GROMACS

From SC07 Student Competition

This problem uses the GROMACS molecular dynamics package.

The GROMACS binaries, etc. are in /cluster/bobsced/{bin, lib, share, etc.}.

This instance of GROMACS is built with MPICH.

The villin molecular system can be found in your home directory on BobSCEd.

Consider the best order in which to answer these questions.

1) Which calculation performed by mdrun takes the majority of the wall time?

2) Find the mean and standard deviation of the Total Energy parameter for the villin molecular system over 6 runs of 100000 steps at 0.001 time resolution.

3) How many atoms are in the system?

4) Determine the fastest setup to run that configuration on BobSCEd with a maximum of 16 cores (i.e 4 nodes x 4 cores/node) over gigabit ethernet. Calculate the speedup compared to a 1 core run for that configuration.

5) For the fastest setup from 4) how much of a difference in wall-time does running the simulation over Infiniband make as compared to gigabit Ethernet? Calculate the speedup compared to a 1 core run (also over Infiniband) for that configuration.