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Nico Sanna Nico.Sanna@caspur.it Co-Chair of the HPC Division &

MS Faculty Days 2010, Rome - Sep 16th 2010. Experience many-core architectures at CASPUR: developing biochemistry application on Microsoft HPC 2008 environment. Nico Sanna Nico.Sanna@caspur.it Co-Chair of the HPC Division & Manager of HPC Support Group in (Bio)Chemical-Physics.

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Nico Sanna Nico.Sanna@caspur.it Co-Chair of the HPC Division &

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  1. MS Faculty Days 2010, Rome - Sep 16th 2010 Experience many-core architectures at CASPUR: developing biochemistry application on Microsoft HPC 2008 environment Nico Sanna Nico.Sanna@caspur.it Co-Chair of the HPC Division & Manager of HPC Support Group in (Bio)Chemical-Physics

  2. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR

  3. Numeric Simulation S = f (..,..,T,..,..) MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR HPC @ CASPUR Science Database (experiment) Technology

  4. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR HPC @ CASPUR Computational fields • Computational Physics • Computational Chemistry • Computational Biology • Computational Fluid-Dynamics • Applied Mathematics • Computational Material Science • ………

  5. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR HPC Computational (bio)-chemical-physics Quantum Chemistry • WaveFunction Methods • Density Functional (DFT) Methods Molecular Dynamics • Classical MD • Molecular Modeling Atomic & Molecular Physics • E-mol scattering • DNA Radiation Damage Data mining / warehousing • Genome/Protein databases (GCG/EMBOSS/user-db) • Microarray Experiment databases

  6. CASPUR Matrix cluster 15.0 TFLOPS of sustained performance MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR 2.2 Kcores AMD 23xx @ 2.1 GHz 6 TB RAM 200 TB IB storage sustainable green performance

  7. CASPUR Jazz Fermi GPU cluster 14.3 TFLOPS Peak performance MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR 192 cores Intel X5650 @ 2.67 GHz 14336 cores on 32 Fermi C2050 GPUs 1 TB RAM 200 TB IB storage Peak green performance

  8. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Beyond (… with) multi-core? Many-core computing could be an alternative… Accelerating co-processors become to be viable solutions to intensive computing Exploit GPU (&FPGA) computing at its best

  9. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Beyond (… with) multi-core? Reproduced w/ permission of Prof. E. Stahlberg

  10. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR CASPUR@XLrate project

  11. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR CASPUR@XLrate

  12. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR CASPUR@XLrate

  13. CASPUR: XLRATE environment MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Linux NFS server-HA 192.168.192.2 DNS 192.168.192.3 domain: XLRATE DNS domain: .xlrate.caspur.it network: 193.205.219.x/25 DNS .129 .240 00:17:A4:77:00:08 00:22:19:91:16:23 00:22:19:91:26:1D .246 .247 New HP SE2210 .243 .245 .250 .244 HP BL460c-G1 DELL 2950 DELL M600 DELL M600 HP BL460c-G1 HN LN CN CN LN CN hpchn01 hpcln01 hpccn01 hpccn02 hpcln02 hpcn03 Clear Speed GPU NVIDIA TESLA-S 00:22:19:91:16:25 blade10 00:22:19:91:26:1F 00:17:A4:77:00:0A blade9 .11 .15 .16 .14 .13 .12 network: 192.168.100.x/24 • hpccn01 (DELL 2950) • Quad Core 2,33GHz • HD RAID1: 2x73GB 15RPM • L2 cache: 2x6MB • 2x Broadcom BCM5708C • hpccn02 (HP BL460c-G1) • 2xDual Core Intel Xeon 3.0GHz • 8GB RAM • HD RAID1: 2x73GB 15RPM • 2x Broadcom BCM5708C

  14. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR CASPUR@XLrate

  15. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR CASPUR@XLrate project

  16. e- M+ X rays R• g rays a particles b particles Neutrons Cosmic rays R* Living tissue MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Radiation Damage: effect of the secondary species Ionizing radiation The genotoxic effects, due to various DNA lesions, are not only produced by the direct impact of the initial high energy particles (direct ionization) Role of SECONDARY SPECIES: excited atoms and molecules, radicals, ions, low-energy electrons (LEEs) 1 eV < E < 20 eV (the most abundant, carrying most of the energy of the initial radiation)

  17. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR U

  18. e- SCELib2 + VOLSCAT Cross Sections & Resonances E3 E2 E1 High Intensity Resonances Low Intensity Resonances GTGATAGAG T A G T G A T A G A G

