The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 -...

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The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007

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Page 1: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

The Avian Flu Grid Project

Rommie Amaro & Dong Xu

University of California, San Diego

PRAGMA 13 - NCSA

Sept 25, 2007

Page 2: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Outline

• Meet the Team• Project goals & motivation• Overall scheme• Running jobs on the PRAGMA grid• Analyze the results w/ AutoDockTools

Page 3: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Meet the Avian Flu Team

Page 4: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Neuraminidase as Drug Target

Developed against N9

sialic acid DANA zanamivir (Relenza)

Oseltamivir (Tamiflu)

Clercq, Nat Rev. Drug Disc.,5: 1015-1025 (2006)Moscana, New Eng. J. Med., 353: 1363-1373 (2006)

Page 5: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Group 1 and 2 Neuraminidases

Russell et al, Nature, 443: 45-49 (2006).

Page 6: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Relaxed Complex Method

Page 7: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Cluster

Cluster

Cluster

Autodock

NAMDOther

Resource

12 CPUs

Autodock

BLAST

Other Resource

64 CPUs

NAMD

Autodock 8 CPUs

Other Resource

CSF4 Meta-Scheduler

Available Resource Lists

Resource

Scheduling Modules

Resource Requirements

Autodock1990 CPUs

NAMD24 CPUs

Autodock100 CPUs

Autodock1 CPU

ˇˇ

ˇˇ

User

Grid Job Submission

Page 8: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Demo

• Submit docking jobs on grid

• Analyze results with AutoDockTools

Page 9: The Avian Flu Grid Project Rommie Amaro & Dong Xu University of California, San Diego PRAGMA 13 - NCSA Sept 25, 2007.

Molecular Dynamics Simulations

• Start with the crystal structure• Ligands (tamiflu), ions• Explicit solvent, 0.15M NaCl• 112,457 atoms

• NAMD2, Amber99 force field• 2 fs timestep, PBC, PME• SDSC Datastar Benchmark: 112

processors, 0.21 days/ns need fast interconnect between processors - not for grid

• Data: tens - hundreds of GB


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Medi Pragma 2012

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Historia Pragma Consultores

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Pragma On Key

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Mini Pragma - Filkab.com

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Acknowledgment of Reviewers, 2016 · Rama R. Amara Luis A. Nunes Amaral Gaya K. Amarasinghe Rommie E. Amaro Richard M. Amasino Stanley H. Ambrose Andre L. B. Ambrosio Indu S. Ambudkar

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GNAT Reference Manual - GNU Projectiv 2.134 Pragma PrefixException Messages ::::: 67 2.135 Pragma Pre Class ::::: 68 2.136 Pragma Priority SpecificDispatching ::::: 68 2.137 Pragma

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Parallel Programming Course OpenMP - Intel · #pragma omp parallel {#pragma omp task foo(); #pragma omp barrier #pragma omp single {#pragma omp task bar();}} task : Multiple foo()

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GNAT Reference Manual - GNU Projectgcc.gnu.org/onlinedocs/gcc-7.2.0/gnat_rm.pdfiv 2.134 Pragma PrefixException Messages ::::: 67 2.135 Pragma Pre Class ::::: 68 2.136 Pragma Priority

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Investment for the Future of PRAGMA Progress Since PRAGMA 10: PRAGMA 11 Osaka University 15 – 17 October 2006.

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Pedro Amaro

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Company Profile Pragma Africa - Pragma Latam · The Pragma Way 4 The Pragma Group Pragma Holdings acts as an investment vehicle for the group and provides strategic and operational

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