First of all, the link from Linux-Bench pointing to the forum
https://forums.servethehome.com/linux-bench/
is dead. So I hope I'm at the right place here.
I am wondering if there is a particular reason you have NAMD as a molecular dynamics benchmark over other programs?
I would like to suggest to add a Gromacs Molecular dynamics benchmark and I'm happy to provide a system.
(http://manual.gromacs.org/documentation ,
GitHub - gromacs/gromacs: Public/backup repository of the gromacs molecular simulation toolkit )
The reasons for the suggestion are the following:
- Gromacs is LGPLv2.1 vs. NAMDs own licence (NAMD License)
- Gromacs is much easier to install using cmake, can run threaded without MPI
- Gromacs GPU code path has almost feature parity of CUDA and OpenCL, NAMD is CUDA only (GROMACS 2016 Release Notes — GROMACS 2016 Release Notes 2016 documentation)
- Gromacs is FAST and widely adopted
- Gromacs makes heavy usage of the newest vector extensions (AVX2, AVX512ER/F, Neon/asimd in Aarch64, VSX in Power8, New low-level SIMD support — GROMACS 5.1 Release Notes 5.1 documentation)
- Gromacs needs no other external dependencies, only fetches and compiles fftw (FFTW Home Page) via cmake installation
If you are interested, I'm happy to provide a simple install/compile script and a production test system!
cheers, Johannes
https://forums.servethehome.com/linux-bench/
is dead. So I hope I'm at the right place here.
I am wondering if there is a particular reason you have NAMD as a molecular dynamics benchmark over other programs?
I would like to suggest to add a Gromacs Molecular dynamics benchmark and I'm happy to provide a system.
(http://manual.gromacs.org/documentation ,
GitHub - gromacs/gromacs: Public/backup repository of the gromacs molecular simulation toolkit )
The reasons for the suggestion are the following:
- Gromacs is LGPLv2.1 vs. NAMDs own licence (NAMD License)
- Gromacs is much easier to install using cmake, can run threaded without MPI
- Gromacs GPU code path has almost feature parity of CUDA and OpenCL, NAMD is CUDA only (GROMACS 2016 Release Notes — GROMACS 2016 Release Notes 2016 documentation)
- Gromacs is FAST and widely adopted
- Gromacs makes heavy usage of the newest vector extensions (AVX2, AVX512ER/F, Neon/asimd in Aarch64, VSX in Power8, New low-level SIMD support — GROMACS 5.1 Release Notes 5.1 documentation)
- Gromacs needs no other external dependencies, only fetches and compiles fftw (FFTW Home Page) via cmake installation
If you are interested, I'm happy to provide a simple install/compile script and a production test system!
cheers, Johannes
