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Sphere, a Smoothed Particle Hydrodynamics (SPH) Simulation Software

Set up Sphere

Preparations

Create installation dir and setup PREFIX variable used in this document’s examples:

export PREFIX=$HOME/sw/sph-new
mkdir $PREFIX

Install required system packages:

sudo apt-get install make g++ libhdf5-dev libvtk5-dev freeglut3-dev octave

Optionally, for viewing VTK files we recommend to use Paraview and for HDF5 files the hdf5-tools package contains some utility programs

sudo apt-get install paraview hdf5-tools

Set up H5Part

Obtain H5Part library

Download H5Part library

wget https://codeforge.lbl.gov/frs/download.php/170/H5Part-1.6.1.tar.gz

Unpack H5Part library

tar -xzf H5Part-1.6.1.tar.gz

Prepare system

On a current Debian Testing system the layout of paths of libhdf5-dev is different from what H5Part expects. Therefore we create a directory with two symlinks that point to the correct locations:

pushd /usr/local
mkdir hdf5
cd hdf5
ln -sfT /usr/include/hdf5/serial include
ln -sfT /usr/lib/x86_64-linux-gnu/hdf5/serial lib
popd

Check result:

ls -l /usr/local/hdf5

Compile and install

Now, change directory to h5part-1.6.1 and run configure and make install

cd H5Part-1.6.1
./configure --prefix=$PREFIX/h5part --with-hdf5path=/usr/local/hdf5
make -j8 install
cd ..

Set up GenNC

Download the Name Constant Generator tool from https://savannah.nongnu.org/projects/named-constant/:

wget http://download.savannah.gnu.org/releases/named-constant/named-constant-0.3.1.tar.gz

Unpack:

tar -xzf named-constant-0.3.1.tar.gz
cd named-constant-0.3.1
make prefix=$PREFIX install
cd ..

Now set the GENNC_HOME variable in your shell and also add the /bin directory to the $PATH:

export GENNC_HOME=$PREFIX/gennc
export PATH=$PATH:$GENNC_HOME/bin

Compile Sphere

First, you can set up some environment variables to control the compiler flags during the build. Recommended settings are:

export CXXFLAGS="-Wall -Wextra -m64 -O3 -march=native"
export CPPFLAGS="-DNDEBUG"
export LDFLAGS="-m64"

Run the script bootstrap to invoke the autotools, which will generate the configure script, and some other files:

./bootstrap

Now, run configure, setting the location of the H5Part library that we installed and also using the make shift HDF5 directory that we created:

./configure --prefix=$PREFIX/sph-v1.0.0 --with-h5part=$PREFIX/h5part --with-hdf5=/usr/local/hdf5

An alternative is to specify the HDF5 include and library directories separately:

./configure --prefix=$PREFIX/sph-v1.0.0 --with-h5part=$PREFIX/h5part \
 --with-hdf5-incdir=/usr/include/hdf5/serial --with-hdf5-libdir=/usr/lib/x86_64-linux-gnu/hdf5/serial
make -j8 install
export PATH=$PATH:$PREFIX/sph-v1.0.0/bin

Build test input files (scenes)

This takes about an hour

cd sph/vtk
make

Running Sphere

sphere -2 -d1e-5 -S1000 -irk3 vtk/test-cases2/2D/monaghan-ellipsis/mittel/test.vtk

This command runs Sphere in 2D mode, with fixed timestep of 1/100000 s using the RK3 (Simpson rule) integrator with a save rate of 1000 Hz. The last argument is the inititial state in a VTK file. The simulation creates a file sph-result-2d.h5 which contains the particle data at each of the save time steps. Also, information about the simulation is printed to the console in XML format and saved also in the file sph-result-2d.sphrun.xml.

For more information on sphere options, run

sphere -h

sphere is just a shell script that launches the actual SPH binary. Some settings are not yet available as options in sphere but can only be triggered using environment variables.

Converting output to VTK

There is the script h52vtk.sh, which converts a single HDF5 file into a series of VTK files, which can be viewed with Paraview.

h52vtk.sh sph-result-2d.h5

This creates a directory sph-result-2d with files res_00000.vtk, res_00001.vtk, … which contain the dynamic particle data and a file boundary.vtk which contains the static (boundary) particle data.