Part 1
In this section you will run a benchmark simulation and investigate the strong scaling parallel performance.
The benchmark system
The system we will used from the HECBIOSIM bechmark suite: https://www.hecbiosim.ac.uk/access-hpc/benchmarks
We will focus on the 465K atom system:
465K atom system - hEGFR Dimer of 1IVO and 1NQL - Total number of atoms = 465,399 - Protein atoms = 21,749 Lipid atoms = 134,268 Water atoms = 309,087 Ions = 295
The input file can be obtained from https://www.hecbiosim.ac.uk/access-hpc/benchmarks, or from our git repo: TODO
Running the benchmark
An example slurm script to run the benchmark on ARCHER2 is shown below
#!/bin/bash
#SBATCH --job-name=gmx_bench
#SBATCH --nodes=1
#SBATCH --tasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --time=00:10:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=z19
#SBATCH --partition=standard
#SBATCH --qos=standard
# Setup the environment
module load gromacs
export OMP_NUM_THREADS=1
srun --distribution=block:block --hint=nomultithread gmx_mpi mdrun -s bench_465kHBS.tpr -v
The bottom of the md.log file will contain the performance timings, e.g:
Core t (s) Wall t (s) (%)
Time: 12283.520 95.966 12799.9
(ns/day) (hour/ns)
Performance: 18.008 1.333
The most useful numbers to us are the wall-time 95.966s , and the performance: 18.008 ns/day which tells us how much simulation time (in nano-seconds) can be simulated for 1 day of wall-clock time.
Things to investigate
- You should vary the number of nodes of plot the performance. This investigates the strong scaling of the program.
- What node count would you use for a long production simulation?
- Previous benchmarks for this system can be found here: https://www.hecbiosim.ac.uk/access-hpc/our-benchmark-results/archer2-benchmarks
We have plotted our results for version 2021.3 of gromacs on ARCHER2 here:
