Are these timings fine?

lutek14
Tue, 14 Nov 2023 07:02:14 +0000
User discussions

GROMACS version: gromacs/2021.4_mpi_plumed
GROMACS modification: No

Hello,
I am running Gromacs on HPC for the first time, and I am unsure if the timings are fine. I am not sure whether I have allocated too many or too few resources.

The system consists of 57,810 atoms.
The timings are listed below:

NVT

          Core t (s)   Wall t (s)        (%)
Time:    22796.285      474.923     4800.0
                   (ns/day)    (hour/ns)
Performance:       18.193        1.319

NPT

               Core t (s)   Wall t (s)        (%)
       Time:    23881.127      497.524     4800.0
                 (ns/day)    (hour/ns)
Performance:       17.366        1.382

Currently running production from 0 to 10, and then will start 10 to 100.

As per GROMACS description…
“Running on 1 node with total 48 cores, 48 logical cores.[…] Brand: Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz”

What do you think about those timings? Once I have observed that ns/day can reach over 30-40ns/day, so it appears that my results are rather subpar…
Would running it on a GPU be a wise decision? I have access to those, but only nine processors are available. As a result, they are often occupied.

Thank you in advance

4 posts - 2 participants