Running and Verifying LAMMPS

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to create the working directory:

   mkdir -p path/to/CASE

3. Perform the following commands to switch to the working directory and copy the computing instance and binary files to the working directory.

   cd /path/to/CASE
   cp /path/to/LAMMPS/lammps-stable_5Jun2019/bench/in.lj  ./
   cp /path/to/LAMMPS/lammps-stable_5Jun2019/src/lmp_g++_openmpi ./

4. Run the following command:

   mpirun --allow-run-as-root -np 96  --mca btl ^openib  ./lmp_g++_openmpi -in in.lj

   Check the value (in the unit of timesteps/s) of Performance in the log.lammps log file. A higher value indicates better performance.

   The following is an example of the test result.

   Performance: 593019.799 tau/day, 1372.731 timesteps/s
   98.1% CPU use with 96 MPI tasks x no OpenMP threads
   MPI task timing breakdown:
   Section |  min time  |  avg time  |  max time  |%varavg| %total
   ---------------------------------------------------------------
   Pair    | 0.028215   | 0.040367   | 0.051175   |   3.4 | 55.41
   Neigh  | 0.0036562  | 0.0049894  | 0.0061901  |   1.2 |  6.85
   Comm  | 0.013968   | 0.026072   | 0.039602   |   4.8 | 35.79
   Output  | 7.905e-05  | 0.000128   | 0.00023195  |   0.0 |  0.18
   Modify  | 0.00056847 | 0.00080538  | 0.00099514 |  0.0 |  1.11
   Other   |            | 0.0004857  |          |      |  0.67