The SC15 Student Cluster Competition will use a modified version of the zombie model for HPC Repast. This version (with modifications provided by Hoony Park of ORNL) allows for input from HDF5 files, as well as output to HDF5 on a cadence set by the user.
The installation of the modified zombie model follows the basic instructions presented in the INSTALL.txt files. However, there is an additional requirement of an HDF5 library. After installing a version of HDF5 > 1.8.14, modify the makefile to reference the installed HDF5 libraries. Following installation of all prerequisites (using the install.sh script if you wish) and all appropriate makefile modifications a
make hzombie_model
should build all of the modified zombie model code and its prerequisite HPC Repast libraries.
The configuration file model.props contains the variables for human and zombie input files. Here we describe the human files, but the zombie files are similar.
human.input.filethe file containing the HDF5 input of the initial human distributionhuman.output.filethe file to hold the output of the human distribution at the given cadencehuman.datanamethe name of the HDF5 data block
In addition, the variable output.interval has been added to determine the frequency in timesteps at which the human and zombie population distributions are written to the output file.
Input can be generated by producing HDF5 files natively, or converting .csv files to HDF5 files. The python script csv2hdf.py in the src/scripts directory will convert a given .csv file to HDF5 format.
sample.csv is a 100x100 grid with a distribution of population members that you can experiment with.