NAMD Molecular Dynamics Performance Improves Well With NVIDIA Blackwell / RTX 5090

Written by Michael Larabel in NVIDIA on 27 January 2025 at 06:46 AM EST. 2 Comments
NVIDIA
With now having a Linux driver for running GPU compute workloads on the GeForce RTX 5090 (as mentioned, Linux gaming benchmarks will come following the formal R570 Linux driver release in the coming days that is better optimized for gaming), I ran some additional GPU compute benchmarks on the GeForce RTX 5090 "Blackwell" graphics card over the weekend.

With this morning's quick article is a look at the NAMD molecular dynamics performance on the GeForce RTX 5090 using CUDA. This is just some quick testing with a few workloads while some other more interesting compute benchmarks will be out later.

NVIDIA GeForce RTX 5090


All of these NVIDIA GeForce graphics cards were freshly re-tested using NAMD 3.0.1 and using the CUDA 12.8 / NVIDIA 570.86.10 Linux driver.
NAMD NVIDIA GeForce RTX 5090

The GeForce RTX 30/40 series consumer graphics cards appeared rather bottlenecked with NAMD and these simulations... With the smaller ATPase simulation, there wasn't even a real difference between the RTX 4080 and RTX 4090 performance. But now a nice leap forward with the GeForce RTX 5090. A much bigger improvement from RTX 4090 to RTX 5090 than from the RTX 3090 to RTX 4090.
NAMD CUDA benchmark with settings of Input: ATPase with 327,506 Atoms. RTX 5090 was the fastest.

With the Blackwell GPU and GDDR7 video memory, the GeForce RTX 5090 provides nice uplift for NAMD accelerated by CUDA.
NAMD CUDA benchmark with settings of Input: STMV with 1,066,628 Atoms. RTX 5090 was the fastest.

Apologies for not having these NAMD results completed in time for the other GeForce RTX 5090 compute benchmarks on Friday due to the short time-frame of having this R570 Linux driver build for compute testing. Some additional compute tests with this $1999 USD graphics card will continue over the days ahead while waiting for the new public driver build around 30 January that is better suited for gaming. Later today should be some Llama.cpp benchmarks on the RTX 5090 as the next set of results. Thanks to NVIDIA for providing the GeForce RTX 5090 review sample for Linux testing.
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Michael Larabel

Michael Larabel is the principal author of Phoronix.com and founded the site in 2004 with a focus on enriching the Linux hardware experience. Michael has written more than 20,000 articles covering the state of Linux hardware support, Linux performance, graphics drivers, and other topics. Michael is also the lead developer of the Phoronix Test Suite, Phoromatic, and OpenBenchmarking.org automated benchmarking software. He can be followed via Twitter, LinkedIn, or contacted via MichaelLarabel.com.

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