Run a simulation using mpiexec#

The application mpiexec is used to run multi-node simulations in parallel. Eradication.exe is “single threaded”, so it uses only one core for processing. If you run a simulation with multiple geographic nodes using mpiexec instead of invoking Eradication.exe directly, multiple copies of Eradication.exe will be running, with one copy per core processing data for a single node at a time. Message Passing Interface (MPI) communicates between the cores when handling the migration of individuals from one node to another.

Although mpiexec can be used to run a simulation in parallel on your local computer, it is more often used to run complex simulations in parallel on an HPC cluster or several linked computers.

Mpiexec is part of the Microsoft HPC Pack 2019 SDK (64-bit) installed as a prerequisite for building Eradication.exe from the EMOD source code. See EMOD source code installation for more information.

Note

If you get an error that the mpiexec command cannot be found, you must add the path to mpiexec to the PATH environment variable. For example, open Control Panel and add the path C:\Program Files\Microsoft HPC Pack 2012\Bin to PATH.

Usage#

  1. Take note of the number of cores on your computer or cluster.

    If running locally, we recommend running mpiexec with one fewer cores than are available, so one core is reserved for the operating system. The simulation can be run on all available cores and will complete faster, but the desktop will not be responsive.

  2. Open a Command Prompt window and navigate to the directory that contains the configuration and campaign files for the simulation.

  3. Invoke Eradication.exe using mpiexec as follows, replacing the number of cores, paths, and command options as necessary for your environment. See Run a simulation using the command line for more information about the command options available for use with Eradication.exe.

    mpiexec -n 3 ..\Eradication.exe --config config.json --input-path ..\InputDirectory\Garki --output-path OutputGarki

Mpiexec will start multiple copies of Eradication.exe as specified by -n. Those instances will communicate with each other via MPI. If all cores are on a single computational node or host, they will use internal networking to carry the MPI packets.

You can also link together several computers with MPI using the mpiexec -host option. For example, if you were using six cores on two computers, you could run three copies of Eradication.exe on the first computer, and three more could be run on the second computer. Again, this assumes that each computer has at least three cores.

For more information about mpiexec, see MSDN.