Performance (ns/day) returns negative number

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No

Hello,
I am running md simulations using gmx on Expanse supercomputer at SDSC. My system has 648, 379 atoms. Running the simulation, on one compute node, returns a performance output of

           Core t (s)   Wall t (s)        (%)
   Time:   284153.583    35519.199      800.0
                     9h51:59

                     (ns/day)          (hour/ns)
      Performance:    -18.071        -1.328

I was testing out various configurations (one node, 2 nodes, 1 one node gpu, etc.). Using one gpu provides around 3 ns/day. I am not sure what that negative number means. Is gmx complaining about improper usage of resources, or is something else wrong with the simulation set up?

Any advice is appreciated. If anyone has used the Expanse supercomputer and has some insight into setting up jobs properly, that is also highly appreciated.

Thank you,

2

Negative numbers should not occur and these are strange. The past years I have only seen negative numbers when clocks on different cores on a CPU were not in sync. That might also be the cause here.

You can compute the correct performance yourself by dividing the number of nanoseconds you simulated by the wallclock time you show above.

3

Thank you so much for your response.