Basic Charm++ Example Run

In this exercise we will learn:

• How to run a basic Charm++ progam
• And how to visualize analysis data

LeanMD is a molecular dynamics simulation program written in Charm++. This benchmark simulates the behavior of atoms based on the Lennard-Jones potential, which is an effective potential that describes the interaction between two uncharged molecules or atoms. The computation performed in this code mimics the short-range non-bonded force calculation in NAMD, and resembles the LJ force computation in miniMD benchmark in the Mantevo benchmark suite maintained by Sandia National Laboratories.

Instructions:

1. Download the code:
   
   wget http://charm.cs.illinois.edu/tutorial_anl/leanmd-tut.tar.gz
   
   OR
   
   Copy from /projects/ATPESC2016/anl_charm_tutorial/leanmd-tut
2. Compile Code
   
   tar xzf leanmd-tut.tar.gz
cd leanmd-tut
make
3. Submit Code
   
   qsub -A ATPESC2016 -t 5 -n 4 --mode script myjob.sh
4. Download Projections
   
   wget http://charm.cs.illinois.edu/distrib/binaries/projections/projections_6.7.0.tar.gz
   
   OR
   
   Copy from /projects/ATPESC2016/anl_charm_tutorial/projections_6.7.0
5. Download Test Projections Data
   
   wget http://charm.cs.illinois.edu/tutorial_anl/leanmd_proj_64.tar.gz
6. Visualize Test Projections data
   
   cd leanmd_proj_64
/path/to/projections_6.7.0/bin/projections leanmd.sts
OR
/projects/ATPESC2016/anl_charm_tutorial/projections_6.7.0/bin/projections leanmd.sts
7. Now, try it on your new data!
   
   If you're having trouble with projections, make sure you connect with ssh -X