  19. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR The SCELib Package The SCELib package: study of e-/p+ scattering from molecular targets. Properties Library (w/ API) of the molecular target N. Sanna, & F. A. Gianturco, Comp. Phys. Comm. 128(2) (2000) 615 N. Sanna & G. Morelli, Comp. Phys. Comm. 162(1) (2004) 51 N. Sanna, I. Baccarelli & G. Morelli, Comp. Phys. Comm., submitted (2009)

  20. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR The SCE part of SCELib: implementation on the GPUs Multi centered Basis Functions Multi centered Molecular Orbitals Single centered Molecular Orbitals our target in electron-molecule scattering

  21. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR The G80 architecture

  22. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR The G80 architecture

  23. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Measuring intrinsic functions performance Grid 1 1 1 Block 256 2 1 Size = 512 # Iterations = 100000

  24. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Measuring our GTO function performance Grid 1 1 1 Block 256 2 1 Size = 512 # Iterations = 100000 (*) Single process Intel QX7600 quad-core running @ 2.67 GHz DEVICE HOST F1 : (float) CSN[tid] * exp ( -EXP[tid] * RSQ[tid] ) F2 : (float) CSN[tid] * __expf ( -EXP[tid] * RSQ[tid] ) F3 : (float) CSN[tid] fmul __expf ( -EXP[tid] fmul RSQ[tid] )

  25. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Profiling CalcMO() GTO calculation w/ VisualProfiler 0.1 - GPU TIME

  26. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Profiling CalcMO() GTO calculation w/ VisualProfiler 0.1 - SIGNAL

  27. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Current implementation of SCELib 3.0 on GPUs SCE algorithm 1) Primitive GTO mapping 2) MOs Single Center Expansion

  28. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs - optimal parameters (warp size, arrays’ dimension in constant memory). Still work in progress • scalability for CH4 with respect to the number of grid points Execution time (in msec) and speed-up with respect to Host SPP calculation

  29. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs • scalability for CH4 with respect to the number of primitive GTOs G9800 Speed-up with respect to Host SPP calculations

  30. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs • scalability with respect to the type of molecular system

  31. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs Timing (in msec) for individual sections of a SCELib run for SO2 molecule (32 electrons, NOTHRDS=32, NPBSIZE=884), transfer Bandwidth and final Speed-up with respect to Host SPP calculations. AD: Allocated Data (in MB) in the Device Global Memory (A) G9800 GX2; (B) Quadro FX5600; (C) Tesla C1060

  32. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs • scalability with respect to the type of molecular system

  33. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs • scalability with respect to the type of molecular system

  34. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib3.0 performance on GPUs • scalability with respect to the type of molecular system

  35. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib4.0 performance on GPUs • SO2Running on MS HPC 2008 Server. One Tesla C1060 GPU

  36. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib4.0 performance on GPUs • SO2 Running on Linux. One Fermi C2050 GPU

  37. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib4.0 performance on GPUs • CPU scalability. Intel X5650 @ 2.67 GHz

  38. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib4.0 performance on GPUs • CPU scalability. Intel X5650 @ 2.67 GHz

  39. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR SCELib4.0 performance on GPUs • CPU/GPU scalability. Intel X5650 @ 2.67 GHz & C2050 GPU

  40. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Conclusions • GPU computing more than FPGA/FPA • CPU/GPU hybrid architectures are becoming mainstream in HPC • Green Computing & Power Awareness HPC w/ many-core (Matrix = 120 KW / Jazz = 13 KW) • Linux OS is there, but look at MS for low latency & data-intensive applications

  41. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Gaussian 03 performance on CPUs (PGI version) • B3LYP/6-31G** SPE calculation running on AMD/Intel procs

  42. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Gaussian 03 performance on CPUs (PGI version) • B3LYP/6-31G** SPE calculation running on AMD/Intel procs

  43. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Gaussian 03 performance on CPUs (PGI version) • B3LYP/6-31G** SPE calculation running on AMD/Intel procs

  44. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Gaussian 03 performance on CPUs (PGI version) • B3LYP/6-31G** SPE calculation running on AMD/Intel procs

  45. MS Faculty Days 2010 // Rome, Sep 16th 2010 Nico Sanna - CASPUR Gaussian 03 performance on CPUs (PGI V10.8) • B3LYP/6-31G** SPE calculation running on AMD/Intel procs

  46. Amber 11 performance on CPUs/GPU • Nucleosome (25095 atoms) Implicit Solvent

  47. Amber 11 performance on CPUs/GPU • Nucleosome (25095 atoms) Implicit Solvent Nanoseconds/day

  48. Amber 11 performance on CPUs/GPU • FactorIX (90906 atoms) Explicit Solvent

  49. Amber 11 performance on CPUs/GPU • FactorIX (90906 atoms) Explicit Solvent Nanoseconds/day

  50. Amber 11 performance on CPUs/GPU • DHFR (23558 atoms) Explicit Solvent

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