Requirements

A UNIX-like operating system such as GNU/Linux, or the Windows subsystem for linux (see Windows subsystem for linux)
A recent Fortran compiler such as gfortran, which supports Fortran 2008
A recent C compiler such as gcc to compile the included libraries
git to download and update the source code
python3 with numpy, pandas and matplotlib for some of the included tools

Obtaining the source code

Run the following command in a folder to clone the complete repository:

git clone https://github.com/MD-CWI/afivo-streamer.git

If you only want the master branch, then you can use

git clone -b master --single-branch https://github.com/MD-CWI/afivo-streamer

The code can also be downloaded as a zip file. If there are difficulties accessing Github, there is also a Gitlab mirror, but it can lag a bit behind.

Compiling the source code

Go into the afivo-streamer folder and compile the code:

cd afivo-streamer
make

This will first compile the afivo library and its dependencies, and afterwards compile most of the programs included with afivo-streamer. To test whether the code is working as expected, you can run several tests using

bash run_test.sh

To run some of the examples, see running examples.

Updating to the latest version

If you want to update your previously downloaded code, go into your afivo-streamer folder and pull the new version:

git pull

Afterwards, you can recompile the code by typing

make

either in the afivo-streamer folder, or in a specific program folder with a Makefile.

Compilation flags and recompilation

A number of flags can be set to help with debugging or performance testing. To apply these, first remove all previously compiled files:

make allclean

This is also useful when upgrading e.g. the compiler on your system. Afterwards, a number of flags can be applied, most importantly:

make DEBUG=1 leads to a much slower executable that does all kinds of error checking (array bounds, division by zero etc.)
make PROF=gprof compile with -pg support for gprof
make PROF=gperftools link with libprofiler to enable gperftools, see https://teunissen.net/afivo/md_documentation_profiling.html
make COMPILER=ifort to use the ifort compiler

Afterwards, perform make allclean again to revert to the standard compilation settings.

Windows subsystem for linux

Follow the instructions on https://learn.microsoft.com/en-us/windows/wsl/install to install wsl (windows subsystem for linux). After installation, launch wsl. For Ubuntu/Debian (Ubuntu is the default), the required compilers and python tools can be installed with:

sudo apt update
sudo apt install gfortran gcc g++ make git python3 python3-numpy python3-pandas python3-matplotlib

Afterwards, the regular installation instructions can be followed. The Linux files are also accessible from Windows, so simulation output can be visualized from the Windows environment.

Potential issues and solutions

Compilation errors after pulling a new version

Remove the old compiles with make allclean
Rarely, the Silo or Hypre libraries have to be recompiled. To do this, go to afivo/external_libraries and execute the build_... scripts.

Specifying the compilers to use

Sometimes, no suitable compilers are found (or used). This can be overcome by manually specifying which compilers to use. If gcc, g++ and gfortran can be found in /usr/bin/, then this can for example be done with:

export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FORT=/usr/bin/gfortran

Missing libraries

/usr/bin/ld: cannot find -lsz. Solution (on Fedora) sudo dnf install libaec-devel

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