GENESIS

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

• Benchmark sets for DHFR, ApoA1, and UUN

 

Previous benchmarks

• Benchmark of GENESIS 1.0-1.4