1 The Performance Analysis of Molecular dynamics RAD GTPase with AMBER application on Cluster...

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The Performance Analysis of The Performance Analysis of Molecular dynamics RAD GTPase Molecular dynamics RAD GTPase

with AMBER application onwith AMBER application onCluster computing environtment.Cluster computing environtment.

Universitas Indonesia

Heru Suhartanto, Arry Yanuar

Toni Dermawan

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Molecular Dynamics Molecular Dynamics SimulationSimulation

MD simulation on virus H5N1 [3]

Computer Simulation Techniques

Computer Simulation Techniques

Molecular Dynamic

Simulation

Molecular Dynamic

Simulation

2Fakultas Ilmu Komputer Universitas Indonesia

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““MD simulation : MD simulation : computational tools used to computational tools used to describe the position, speed describe the position, speed an and orientation of an and orientation of molecules at a certain time” molecules at a certain time” Ashlie Martini Ashlie Martini [4][4]


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MD simulation MD simulation purposes/benefits:purposes/benefits:

Sumber gambar: [5], [6], [7]4Fakultas Ilmu Komputer Universitas Indonesia

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Challenges in MD Challenges in MD simulationsimulation


•O(N2) time complexity

•Timesteps (simulation time)

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Focus of the experimentFocus of the experiment


•Study the effect of MD simulation timestep on the executing / processing time;

•Study the effect of in vacum and implicit solvent technique with generalied Born (GB) model on the executing / processing time;

•Study (scalability) how the number of processors improve executing / processing time;

•Study how the output file grows as the timesteps increase.

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Scope of the experimentsScope of the experiments


•Preparation and simulation with AMBER packages

•Performance is based on the execution time of the MD simulation

•No parameter optimization for the MD simulation

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Molecular Dynamics basic process Molecular Dynamics basic process [4][4]


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Flow of data in AMBER [8]

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Flows in AMBER [8]Flows in AMBER [8]

Preparatory programPreparatory program LEaP is the primary program to create a new system in LEaP is the primary program to create a new system in

Amber, or to modify old systems. It combines the Amber, or to modify old systems. It combines the functionality of prep, link, edit, and parm from earlier functionality of prep, link, edit, and parm from earlier versions.versions.

ANTECHAMBER is the main program from the ANTECHAMBER is the main program from the Antechamber suite. If your system contains more than Antechamber suite. If your system contains more than just standard nucleic acids or proteins, this may help you just standard nucleic acids or proteins, this may help you prepare the input for LEaP.prepare the input for LEaP.

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SimulationSimulation SANDER is the basic energy minimizer and molecular SANDER is the basic energy minimizer and molecular

dynamics program. This program relaxes the dynamics program. This program relaxes the structure by iteratively moving the atoms down the structure by iteratively moving the atoms down the energy gradient until a sufficiently low average energy gradient until a sufficiently low average gradient is obtained.gradient is obtained.

PMEMD is a version of sander that is optimized for PMEMD is a version of sander that is optimized for speed and for parallel scaling. The name stands for speed and for parallel scaling. The name stands for "Particle Mesh Ewald Molecular Dynamics," but this "Particle Mesh Ewald Molecular Dynamics," but this code can now also carry out generalized Born code can now also carry out generalized Born simulations.simulations.

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AnalysisAnalysis PTRAJ is a general purpose utility for PTRAJ is a general purpose utility for

analyzing and processing trajectory or analyzing and processing trajectory or coordinate files created from MD simulationscoordinate files created from MD simulations

MM-PBSA is a script that automates energy MM-PBSA is a script that automates energy analysis of snapshots from a molecular analysis of snapshots from a molecular dynamics simulation using ideas generated dynamics simulation using ideas generated from continuum solvent models.from continuum solvent models.

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RAD (Ras Associated with Diabetes) is a family of RGK small GTPase located inside human body with diabetes type 2. The crystal form of Rad GTPase has resolution of 1,8 angstrom.

The crystal form of RAD GTPase is stored in d Protein Data Bank (PDB) file.

Ref: A. Yanuar, S. Sakurai, K. Kitano, Hakoshima, dan Toshio, “Crystal structure of human rad gtpase of the rgk-family,” Genes to Cells, vol. 11, no. 8, pp. 961-968, Agustus 2006

The The RAD GTPaseRAD GTPase Protein Protein

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RAD GTPaseRAD GTPase Protein Protein


Reading from PDB with NOC:

The leap.log reading:

number of atom 2529

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Parallel approach in MD Parallel approach in MD simulationsimulation


AlgoritAlgorithms forhms for fungsi fungsi forceforce:: data replidata replicationcation DataData distribution distribution

DataData decomposition decomposition Particle decompositionParticle decomposition Force decompositionForce decomposition Domain decompositionDomain decomposition Interaction decompositionInteraction decomposition

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Parallel implementation inParallel implementation in AMBERAMBER


•Atoms are distributed among available processors (Np)

•Each Execution nodes / processors compute force function

•Updating position, computing parsial force, ect.

