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There are two data sets in UEABS for Gromacs.
1. ion_channel that use PME for electrostatics, for Tier-1 systems
2. lignocellulose-rf that use Reaction field for electrostatics, for Tier-0 systems. Reference : http://pubs.acs.org/doi/abs/10.1021/bm400442n
The input data file for each benchmark is the corresponding .tpr file produced using
tools from a complete gromacs installation and a series of ascii data files
(atom coords/velocities, forcefield, run control).
If it happens to run the tier-0 case on BG/Q use lignucellulose-rf.BGQ.tpr
instead lignocellulose-rf.tpr. It is the same as lignocellulose-rf.tpr
created on a BG/Q system.
The general way to run gromacs benchmarks is :
WRAPPER WRAPPER_OPTIONS PATH_TO_MDRUN -s CASENAME.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile
CASENAME is one of ion_channel or lignocellulose-rf
maxh : Terminate after 0.99 times this time (hours) i.e. gracefully terminate after ~30 min
resethwat : Reset Timer counters at half steps. This means that the reported
walltime and performance referes to the last
half steps of sumulation.
noconfout : Do not save output coordinates/velocities at the end.
nsteps : Run this number of steps, no matter what is requested in the input file
logfile : The output filename. If extension .log is ommited
it is automatically appended. Obviously, it should be different
for different runs.
WRAPPER and WRAPPER_OPTIONS depend on system, batch system etc.
Few common pairs are :
CRAY : aprun -n TASKS -N NODES -d THREADSPERTASK
Curie : ccc_mrun with no options - obtained from batch system
Juqueen : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
Slurm : srun with no options, obtained from slurm if the variables below are set.
#SBATCH --nodes=NODES
#SBATCH --ntasks-per-node=TASKSPERNODE
#SBATCH --cpus-per-task=THREADSPERTASK
The best performance is usually obtained using pure MPI i.e. THREADSPERTASK=1.
You can check other hybrid MPI/OMP combinations.
The execution time is reported at the end of logfile : grep Time: logfile | awk -F ' ' '{print $3}'
NOTE : This is the wall time for the last half number of steps.
For sufficiently large nsteps, this is half of the total wall time.