Benchmark


Benchmark of GENESIS 2.0 beta / 1.6 on FUGAKU

CPU: A64FX (2.0 GHz)
Compile conditions: Fujitsu compiler 4.3.0a tcsds-1.2.28 / Single precision
Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
Time step: 2 fs (VV), 2.5 fs / 5.0 fs (MTS, ver. 1.6), 3.5 fs / 7.0 fs (MTS, ver. 2.0)
Input and control files are available for DHFR, ApoA1, and UUN.

DHFR (27,346 atoms)

Force field: AMBER
Ensemble: NVT
switch, cutoff, pairlist = 8, 8, 9.5 Å

DHFR (27,346 atoms)

Force field: AMBER
Ensemble: NPT
switch, cutoff, pairlist = 8, 8, 9.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble: NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble: NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble: NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble: NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble: NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble: NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Huge Crowding System

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Compiler: Fujitsu compiler 4.1.0 tcsds-1.2.24


Benchmark of GENESIS 2.0 beta on CPU+GPU cluster

CPU: Intel Xeon Gold 6142 (2.6 GHz)
GPU: GeForce GTX 1080Ti
Compile conditions: Intel MPI ver. 19.1 / Intel compiler ver. 19.1 / Single precision
Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
Time step: 2 fs (VV),  3.5 fs / 7.0 fs (MTS)
Input and control files are available for DHFR, ApoA1, and UUN.

DHFR (27,346 atoms)

Force field: AMBER
Ensemble : NVT
switch, cutoff, pairlist = 8, 8, 9.5 Å

DHFR (27,346 atoms)

Force field: AMBER
Ensemble : NPT
switch, cutoff, pairlist = 8, 8, 9.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å


Benchmark of GENESIS 1.6 on CPU+GPU cluster

CPU: Intel Xeon Gold 6142 (2.6 GHz)
GPU: GeForce GTX 1080Ti
Compile conditions: Intel MPI ver. 19.1 / Intel compiler ver. 19.1 / Mixed precision
Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
Time step: 2 fs (VV),  2.5 fs / 5.0 fs (MTS)
Input and control files are available for DHFR, ApoA1, and UUN.

DHFR (27,346 atoms)

Force field: AMBER
Ensemble : NVT
switch, cutoff, pairlist = 8, 8, 9.5 Å

DHFR (27,346 atoms)

Force field: AMBER
Ensemble : NPT
switch, cutoff, pairlist = 8, 8, 9.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

ApoA1 (92,224 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

UUN (216,726 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble : NVT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Crowding System (1,578,958 atoms)

Force field: CHARMM
Ensemble : NPT
switch, cutoff, pairlist = 10, 12, 13.5 Å

Input and control files of the benchmark

 

Previous benchmarks