PanSim: A Distributed Pandemic Simulator

PanSim is a distributed pandemic simulator.

Local Test Instructions

Step 1: Clone PanSim repository

$ cd ~
$ git clone https://github.com/parantapa/pansim.git
$ cd pansim

Step 2: Create a Anaconda environment

To create a new virtual environment with conda, have Anaconda/Miniconda setup on your system. Installation instructions for Miniconda can be found at https://docs.conda.io/en/latest/miniconda.html#linux-installers After installation of Anaconda/Miniconda execute the following commands:

$ conda env create -f environment.yml

The above command creates a new conda environment called pansim.

Step 3: Install PanSim in the environment

PanSim can be installed using pip.

$ conda activate pansim
$ pip install -U -e .

Step 4: Test Pansim

Executing the following command to figure if installation was successful.

$ pansim --help

To run the simple tests using the serial and parallel version do the following.

$ cd tests
$ ./simplesim_test_cva_1.sh
$ ./distsim_test_cva_1.sh

Local Test Instructions with Java

Step 1: Compile the simple java behavior model using maven

$ mvn -U clean compile assembly:single

Step 2: Run the simple tests (using java behavior model)

$ cd tests
$ ./simplesim_java_test_cva_1.sh
$ ./distsim_java_test_cva_1.sh

Known Issues

Executing Pansim shows error "undefined symbol: _ZSt28__throw_bad_array_new_lengthv"

This is caused by differing versions of gcc/stdlib in conda compared to on the host system. Try the following set of commands:

$ conda activate pansim
$ cd $CONDA_PREFIX/lib
$ mv libstdc++.so.6.0.28 libstdc++.so.6.0.28.old                                                                                      (pansi
$ ln -s /usr/lib64/libstdc++.so.6.0.29 libstdc++.so.6.0.28
$ cd ~/pansim
$ pip install -U -e .
$ pansim --help

More details can be found at:

conda/conda#10757

AJdeMooij/pansim