Gmx mdrun on AMD CPU

User discussions
1

GROMACS version: 2023.4
GROMACS modification: No
Hi there, I tried to run the same simulation on two servers

  1. a GPU server with Nvidia V100
  2. a CPU server with AMD 64 core CPU

The test script is as follows:

wget http://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
tar -xvf water_GMX50_bare.tar.gz
cd water-cut1.0_GMX50_bare/3072/
start=$(date +%s)
gmx grompp -f pme.mdp -c conf.gro -p topol.top -o water_pme.tpr
gmx mdrun -notunepme -dlb yes -v -resethway -noconfout -nsteps 1000 -s water_pme.tpr
end=$(date +%s)
echo "Elapsed Time: $(($end-$start)) seconds"

It takes 49 seconds for server 1 to finish the simulation, and 129 seconds for the server 2.

Is this duration typical for a server equipped with an AMD CPU of this specification?

2

Hello,

I would say that it is quite impossible to give a general answer without knowing the details of the run, e.g., how big the system is, how many resources are taken up by GROMACS (you are launching a mdrun without any additional flags on the resources usage, so GROMACS will decide itself what to use), etc.
In line of principle, the fact that the GPU one is faster makes sense, but again, depends on the system, there are cases where GPUs actually are bottlenecks. Also, the speed is in ns/day, you can see it at the end of the .log files of your sims. I don’t think the machine time you calculate is a good indicator, as this is not necessarily a good representation of the time takes by GROMACS but can also include other processes, e.g., you are taking into account the time taken for the grompp passage which is irrelevant in terms of simulation speed.

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