- switch to the MC barostat (barostat=2)
- use H mass repartitioning and a dt=0.004
On Tue, Nov 4, 2025 at 11:13 AM Daniel Hall via AMBER <amber.ambermd.org>
wrote:
> Hello amber community,
>
> I hope everyone is well.
>
> I am experiencing a poorer than expected performance when running explicit
> solvated system, with performances ~330 ns/day for a system of size ~18k
> atoms using amber24 on an Ubuntu 24.02 system. Here is my workstation
> hardware;
>
> CPU: Intel Xeon W-2295, 18 cores . 3 GHz
> GPU: NVIDIA GeForce RTX 3080 10GB
> Storage: 1 TB M.2 2280 PCIe NVMe Gen4x4 + 2 TB M.2 2280 PCIe NVMe Gen4x4
> RAM: 64GB (4 x 16GB) DDR4 2933 MHz
> PSU: 1000W
>
> This is the prod.in using pmemd.cuda;
>
> igb = 0, imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 2.0,
> nstlim = 250000000, dt = 0.002,
> ntpr = 50000, ntwx = 50000, ntwr = 50000,
> tol = 0.00001
> /
>
> Troubleshooting I’ve already performed;
>
> * I have checked that the GPU is being utilized, although the memory
> usage is only 472 Mb. Both the NVIDIA drivers (580.95.05) and CUDA versions
> (13.0) are up-to-date, and the correct version of CUDA is being used.
> * The GPU is in the correct PCIe slot, x16 gen 3, and is forced x16
> speed in the BIOS.
> * The GPU isn’t thermal throttling, as it doesn’t exceed 75 °C.
> * The maximum power performance option is selected by the workstation.
> * The simulation is being in single-precision and not double-precision.
> * I would normally use 5000 for ntpr, ntwx and ntwr but increasing to
> 50000 did not make a difference.
> * Utilising more CPU cores made performances worse.
>
> Is there anything else that I have missed or could do to improve
> simulation performance.
>
> Any suggestions are greatly appreciated 😊
>
>
> Regards
> Dan.
>
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Received on Tue Nov 04 2025 - 09:00:03 PST