•Write to output files

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HastinapuraHastinapura Cluster ClusterNama Nama

NodeNode

Head NodeHead Node Worker NodesWorker Nodes Storage Storage

NodeNode

ArsitektuArsitektu

rr

Sun Fire Sun Fire

X2100X2100

Sun Fire X2100Sun Fire X2100 --

ProsesorProsesor AMD Opteron AMD Opteron

2.2 GHz (Dual 2.2 GHz (Dual

Core)Core)

AMD Opteron AMD Opteron

2.2 GHz (Dual 2.2 GHz (Dual

Core)Core)

Dual Intel Dual Intel

Xeon 2.8 GHz Xeon 2.8 GHz

(HT(HT))

RAMRAM 2 GB RAM2 GB RAM 11 GB RAM GB RAM 2 GB RAM2 GB RAM

HarddiskHarddisk 80 GB80 GB 80 GB80 GB 3 x 320 GB3 x 320 GB


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SoftwareSoftwaress Hastinapura Hastinapura ClusterCluster


FunctionsFunctions Applications Applications (versi)(versi)

11 compilerscompilers ggcccc ( (3.3.53.3.5); ); g++g++ ( (3.3.53.3.5, ,

GCC); GCC); g77g77 ( (3.3.53.3.5, GNU , GNU

Fortran); Fortran); g95g95 (0.91, GCC (0.91, GCC

4.0.3)4.0.3)

22 Aplikasi MPI 1Aplikasi MPI 1 MPICH (MPICH (1.2.7p11.2.7p1, , Release Release

date: 2005/11/04 date: 2005/11/04

11:54:5111:54:51))

33 Operating systemOperating system Debian/Linux OS (3.1 Debian/Linux OS (3.1

“Sarge”)“Sarge”)

44 Resource managementResource management Globus Toolkit [2] (4.0.3)Globus Toolkit [2] (4.0.3)

55 Job schedulerJob scheduler Sun Grid Engine (SGE) Sun Grid Engine (SGE)

(6.1u2)(6.1u2)

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Experiment resultsExperiment results

Fakultas Ilmu Komputer Universitas Indonesia

2020

Execution time withExecution time with In In VacuumVacuum



Execution time for Execution time for In VacuumIn Vacuum

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Execution time for Execution time for Implicit Implicit Solvent Solvent with GB with GB Model Model



Execution time for Execution time for Implicit SolvenImplicit Solven with GBwith GB Model Model


Execution time comparison betweenExecution time comparison between In In Vacuum Vacuum and and Implicit Solvent Implicit Solvent withwith GB GB model model


The effect of The effect of ProsesorProsesor number on number on MD MD simulation withsimulation with In VacuumIn Vacuum


The effect of processors number at MD The effect of processors number at MD simulation with simulation with Implicit Solvent Implicit Solvent dengan dengan

Model GBModel GB

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Number of processors and output file sizes Simulation time - (ps)

1 2 4 8 MB

(Megabytes) 100 6.148.096 6.148.096 6.148.096 6.148.096 5,86

200 12.292.096 12.292.096 12.292.096 12.292.096 11,72

300 18.440.192 18.440.192 18.440.192 18.440.192 17,59

400 24.584.192 24.584.192 24.584.192 24.584.192 23,45

Output file sizes as the simulation time grows – in vacum

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Jumlah prosesor

Simulation time (ps)

1 2 4 8 Konversi ke

MB (Megabytes)

100 6.148.096 6.148.096 6.148.096 6.148.096 5,86

200 12.292.096 12.292.096 12.292.096 12.292.096 11,72

300 18.440.192 18.440.192 18.440.192 18.440.192 17,59

400 24.584.192 24.584.192 24.584.192 24.584.192 23,45

Output file sizes as the simulation time grows –

Implicit solvent with GB model

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Problems encounteredProblems encountered

Electrical supplies instabilitiesElectrical supplies instabilities.. Some nodes are not functioning Some nodes are not functioning

during one or two experimentsduring one or two experiments Another cluster with head node Another cluster with head node

functions also as worker node: some functions also as worker node: some nodes are not functioning / downs nodes are not functioning / downs during some experiments.during some experiments.


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ReferencesReferences[1]http://www.cfdnorway.no/images/PRO4_2.jpg[1]http://www.cfdnorway.no/images/PRO4_2.jpg[2]http://sanders.eng.uci.edu/brezo.html[2]http://sanders.eng.uci.edu/brezo.html[3]http://www.atg21.com/FigH5N1jcim.png[3]http://www.atg21.com/FigH5N1jcim.png[4] A. Martini, “Lecture 2: Potential Energy Functions”, 2010, [4] A. Martini, “Lecture 2: Potential Energy Functions”, 2010, [Online]. Tersedia di: http://nanohub.org/resources/8117. [Online]. Tersedia di: http://nanohub.org/resources/8117. [Diakses pada 18 Juni 2010].[Diakses pada 18 Juni 2010].[5]http://www.dsimb.inserm.fr/images/Binding-sites_small.png[5]http://www.dsimb.inserm.fr/images/Binding-sites_small.png[6]http://thunder.biosci.umbc.edu/classes/biol414/spring2007/[6]http://thunder.biosci.umbc.edu/classes/biol414/spring2007/files/protein_folding(1).jpgfiles/protein_folding(1).jpg[7]http://www3.interscience.wiley.com/tmp/graphtoc/[7]http://www3.interscience.wiley.com/tmp/graphtoc/72514732/118902856/118639600/ncontent72514732/118902856/118639600/ncontent[8] D. A. Case et al., “AMBER 10”, University of California, San [8] D. A. Case et al., “AMBER 10”, University of California, San Francisco, 2008, [Online]. Tersedia di: Francisco, 2008, [Online]. Tersedia di: http://www.lulu.com/content/paperback-book/amber-10-users-http://www.lulu.com/content/paperback-book/amber-10-users-manual/2369585. [Diakses pada 11 Juni 2010].manual/2369585. [Diakses pada 11 Juni 2010].


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