder.

Boost Graph Library

Version >= 1.61.0 required.

You can download it from here: https://sourceforge.net/projects/boost/files/.

You don't need to compile anything, since the BGL is a header only library.

VTK library

Version >= 5.10 required

For more information see: http://www.vtk.org/download/

Alternatively, at Mox cluster just load the correspondent module:

module load vtk/5

Eigen

Version >= 3 required.

For more information see: http://eigen.tuxfamily.org/index.php?title=Main_Page

You do not have to compile anything, since the Eigen is a header only library.

Alternatively, at Mox cluster just load the correspondent module:

module load eigen/3

Installation

Configuration variables

Along with this project you are provided with a Makefile.inc in this folder. Before doing anything, edit it and change:

• PROJECT_FOLDER with the path where this folder resides in your system
• INSTALL_PATH with the path you want to install the library to
• mkBGLInc with the path where the BGL resides in your system
• mkGetFEMHome with the path to the home folder of the GetFEM library (needed only to compile the network_diffusion application)
• mkMANworksHome with the path to the home folder of the MANworks library (needed only to compile the network_diffusion application)
• TOL_VALUE with a value which represents the tolerance on being zero in the comparison of points. If you do not provide any value, a default one will be used.

Only if you do not use the module system at MOX department or you installed a new version of the vtk library, you also need to change:

• mkVtkInc with the path where the include files of the VTK library resides.
• mkVtkLib with the path where the VTK library resides
• mkEigenInc with the path where the Eigen library resides

Now you are ready to build the library.

Build the library

Just type

make RELEASE=yes all

to compile the library (static and dynamic version), the associated tests, the documentation (LaTeX and html) and to install the library. Omit RELEASE=yes if you want to compile them in debug mode.

NOTE: you will always have to specificy RELEASE=yes if you want full optimization for the code. Debug mode mainly enables some further controls and output messages.

Another way to compile the library is to enter the folder libBGLgeom and compile it from there. Type

make help

to view all possible commands and details.

Tests and documentation

To see the library's documentation and to run tests, enter the libBGLgeom directory and see the README file.

---

How to build applications

---

To have information on how to build the applications, view documentation, etc, you will find a README file in each one of the two folders.

Remember that you have to compile the BGLgeom library first.

---

DEV ENVIRONMENT

---

OS : Scientific Linux 6.8 (Carbon) 64-bit

Processor : Intel® Core™ i5-2430M CPU @ 2.40GHz × 4

Compiler : g++-4.9

vtk lib : 5.10

GetFEM++ lib: 5.0

Eigen lib: 3

Boost Graph Library: 1.61.0

MANworks lib: 1