Advanced user support
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Advanced User Support. Amit Majumdar 8/13/09. Outline. Three categories of AUS Operational Activities AUS.ASTA AUS.ASP ASTA example. Three Categories of AUS. A dvanced S upport for T eraGrid A pplications ( AUS . ASTA )

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Advanced user support

Advanced User Support

Amit Majumdar

8/13/09


Outline

Outline

  • Three categories of AUS

  • Operational Activities

  • AUS.ASTA

  • AUS.ASP

  • ASTA example


Three categories of aus

Three Categories of AUS

  • Advanced Support for TeraGrid Applications (AUS.ASTA)

    • AUS staff work on a particular user’s code (some community codes)

    • Guided/initiated by the allocations process

  • Advanced Support for Projects (AUS.ASP)

    • Project initiated by AUS staff (jointly with users) – impacts many users

    • Optimally install software, maintain, train users

  • Advanced Support for EOT (AUS.ASEOT)

    • Advanced HPC/CI trainings

    • Participate in workshops, tutorials (TG09, PetaScale, SCXY)

    • Interaction with other CI programs PlantCI, DataNet etc.


Update on operational activities

Update on Operational Activities

  • Bi-weekly telecon among AUS POCs from every RP site

    • Matching of AUS staff to ASTA projects, discussion about ASP, EOT activities

    • Program plans, annual reports etc.

  • Web/Tele-con among AUS technical staff

    • Biweekly technical tele/web-conference on ASTA and other projects - using readytalk

    • Since we started (early October, 2008) 20 tele/web-con sessions and 31 technical presentations (including today)


Astas started in october 2008 trac

ASTAs Started in October 2008 - TRAC


Startup supplemental astas

Startup/Supplemental ASTAs


Astas started in january 2009 trac

ASTAs Started in January 2009 - TRAC


Astas started in april 2009 trac

ASTAs Started in April 2009 - TRAC


Astas started in july 2009 trac

ASTAs Started in July 2009 TRAC


Astas

ASTAs

New Supplemental ASTAs Since last Round Table

  • Total ASTAs: 44

  • Two more Startup/Supplemental ASTAs approved


Advanced support projects

Advanced Support Projects

  • Three projects (two completed first phase)

    • Benchmarking Molecular Dynamics codes (SDSC, PSC) – completed first phase

    • Benchmarking Materials Science codes (PSC, TACC, LONI, NCSA, NICS) – completed first phase

    • Hybrid Programming model for multi-core (TACC, SDSC, PSC, NICS) jointly with XS-WG - continuing


Asp benchmark webpage

ASP Benchmark Webpage

Doc group has helped in setting up of AUS benchmark pages

Moved from earlier staging area webpage to production doc page:

http://www.teragrid.org/userinfo/aus/benchmark.php


Asta example as a part of adrian roitberg asta

ASTA Example:As a part of Adrian Roitberg ASTA

GPU Implementation of AMBER by Ross Walker (SDSC) jointly with NVIDIA experts

Other ASTA team members

SudhakarPamidighantam (NCSA ), Christian Halloy (NICS )


Gpu support

GPU Support

  • Collaboration with NVIDIA to produce CUDA version of AMBER.

    • PMEMD Engine

    • Implicit Solvent GB (V1.0 complete)

    • Explicit Solvent PME (in progress)

  • Focus on accuracy.

    • It MUST pass the AMBER regression tests.

    • Energy conservation MUST be comparable to double precision CPU code.


Gpu accuracy

GPU Accuracy

  • Use of double precision in all places severely limits performance.

    • Make careful use of double precision where needed.

    • Calculate in single precision.

    • Accumulate in double precision.

    • Avoid large dynamic ranges in arithmetic expressions.

    • Switch over to double precision automatically if the dynamic range is too high.


Provisional performance

Provisional Performance

  • 1 x Tesla C1060 (NCSA Lincoln S1070 – 4X)

Timings

-------

System Wall Time (s) NS/day

ACE-ALA3-NME(GPU) 48.57 355.92

ACE-ALA3-NME(4xCPU)* 34.78 496.84

(*Note 4 cpu since we need 10x > atoms than processors)

TRPCage(GPU) 62.48 276.57

TRPCage(8xCPU) 150.84 114.56

Myoglobin(GPU) 62.22 27.72

Myoglobin(8xCPU) 392.34 4.04

Nucleosome(GPU) 332.03 0.520

Nucleosome(8xCPU) 2877.60 0.060

Cray XT5 (1024xCPU) 175.49 0.985


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