Slide 1: AMBER 16 on P100s
AMBER 16 on P100s February 2017
Slide 2: PME-Cellulose_NPT on P100s PCIe
PME-Cellulose_NPT on P100s PCIe 40 35 PME-Cellulose_NPT 30.00 Running AMBER version 16.3 30 The blue node contains Dual Intel Xeon 25 E5-2699 v4@2.2GHz [3.6GHz Turbo] 12.8X ns/day 21.85 (Broadwell) CPUs 20 15 9.3X The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) C
Slide 3: PME-Cellulose_NPT on P100s SXM2
PME-Cellulose_NPT on P100s SXM2 40 35 PME-Cellulose_NPT 36.65 32.22 30 15.6X Running AMBER version 16.3 13.7X The blue node contains Dual Intel Xeon 25 23.37 E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 20 15 9.9X The green nodes contain Dual Intel Xeon E5-2698 v4@2.2GHz [3.6GHz Turbo] (
Slide 4: PME-Cellulose_NVE on P100s PCIe
PME-Cellulose_NVE on P100s PCIe 40 35 PME-Cellulose_NVE 32.55 Running AMBER version 16.3 30 25 23.34 13.2X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 20 15 9.4X The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) C
Slide 5: PME-Cellulose_NVE on P100s SXM2
PME-Cellulose_NVE on P100s SXM2 45 40 PME-Cellulose_NVE 40.88 35.16 35 Running AMBER version 16.3 30 16.6X The blue node contains Dual Intel Xeon 25 24.94 14.2X E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 20 The green nodes contain Dual Intel 15 10.1X Xeon E5-2698 v4@2.2GHz [3.6GHz Turb
Slide 6: PME-FactorIX_NPT on P100s PCIe
PME-FactorIX_NPT on P100s PCIe 140 132.86 120 PME-FactorIX_NPT 98.77 11.6X Running AMBER version 16.3 100 The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] 80 (Broadwell) CPUs ns/day 60 8.6X The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CP
Slide 7: PME-FactorIX_NPT on P100s SXM2
PME-FactorIX_NPT on P100s SXM2 180 160 PME-FactorIX_NPT 159.80 140 144.11 14.0X Running AMBER version 16.3 120 12.6X The blue node contains Dual Intel Xeon 106.25 E5-2699 v4@2.2GHz [3.6GHz Turbo] 100 (Broadwell) CPUs 9.3X ns/day 80 The green nodes contain Dual Intel Xeon E5-2698 v4@2.2GHz [3.6GHz 60
Slide 8: PME-FactorIX_NVE on P100s PCIe
PME-FactorIX_NVE on P100s PCIe 160 140 PME-FactorIX_NVE 145.83 120 12.2X Running AMBER version 16.3 105.86 The blue node contains Dual Intel Xeon 100 E5-2699 v4@2.2GHz [3.6GHz Turbo] 8.8X (Broadwell) CPUs ns/day 80 The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz 60 Turbo] (Broadwel
Slide 9: PME-FactorIX_NVE on P100s SXM2
PME-FactorIX_NVE on P100s SXM2 200 180 PME-FactorIX_NVE 178.02 159.24 160 140 14.9X Running AMBER version 16.3 120 114.88 13.3X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 100 80 9.6X The green nodes contain Dual Intel Xeon E5-2698 v4@2.2GHz [3.6GH
Slide 10: PME-JAC_NPT on P100s PCIe
PME-JAC_NPT on P100s PCIe 350 PME-JAC_NPT 327.69 300 283.60 250 7.1X Running AMBER version 16.3 6.2X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] 200 (Broadwell) CPUs ns/day The green nodes contain Dual Intel 150 Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs + Tes
Slide 11: PME-JAC_NPT on P100s SXM2
PME-JAC_NPT on P100s SXM2 450 PME-JAC_NPT 423.09 400 350 360.64 9.2X Running AMBER version 16.3 300 310.52 7.9X The blue node contains Dual Intel Xeon 250 6.8X E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 200 The green nodes contain Dual Intel Xeon E5-2698 v4@2.2GHz [3.6GHz 150 Turbo] (B
