Simplified Tutorial for New Users

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Here you will find a step by step guide to downloading, installing, and running the Einstein Toolkit. For a more detailed tutorial, view the Tutorial for New Users.

Prerequisites

You will need a number of packages installed in order to download the Einstein Toolkit components, and if you follow the instructions in this tutorial. Instructions for the installation of such packages can be found at the beginning of each optionlist. The correct

For instance, on a Fedora-based system, the user is instructed to run:

yum -y install mpich2 mpich2-devel \
 gsl gsl-devel libjpeg-devel hdf5 hdf5-devel \
 gcc gcc-c++ gcc-gfortran patch \
 numactl-devel hdf5-mpich-devel \
 numactl hwloc subversion \
 git openssl-devel lapack-static

Please check the optionlist that is relevant for your system and make sure all required packages are installed before proceeding with the next step.

Downloading

A script called GetComponents is used to fetch the components of the Einstein Toolkit. GetComponents serves as convenient wrapper around lower level tools like git and svn to download the codes that make up the Einstein toolkit from their individual repositories. You may download and make it executable it as follows:

curl -O -L https://raw.githubusercontent.com/gridaphobe/CRL/ET_2015_11/GetComponents
chmod a+x GetComponents

GetComponents accepts a thorn list as an argument. To check out the needed components:

./GetComponents --parallel https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2015_11/einsteintoolkit.th

which downloads the master thorn list from the Einstein toolkit server and proceeds to download all thorns. This thornlist checks out Cactus, the Einstein Toolkit, and Simulation Factory.

Configuring

You may proceed to configure Simfactory which requires some changes for some OS.

cd Cactus
# for Debian
./simfactory/bin/sim setup --optionlist=debian.cfg --runscript debian.sh
# for Ubuntu, Mint
./simfactory/bin/sim setup --optionlist=ubuntu.cfg --runscript debian.sh
# for Fedora (you may have to log out and back in if you have just intalled mpich to make the module command work)
module load mpi
./simfactory/bin/sim setup --optionlist=fedora.cfg --runscript debian.sh
# OSX+MacPorts (last tested with Yosemite)
./simfactory/bin/sim setup --optionlist=osx-macports.cfg --runscript osx-macports.run
# OSX+Homebrew (last tested with Yosemite)
export CPATH=/usr/local/include LIBRARY_PATH=/usr/local/lib
./simfactory/bin/sim setup --optionlist=osx-homebrew.cfg --runscript generic-mpi.run

Accept the default values for all options.

Building

Now that you have configured Simfactory, you may build:

./simfactory/bin/sim build --mdbkey make 'make -j2' --thornlist=manifest/einsteintoolkit.th

Adjust -j2 to match the number of cores your machine possesses if you want to use more or less than 2 parallel build processes. This may take a while, as it compiles all the thorns specified in manifest/einsteintoolkit.th.

Running

The example files provided are mostly too large to run on a single machine. You can try however to run the static_tov example which is smallest and requires about 1.3GB of RAM to run and will run for about 24 hours using a single core. To speed up the run, you can try and reduce the resolution by increasing the parameters "CoordBase::dx", "CoordBase::dy", and "CoordBase::dz" from 8 to 12 which will reduce runtime to roughly 5 hours and memory consumption to 800MB.

 # modify parameter file for smaller memory footprint using sed
 sed '/CoordBase::d[xyz]/s/8/12/' <par/static_tov.par >par/static_tov_small.par
 # start simulation, watch log output
 ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --procs=1 --walltime=8:0:0
 ./simfactory/bin/sim show-output --follow static_tov

Cactus will use a sinlge MPI process and (unless you have set OMP_NUM_THREADS) will use as many OpenMP threads as you have cores on your computer. Under Linux use can use top -H to show all running threads.

Look at Results

When the simulation is complete (ie. when "All done" appears in the output), stop simfactory by pressing CTRL-C and move to the output directory. The command should be:

cd ~/simulations/static_tov/output-0000/static_tov_small

You should see a number of files with the extenstion .asc. These are 0-D (reductions of 3-D grid functions to scalar values) and 1-D ASCII output files that can be plotted with gnuplot.

In this case it's interesting to look at the maximum of the density (in the file hydrobase-rho.maximum.asc). Start gnuplot with the command:

gnuplot

and at the gnuplot prompt type:

plot 'hydrobase-rho.maximum.asc' using 2:3 with linespoints

This plots the data in column 3 (rho) as a function of the data in column 2 (time).

Rho of time lowres.png

As can be seen from the plot, the maximum of the density oscillates with decreasing amplitude around the initial value with a small drift upwards. Even though the initial model is supposed to be in equilibrium, numerical errors means that the numerical model is not exactly in equilibrium and it starts to oscillate. The oscillation energy is slowly dissipated by shocks, decreasing the oscillation amplitude, while the star contracts in response, increasing the maximum density.

A consistent picture can be seen by plotting the minimum of the lapse:

p 'admbase-lapse.minimum.asc' u 2:3 w lp

Lapse of time lowres.png

The quantity shows the same features as the maximum of the density, except the drift is downwards. The downwards trend stems from the contraction of the star. As the star contracts, the curvature of spacetime increases slightly. In response, the singularity avoiding lapse condition used here decreases the lapse.

As the oscillations and subsequent drift of the density and the lapse are caused by numerical error, increasing the numerical resolution will decrease these effects.

Further reading

The following resources provide more in-depth explanations of the tools and concepts used in this tutorial

  • Cactus users guide containing detailed information on a thorn structure and the support routines offered by Cactus. Also available in the 'doc' folder of your Cactus checkout in the file 'doc/UsersGuide.pdf'
  • Simfactory users guide which describes the available command for simfactory
  • visualization the visualization lecture of the new user's tutorial held at the APS meeting in Atlanta 2012
  • course page of the new user's tutorial held at the APS meeting in Atlanta 2012