[gmx-users] Worse GROMACS performance with better specs?

Jason Loo Siau Ee JasonSiauEe.Loo at taylors.edu.my
Wed Jan 10 08:00:53 CET 2018

Dear gmx users,

I recently purchased a second GPU workstation and tried compiling GROMACS on it, but despite the better (and more expensive) specs the performance is significantly worse on my test system. To test things I standardized the version (2016.4). Some details below:

Workstation 1:

2 x Intel Xeon E5-2680v4 (14 cores), 2 x GTX 1080

gmx mdrun -ntmpi 8 -ntomp 7 -gpu_id 00001111

Performance: 61ns/day

Workstation 2:

2 x Intel Xeon Gold 6126 (12 cores), 2 x GTX 1080Ti

gmx mdrun -ntmpi 8 -ntomp 6 -gpu_id 00001111

Performance: 49ns/day

I'm guessing it's an issue during compilation but I can't figure it out. I wouldn't claim to have any knowledge about how GROMACS interacts with the hardware, so some observations as below (not sure idea which is actually relevant):

- Compilation command for both: cmake .. -DGMX_BUILD_OWN_FFTW=ON  -DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_GPU=ON  -DCMAKE_INSTALL_PREFIX=/opt/gromacs

- When compiling on Workstation 2 I originally got a CMake error "Cannot find AVX512F compiler flag". Updated my gcc version to 5.3.1 to solve this.

- Some regression tests fail for Workstation 2 during compilation: 4 -FTUnitTest (SEGFAULT), 16 - CorrelationTest

- mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only logical processor count

- Running CPU-only (export CUDA_VISIBLE_DEVICES="") I get 21ns/day versus 23 ns/day , so the CPUs in Workstation 2 are definitely faster.

- Upgraded both to 2018.rc1 (used cmake3) I get a regression test fail for Workstation 1 (9 - GPUUtilUnitTest) and Workstation 2 (8 - FFTUnitTests, 9 - GPUUtilsUnitTest, 26 - CorrelationTest). Performance is 66.5ns/day versus 51.95ns/day. The GPU load actually looks similar to previous versions (~70% for Workstation 1 and 50-60% for Workstation 2). I actually got the best performance with Workstation 1 running 2016.1 (69ns/day).

Any help on how I can optimize performance on Workstation 2 would be appreciated. If there are certain files that would be helpful let me know and I'll send a link.


Jason Loo

PhD, MPharm, RPh


School of Pharmacy

Faculty of Health and Medical Sciences

Taylor's University

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