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The YASARA Benchmarks
Since the first YASARA website went
online in 1999, we have been providing benchmarks to allow an objective
comparison with other programs. Our goal is however not to start 'benchmark wars' with
other groups, as we are all trying to solve the same problems. So
instead of comparing other programs with YASARA directly, we offer
symbolic rewards of 100$ for the first one who can beat YASARA in one
of the following benchmarks. You do not have to use your own program,
just any software you find.
 All benchmarks
involve the enzyme dihydrofolate
reductase (DHFR), which is commonly used for this purpose, a PDB file
of the system
with 23786 atoms can be downloaded here.
The simulation is run with PME (grid spacing <1 A, 4th order
B-splines), 8.0 A
cutoff for Van der Waals and real-space Coulomb forces, correct atom
masses, reproducible trajectory (running the simulation again
gives the same results), Intel turbo boost disabled, and 8 AVX
registers. More details about recommended CPUs and
GPUs are available, the
simulation algorithms are described in:
New
ways to boost molecular dynamics simulations, Krieger E, Vriend
G (2015) J.Comput.Chem. 36, with open access.
The following restrictions apply:
- Benchmarks are shown for a certain CPU and
graphics card.
Your program must be faster on the same
or slower hardware.
- Your program must be available.
- Only the first one who wins a benchmark gets
the reward,
then the benchmark will be removed.
Benchmark 1: 100$
or 1000$ for faster MD simulations on the CPU
On
an Intel Core i7 5960X CPU running at 3.6 GHz (no turbo boost), without
GPU, YASARA simulates DHFR with 160 ns/day, the computer costs around 1700 EUR.
100$ are yours if you can do it faster, or even 1000$ if you can do that with the same compiler
options (GCC 4.8, -O3 -fno-strict-aliasing -march=core-avx2 -mavx2
-mfpmath=sse -ffast-math -m32). YASARA power users reported
199 ns/day with the 5960X CPU clocked at 4.4 GHz, 255 ns/day with a Core i7-6950X at 4.3 GHz. For comparison, a Core i7 6700K at 4.0 GHz yields 125 ns/day, a Core i7 6950X at 3.0 GHz yields 228 ns/day.
Benchmark 2: 100$
for faster MD simulations on AMD Radeon GPUs
On
an Intel Core i7 4770 CPU running at 3.4 GHz (no turbo boost), with an
AMD Radeon R9-290X GPU, YASARA
simulates DHFR with 150 ns/day, the computer costs around 1000 EUR.
100$ are yours if you can do it faster.
Benchmark 3: 100$
for faster MD simulations on nVIDIA GPUs with correct atom masses
On
an Intel Core i7 5960X CPU running at 3.6 GHz
(no turbo boost), with a Geforce GTX 980 GPU, YASARA simulates DHFR
with 253 ns/day, the computer costs around 2300 EUR.
For reasons explained here, YASARA uses
the OpenCL industry standard to program the GPU. nVIDIA's OpenCL
implementation is currently still lacking some functions that are
available in its proprietary CUDA language, which gives CUDA-based
programs an advantage, making it a very tight race. So to avoid a 100$
payment, we added the restriction that the simulation must be run with
correct atom masses. YASARA power users reported
290 ns/day with the 5960X CPU clocked at 4.4 GHz and 322 ns/day with a 4.6 GHz CPU clock.
A BIOS update increased performance by 10%. 321 ns/day were reported for a Core i7 8700K with GTX 1070. 384 ns/day were reported for a Core i7 6950X@4.4 GHz with GTX 1080, 414 ns/day with a Core i7 6950X @ 4.3 GHz (again GTX 1080) and 480 ns/day with a Core i9 7980XE@4.3 GHz with GTX 1080Ti.
Benchmark 4: 100$
for faster interactive MD simulations
Interactive molecular modeling during a real-time
molecular dynamics simulation allows you to pull individual atom and
entire molecules around with the mouse or 3D input devices - or with
your fingers on a touch-screen. As described in our open access articleYASARA View - molecular graphics for all devices -
from smartphones to workstations, Krieger E, Vriend G (2014)
Bioinformatics 30, 2981-2982,
this even works on smartphones, reaching 4 fps for an interactive DHFR
simulation on a Motorola Razr i smartphone.
100$ are yours if you can do it faster.
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