Allegro GPU node benchmarks

This page is for all members to add their personal benchmarks of systems on the Allegro cluster for future reference a qualitative comparisons.

Add a section for the system at hand and be sure to include all relevant details: number of atoms (include in title), ensemble, constraint/cut-off settings, integrator, forcefield, software/libraries (+versions) etc.

GB3 in water (14028 atoms)

NPT-ensemble:

• Andersen Thermostat@300K; collision freq. ps^-1
• MonteCarloBarostat 1bar 300K

Integrator:

• VerletIntegrator, 2fs time-steps

Forcefield:

• Protein: CHARMM22*
• Water: TIP3P

constraints:

• H-bonds
• rigid water

Single precision

Software:

• OpenMM-7.0.1.dev-5e86c4f
• cuda-7.0
• Parmed-2.5.1.0
• mdtraj-1.7.2
• python-2.7.11 and python-3.5.1

Benchmark was run with two different cutoffs for the non-bonded interactions (ParticleMeshEwald)

Node: gpu054 (GeForce GTX 780): for 1nm cutoff: ~67ns/day For 9.5Å cutoff: ~80ns/day

Node gpu071 (GeForce GTX 980): for 1nm cutoff: ~86ns/day For 9.5Å cutoff: ~96ns/day

Synaptotagmin-I C2a domain in water (27,200 atoms)

NPT-ensemble:

• Andersen Thermostat@300K; collision freq. ps^-1
• MonteCarloBarostat 1bar 300K
• Non-bonded cutoff 1 nm

Integrator:

• VerletIntegrator, 2fs time-steps

Forcefield:

• Protein: CHARMM27
• Water: TIP3P

constraints:

• H-bonds
• rigid water

Single precision

Node: gpu073

Software:

• OpenMM-7.0rc1
• cuda-7.0
• Parmed-2.5.1
• mdtraj-1.7.2
• python-3.5.1

Speed: 90 ns/day