Quickstart Guide

[bibshow file=https://www.flexi-project.org/wp-content/uploads/latex_bibfiles/userguide.bib]

Installation

Prerequisites

FLEXI has been tested for various Linux distributions. This includes Ubuntu 14.04 LTS, 16.04 LTS and 18.04 LTS, OpenSUSE 42.1 and CentOS 7.
The suggested packages in this section can of course be replaced by self compiled versions.

The required packages for the Ubuntu Linux distributions are listed in the following table . Under Ubuntu, they can be obtained using the apt environment:

sudo apt-get install git
Package Ubuntu 14.04 Ubuntu 16.04 Ubuntu 18.04
git x x x
cmake x x x
cmake-curses-gui o o o
liblapack3 x x x
liblapack-dev x x x
gfortran x x x
g++ x x x
mpi-default-dev x x x
zlib1g-dev – x x
exuberant-ctags o o o

Table: Debian/Ubuntu packages. x: required, o: optional, -: not available

The required packages for OpenSUSE and CentOS are listed in the following table.

Under OpenSUSE, packages are installed by the following command.

sudo zypper install git

The PATH variable must be extended by the openmpi path

export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin

Under CentOS, packages are installed by the following command.

sudo yum install git

Additionally, the PATH variable must be extended by the openmpi path

export PATH=$PATH:/usr/lib64/openmpi/bin
Package OpenSUSE 42.1 CentOS 7
git x x
cmake x x
lapack-devel x x
openmpi x x
openmpi-devel x x
zlib-devel x x
gcc-fortran x x
gcc x –
gcc-c++ x x

Table: Required Red Hat packages under OpenSUSE and CentOS.

On some systems it may be necessary to increase the size of the stack (part of the memory used to store information about active subroutines) in order to execute FLEXI correctly. This is done using the command

ulimit -s unlimited

from the command line. For convenience, you can add this line to your .bashrc.

Obtaining the source

The FLEXI repository is available at GitHub. To obtain the most recent version you have two possibilities:

  • Clone the FLEXI repository from Github 
    git clone https://github.com/flexi-framework/flexi.git
  • Download FLEXI from Github: 
    wget https://github.com/flexi-framework/flexi/archive/master.tar.gz
tar xzf master.tar.gz

Note that cloning FLEXI from GitHub may not be possible on some machines, as e.g. the machines at the HLRS at the University of Stuttgart due to restricted internet access. Please refer to this section of the user guide for help.

Compiling the code

  • Open a terminal
  • Change into the FLEXI directory
  • Create a new subdirectory and use CMake to configure and compile the code 
    mkdir build; cd build
cmake ../
make

The executables flexi and posti_visu are contained in your FLEXI directory in build/bin/.

Custom configuration of compiler options may be done using

ccmake ../

For a list of all compiler options see the user guide.

Directory Paths

In the following, we write $FLEXIROOT as a substitute for the path to the FLEXI repository. Please replace $FLEXIROOT in all following commands with the path to your FLEXI repository or add an environment variable $FLEXIROOT.

Furthermore, the path to executables is omitted in the following, so for example, we write flexi instead of $FLEXIROOT/build/bin/flexi.

Here is some explanation for Linux beginners:

In order to execute a file, you have to enter the full path to it in the terminal. There are two different ways to enable typing flexi instead of the whole path (do not use both at the same time!)
1. You can add an alias for the path to your executable. Add a command of the form

alias flexi='$FLEXIROOT/build/bin/flexi'
to the bottom of the file ~/.bashrc. Source your ~/.bashrc afterwards with

. ~/.bashrc
2. You can add the FLEXI binary directory to your $PATH environment variable by adding

export PATH=$PATH:$FLEXIROOT/build/bin
to the bottom of the file ~/.bashrc and sourcing your ~/.bashrc afterwards.

Running the code

The following examples assume that the FLEXI environment variables have been made available, see the user guide.

