Running and Verifying GROMACS

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to switch to the directory where the case is stored:

   cd /path/to/CASE

3. Decompress the compute instance files:

   tar xvf water_GMX50_bare.tar.gz

4. Run the following command to switch to the directory generated after the package is decompressed:

   cd water-cut1.0_GMX50_bare/0768

5. Run the following command to create a topol.tpr file:

   gmx_mpi grompp -f pme.mdp

6. Run the following command to view whether the topol.tpr file is created:

   ll topol.tpr

   -rw-r--r-- 1 root root 18448672 Jan 11 16:41 topol.tpr

7. Run the following command to start the GROMACS test:

   mpirun --allow-run-as-root --mca btl ^openib  -np 96 gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 1 -s topol.tpr

   View the value of ns/day in Performance in the md.log file. The unit is ns/day. The higher the value is, the better the performance is.

   The following is an example of the test result:

   Part of the total run time spent waiting due to load imbalance: 1.1%.
   Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
   Average PME mesh/force load: 1.033
   Part of the total run time spent waiting due to PP/PME imbalance: 2.1 %
                  Core t (s)   Wall t (s)        (%)
          Time:    14806.100      154.231     9600.0
                    (ns/day)    (hour/ns)
   Performance:        5.603        4.283
   GROMACS reminds you: "Come on boys, Let's push it hard" (P.J. Harvey)