Slide 12: PME-JAC_NVE on P100s PCIe
PME-JAC_NVE on P100s PCIe 400 350 PME-JAC_NVE 363.79 300 308.46 7.6X Running AMBER version 16.3 The blue node contains Dual Intel Xeon 250 E5-2699 v4@2.2GHz [3.6GHz Turbo] 6.4X (Broadwell) CPUs ns/day 200 The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz 150 Turbo] (Broadwell) CPUs +
Slide 13: PME-JAC_NVE on P100s SXM2
PME-JAC_NVE on P100s SXM2 500 PME-JAC_NVE 473.10 450 400 402.18 9.9X Running AMBER version 16.3 350 339.81 8.4X The blue node contains Dual Intel Xeon 300 E5-2699 v4@2.2GHz [3.6GHz Turbo] 7.1X (Broadwell) CPUs ns/day 250 The green nodes contain Dual Intel 200 Xeon E5-2698 v4@2.2GHz [3.6GHz Turbo] (B
Slide 14: GB-Myoglobin on P100s PCIe
GB-Myoglobin on P100s PCIe 600 GB-Myoglobin 561.94 500 483.37 19.5X Running AMBER version 16.3 400 The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] 16.7X (Broadwell) CPUs ns/day 300 The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz 200 Turbo] (Broadwell) CPUs +
Slide 15: GB-Myoglobin on P100s SXM2
GB-Myoglobin on P100s SXM2 700 GB-Myoglobin 639.37 600 500 534.28 22.2X Running AMBER version 16.3 18.5X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] 400 (Broadwell) CPUs ns/day The green nodes contain Dual Intel 300 Xeon E5-2698 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs +
Slide 16: GB-Nucleosome on P100s PCIe
GB-Nucleosome on P100s PCIe 50 45 GB-Nucleosome 45.92 40 39.91 114.8X Running AMBER version 16.3 35 30 99.8X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] (Broadwell) CPUs ns/day 25 22.77 The green nodes contain Dual Intel 20 Xeon E5-2699 v4@2.2GHz [3.6GHz 15 56.9X Turbo] (
Slide 17: GB-Nucleosome on P100s SXM2
GB-Nucleosome on P100s SXM2 60 50 GB-Nucleosome 48.29 46.29 Running AMBER version 16.3 40 120.7X The blue node contains Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz Turbo] 115.7X (Broadwell) CPUs ns/day 30 25.53 The green nodes contain Dual Intel Xeon E5-2698 v4@2.2GHz [3.6GHz 20 Turbo] (Broadwell) CPU
Slide 18: Rubisco-75K on P100s PCIe
Rubisco-75K on P100s PCIe 4.5 4.0 Rubisco-75K 4.20 3.5 420.0X Running AMBER version 16.3 3.0 The blue node contains Dual Intel Xeon 2.69 E5-2699 v4@2.2GHz [3.6GHz Turbo] 2.5 (Broadwell) CPUs 269.0X ns/day 2.0 The green nodes contain Dual Intel Xeon E5-2699 v4@2.2GHz [3.6GHz 1.5 1.40 Turbo] (Broadwel
Slide 19: Rubisco-75K on P100s SXM2
Rubisco-75K on P100s SXM2 5.0 4.5 Rubisco-75K 4.46 4.0 Running AMBER version 16.3 3.5 446.0X 3.06 The blue node contains Dual Intel Xeon 3.0 E5-2699 v4@2.2GHz [3.6GHz Turbo] 306.0X (Broadwell) CPUs ns/day 2.5 The green nodes contain Dual Intel 2.0 Xeon E5-2698 v4@2.2GHz [3.6GHz 1.57 Turbo] (Broadwel
Slide 20: Recommended GPU Node Configuration for AMBER Computational Chemistry
Recommended GPU Node Configuration for AMBER Computational Chemistry Workstation or Single Node Configuration # of CPU sockets 2 Cores per CPU socket 6+ (1 CPU core drives 1 GPU) CPU speed (Ghz) 2.66+ System memory per node (GB) 16 GPUs P100, V100 1-4 # of GPUs per CPU socket GPU memory preference (