Running and Verification

Procedure

Use PuTTY to log in to the server as the root user.
Go to the test directory.
```
cd /path/to/CASE
```
Decompress the test case file.
```
tar xvf water_GMX50_bare.tar.gz
```
Go to the directory generated after the decompression.
```
cd water-cut1.0_GMX50_bare/0768
```
Create a topol.tpr file.
```
gmx_mpi grompp -f pme.mdp
```
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.

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

Parent topic: GROMACS 2019.3 Porting Guide (CentOS 8.2)