CoMD

Classical molecular dynamics proxy application.

This is CoMD version 1.1

CoMD is a reference implementation of typical classical molecular dynamics algorithms and workloads. It is created and maintained by ExMatEx: Exascale Co-Design Center for Materials in Extreme Environments (exmatex.org). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc.

To view the generated Doxygen documentation for CoMD, please visit the site: http://ecp-copa.github.io/CoMD.

To contact the developers of CoMD send email to [email protected].

ZMQ Add-on

This version of CoMD was modified to generate a ZeroMQ data stream with the main results (basically, atom's id&position) obtained for each timestep (or a set of timesteps).

This ZMQ support was only added to the MPI version. The compilation flag DO_ZMQ=ON/OFF enables/disables this option in the Makefile.

When compiled with ZMQ support, some extra parameters are needed to set the recipient's hostname(s)/port(s) (--help to list them). Examples of use:

• Serial execution with 256000 atoms (4 x 40 x 40 x 40) using ZMQ with default port (9000):

  bin/CoMD-serial --hostDir ~/tmp/ --nx 40 --ny 40 --nz 40

  With --hostDir we indicate the path where a file for each port used sets the hostname (eg. localhost) for the ZMQ connection. In this example this file is needed: ${HOME}/tmp/9000

     cat ~/tmp/9000
  
     dahu-7.grenoble.grid5000.fr
  

• 4 MPI processes using 4 different ZMQ ports:

  mpirun -np 4 bin/CoMD-mpi --hostDir ~/tmp/ --nx 40 --ny 40 --nz 40 --xproc 2 --yproc 2 --zproc 1

  4 files in ${HOME}/tmp are needed: ${HOME}/tmp/9000 ${HOME}/tmp/9001 ${HOME}/tmp/9002 ${HOME}/tmp/9003

Credits for this add-on: Omar A. Mures, Henrique C. Zanúz, Bruno Raffin and Emilio J. Padrón