Running the Simulations

Introduction

This page describes the steps taken to run the simulations using the model of pulse wave propagation, called Nektar1D. Having created the input files to the model, the next step was to use these as inputs to the computational model. This was performed in Linux using a series of commands at the terminal.

Requirements

You will need the following in order to run the simulations:

• An installation of Nektar1D (usually on a Linux platform)
• The input files to the simulations, created in the previous step.
• Some time (approximately 1 hour per simulation, although multiple simulations can be run simultaneously if you have access to multiple cores on your computer).

Steps

Installing Nektar1D

As stated on the Haemod Research Group website, "Nektar1D is our in-house code for solving the nonlinear, one-dimensional (1D) equations of blood flow in a given network of compliant vessels subject to boundary and initial conditions". It can be installed using the following steps:

1. Follow the instructions on this page to request the files required to compile Nektar1D.
2. Having obtained the files, you will then need to prepare the Linux installation for Nektar1D (it requires certain packages to be installed in order to be run), and compile the code. A manual with detailed instructions for doing this is available here. In addition, I have listed some additional notes on the installation process here.

Running the Simulations

Take the following steps to run the simulations:

1. Boot Linux
2. Open a new terminal
3. Set the current directory to that of the shared folder, e.g.

cd <shared folder path>

where <shared folder path> is the path of the shared folder as seen from Linux's perspective.

4. Use the command sh launch_starter to make (and clear any existing contents of) a directory in which to store the files generated whilst running the simulations, and to then copy files from the shared folder into this new directory.
5. Use the command sh launch_sims1 to run a batch of simulations.
6. If you specified to create multiple launch files (as described here), then you will need to repeat steps 2, 3 and 5 for each of the additional launch files. i.e. for each additional launch file open a new terminal, set the current directory the shared folder, and run that launch file (e.g. sh launch_sims2).
7. Once all of the simulations have been run, then run the command sh launch_finisher in one of the terminals to copy the contents of the directory created in step 4. into the shared folder.

The input and output files from the simulations should now be in the shared folder, and therefore visible from the host operating system.