  • Open a terminal
  • Navigate to a directory and copy a case folder 
    cd temp
  • Copy the cavity tutorial folder 
    cp -r $FLEXIROOT/tutorials/cavity/Basic_Re100 .
cd cavity
  • Run flexi 
    $FLEXI_DIR/flexi parameter_flexi.ini
  • Convert the output files to the vtu format 
    posti_visu cavity_State_0000000.200000000.h5
  • Visualize using e.g. ParaView. 

Basic Usage

For a basic overview of the framework and the single components of the flow solver a flowchart is given in the following Figure.

HOPR

A standalone high-order preprocessor HOPR has been developed to generate high-order meshes from input data from external linear mesh generators. Different file formats are supported. HOPR has been recently made open source under the GPLv3 license. It generates a FLEXI conform mesh format in HDF5 for efficient parallel initialization. For a complete overview of HOPR, see https://www.hopr-project.org.

HOPR can be compiled in the same way as FLEXI. The basic command to run HOPR is

hopr parameter.ini

FLEXI

FLEXI, a high order DGSEM based CFD solver, is the core module in the tool chain. Generally FLEXI requires two main files as input, a mesh file in HDF5 format generated by HOPR and a parameter file where the main settings for the CFD simulation are set. The results files generated by FLEXI are also HDF5 files.

The basic command to run FLEXI is

mpirun -np [no. processors] flexi parameter.ini

Parameter file

The parameter.ini file contains the main settings for the CFD simulation. The parameter file defines e.g.

  • CFL number (Courant-Friedrichs-Lewy)
  • polynomial degree,
  • simulation end time and dump/analyze intervals
  • boundary conditions
  • Initial and boundary states

A complete list of all runtime options that can be set in the parameter file is supplied in the user guide.

posti_visu tool

To visualize the results e.g. with ParaView, a converter tool is provided. The posti_visu tool takes the HDF5 files generated by FLEXI.

The basic command to run the posti_visu tool is

mpirun -np [no. processors] posti_visu parameter.ini [flexi_outputfile.h5]

In this case a parameter file is specified in which options like the type and amount of the visualization nodes and mesh options are defined – see the respective section of the userguide for all available options. You can also omit the parameter file argument:

mpirun -np [no. processors] posti_visu [flexi_outputfile.h5]
This runs posti_visu using only standard options, i.e.

  • equidistant visualization nodes
  • amount of visualizaion nodes equals number of collocation points per element
  • allowing for curved meshes
  • visualizing the conservative variables

HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. For further information and to download the software, visit the HDF5 website at https://www.hdfgroup.org.

Feature list

The currently implemented features of Flexi include

  • Equation systems:
    • compressible Euler equations
    • compressible Navier-Stokes equations
    • linear scalar advection and diffusion
  • Space discretization: DGSEM methode [bibcite key=KoprivaGassner2010][bibcite key=hindenlang2012explicit]
    • Legendre Gauss
    • Legendre Gauss Lobatto
  • Time discretization: explicit Runge-Kutta methods
    • standard RK methods
    • low storage RK methods [bibcite key=Carpenter1994]
    • strong stability preserving RK methods [bibcite key=niegemann2012efficient]
  • Two- or three-dimensional domains
  • Riemann solvers:
    • local Lax-Friedrichs
    • HLL
    • HLLC
    • Roe-Pike
  • Curved Meshes
  • Nonconforming Meshes via mortar interfaces [bibcite key=koprivamortar2002]
  • Shock capturing
    • Employing finite volume subcells
    • Several shock indicators avalable
  • Boundary conditions
    • Various subsonic inflow and outflow conditions [bibcite key=carlson2011inflow]
    • exact boundaries (Dirichlet)
    • periodic boundaries
    • slip wall (Euler wall)
    • non-slip walls (Navier-Stokes wall)
      • adiabatic
      • isothermal
  • Splitform discontinuous Galerkin schemes
  • Dealiasing [bibcite key=gassner2013accuracy]
    • filtering
    • overintegration
  • Lifting methods
    • Bassi Rebay 1 [bibcite key=BR1]
    • Bassi Rebay 2 [bibcite key=BR1]
  • Sponge zone [bibcite key=flad2014discontinuous]
  • Time averaging