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Update notebook to generate simple webpage with index and JSON/YAML files #4

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Update notebook to generate simple webpage with index and JSON/YAML files #4

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ae7e470
Update Jupyter notebook to produce HTML analyses of all GPUs and elem…
jchodera Sep 24, 2020
584af2e
Update analysis notebook to produce simple webpage, YAML and JSON ver…
jchodera Sep 24, 2020
2c6e4b7
Add run metadata for benchmark project
jchodera Sep 24, 2020
a4dc299
Merge remote-tracking branch 'origin/master' into generate-plots
jchodera Sep 24, 2020
d998135
Plot max performance instead
jchodera Sep 25, 2020
26511d1
Update analysis with latest benchmark results
jchodera Sep 25, 2020
5163a3a
Update notebook to show performance and speedup
jchodera Sep 25, 2020
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4,590 changes: 4,569 additions & 21 deletions notebooks/core22-cuda.ipynb
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150 changes: 150 additions & 0 deletions notebooks/run-metadata.yaml
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---
RUN0:
name: DHFR PME
description: DHFR Joint AMBER-CHARMM benchmark with PME
num_atoms: 23558
nonbonded_method: PME
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN1:
name: DHFR LJPME
description: DHFR Joint AMBER-CHARMM benchmark with LJPME
num_atoms: 23558
nonbonded_method: LJPME
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN2:
name: DHFR RF
description: DHFR Joint AMBER-CHARMM benchmark with reaction field electrostatics
num_atoms: 23558
nonbonded_method: CutoffPeriodic
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN3:
name: DHFR PME 4fs BAOAB
description: DHFR Joint AMBER-CHARMM benchmark with PME with 4 fs BAOAB
num_atoms: 23558
nonbonded_method: PME
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN4:
name: apoa1 PME
description: ApoA1 benchmark with PME
num_atoms: 92224
nonbonded_method: PME
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN5:
name: apoa1 LJPME
description: ApoA1 benchmark with LJPME
num_atoms: 92224
nonbonded_method: LJPME
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN6:
name: apoa1 RF
description: ApoA1 benchmark with reaction field electrostatics
num_atoms: 92224
nonbonded_method: CutoffPeriodic
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN7:
name: apoa1 RF
description: ApoA1 benchmark with PME with 4 fs BAOAB
num_atoms: 92224
nonbonded_method: PME
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN8:
name: COVID Moonshot Sprint testing complex (constrained)
description: COVID Moonshot Sprint testing perses alchemical free energy calculation ligand in complex
num_atoms: 89705
nonbonded_method: PME
project: 13412
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN9:
name: COVID Moonshot Sprint testing solvent (constrained)
description: COVID Moonshot Sprint testing perses alchemical free energy calculation ligand in solvent
num_atoms: 4071
nonbonded_method: PME
project: 13413
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN10:
name: SARS-CoV-1 full spike
description: SARS-CoV-1 full spike
num_atoms: 371771
nonbonded_method: PME
pdbid: 5x58
project: 14251
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN11:
name: SARS-CoV-2 full spike
description: SARS-CoV-2 full spike
num_atoms: 448584
nonbonded_method: PME
pdbid: 6vxx
project: 14253
timestep: "2*fs"
integrator: simtk.openmm.LangevinIntegrator

RUN12:
name: SARS-CoV-2 Mpro monomer
description: SARS-CoV-2 main viral protease (Mpro) monomer
num_atoms: 62180
nonbonded_method: PME
pdbid: 6lu7
project: 11743
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN13:
name: SARS-CoV-2 RBD:ACE2
description: SARS-CoV-2 RBD:ACE2 (homology model) complex
num_atoms: 182669
nonbonded_method: PME
pdbid: 2afj
project: 11743
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN14:
name: SARS-CoV-2 RBD:S230 Ab
description: SARS-CoV-2 RBD (homology model):S230 antibody
num_atoms: 110730
nonbonded_method: PME
pdbid: 6nb8_2ghv
project: 11745
timestep: "4*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN15:
name: COVID Moonshot Sprint 4 complex (unconstrained)
description: COVID Moonshot Sprint 4 perses alchemical free energy calculation ligand in complex
num_atoms: 90725
nonbonded_method: PME
project: 13424
timestep: "2*fs"
integrator: openmmtools.integrators.LangevinIntegrator

RUN16:
name: COVID Moonshot Sprint 4 solvent (unconstrained)
description: COVID Moonshot Sprint 4 perses alchemical free energy calculation ligand in solvent
num_atoms: 4058
nonbonded_method: PME
project: 13425
timestep: "2*fs"
integrator: openmmtools.integrators.LangevinIntegrator