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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, 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, 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. YASARA uses the OpenCL industry standard to
program the GPU, which is currently less powerful than nVIDIA's
own CUDA toolkit, which gives CUDA-based programs an advantage,
making it a very tight race. So to avoid a 100$ payment, we had to
add the restriction that the simulation must be run with correct
atom masses (i.e. without heavy hydrogens). 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), 480 ns/day with a Core i9 7980XE@4.3 GHz and GTX
1080Ti, and 543 ns/day with an AMD Threadripper PRO 5975WX and
nVIDIA RTX A6000.
Benchmark 4: 100$
for faster interactive MD simulations
Our video on interactive MD in
a virtual reality shows a simulation of the Simian Tobacco
Mosaic Virus with 1.067 million atoms on an AMD Ryzen 9 7950X CPU
with nVIDIA Geforce RTX 4080 GPU (at timestamp 9:38). The scene is
rendered for the Vive Pro with 2016×2240 pixels per eye at 90 fps,
the MD runs somewhat slower as shown in the video. 100$ are yours
if you can do this faster with the simulation parameters listed at
the top and with comparable or better graphical quality.
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