Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the test directory.

   cd /path/to/CASE

3. Decompress the test case file.

   tar xvf water_GMX50_bare.tar.gz

4. Go to the directory generated after the decompression.

   cd water-cut1.0_GMX50_bare/0768

5. Create a topol.tpr file.

   gmx_mpi grompp -f pme.mdp

6. Check whether a topol.tpr file is generated.

   ll topol.tpr

   If the command output contains the topol.tpr file information, an executable file is successfully generated.

7. Start a GROMACS test.

   mpirun --allow-run-as-root   -np 1  gmx_mpi mdrun -pin on  -ntomp 64 -v -nsteps 10000 -resetstep 8000  -noconfout  -pme gpu   -nstlist 400  -s topol.tpr

   View the value of ns/day under Performance in the md.log file. A higher value indicates a higher performance.

   The following is an example of the test result:

                  Core t (s)   Wall t (s)        (%)
          Time:      915.374       14.303     6400.0
                    (ns/day)    (hour/ns)
   Performance:       24.175        0.993