Molecular Dynamic analysis with Gromacs: Part of Indonesian Herbal Farmacological activities screening in

Silico study

On a Cluster computing environment.

Screening aktifitas farmakologis beberapa bahan aktif tumbuhan obat Indonesia secara in silico menggunakan High Performance Computing berbasis Cluster system

Joint research : Arry Yanuar, Dept of Pharmacy,

and Heru Suhartanto, Ari Wibisono,

Faculty of Computer Science,

Universitas Indonesia

Supported by The Indonesian Ministry of Research and Technology Office, 2009-2010,research grant

Gromacs

GROMACS is a one of the best program to perform molecular dynamics for protein and bio-molecule simulation.

GROMACS can be run with single processor or using multiple processor (parallel using standard MPI communication)

Our Research is to study the performance (time) between, on the Cluster computing resources and on the GPU (Graphic Processor Unit)

The InGrid: http://grid.ui.ac.id

Let’s see a 1 minute visit to the portal and the monitor

Hastinapura

Hastinapura.grid.ui.ac.id is the first Cluster computing resources, the Faculty of Computer Science Universitas Indonesia.

 This cluster can be used to run parallel and serial applications (gromacs).

 It consists of 16 dual-core machines that act as worker nodes.

Hardware Specification Head node

Sun Fire X2100 AMD Opteron 2.2GHz (Dual Core) 2 GB RAM Debian GNU/Linux 3.1 “Sarge”

Worker nodes (16) Sun Fire X2100 AMD Opteron 2.2GHz (Dual Core) 1 GB RAM Debian GNU/Linux 3.1 “Sarge”

Storage node Dual Intel Xeon 2.8GHz (HT) 2 GB RAM Debian GNU/Linux 4.0-testing “Etch” Harddisk 3x320 GB

GPU PC Hardware Specification Dual Core 3.2 GHz

4 GB RAM Ubuntu 9.04 64 Bit Harddisk 80 Gb Gromacs 4.05 + OpenMM GeForce GTS 250

CUDA Cores 128Graphics Clock

(MHz)738 MHz

Processor Clock (MHz)

1836 MHz

Texture Fill Rate (billion/sec)

47.2 Memory Clock (MHz)

1100 

Standard Memory Config

512MB or 1 GB GDDR3

Memory Interface Width

256-bit

Memory Bandwidth (GB/sec)

70.4

GPU Engine Specs:Memory Specs:Feature Support:

File Preparation

File Cyp34a

pdb2gmx -f 1TQN.pdb -p 1TQN.top -o 1TQN.gro

editconf -f 1TQN.gro -o 1TQN.gro -d 1.0

genbox -cp 1TQN.gro -cs spc216.gro -p 1TQN.top –o

1TQN-solvate.pdb

grompp -np 16 -f md.mdp -c 1TQN.gro -p 1TQN.top -o 1TQN-md.tpr

Convert File Into .topology & .gro

Periodic Boundary Condition

Adding solvent into the molecule

Energy Minimization

1TQN-md.tpr is ready to be

executed with 16 processor

#!/bin/sh

# CYP34A

#$ -N gromacs

#$ -cwd

# Jumlah prosesor

#$ -pe mpich 16

#$ -l arch=lx24-x86

#$ -o /export/home/nico/cyp3a4/stdout

#$ -e /export/home/nico/cyp3a4/stderr

#$ -i /export/home/nico/cyp3a4/stdin

#

# needs in

# $NSLOTS

# the number of tasks to be used

# $TMPDIR/machines

# a valid machine file to be passed to mpirun

echo "Got $NSLOTS slots."

/usr/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines

/export/home/nico/gromacs/bin/mdrun_mpi

-s /export/home/nico/cyp3a4/1TQN-md.tpr

-o /export/home/nico/cyp3a4/1TQN-md.trr

-c /export/home/nico/cyp3a4/1TQN-after-md.gro

-np 16 -v

Md-job.sh

qsub md-job.sh

File Cyp34a (GPU)

pdb2gmx -f 1TQN.pdb -p 1TQN.top -o 1TQN.gro

editconf -f 1TQN.gro -o 1TQN.gro -d 1.0

genbox -cp 1TQN.gro -cs spc216.gro -p 1TQN.top –o

1TQN-solvate.pdb

grompp -f md.mdp -c 1TQN.gro -p 1TQN.top -o 1TQN-md.tpr

Convert File Into .topology & .gro

Periodic Boundary Condition

Adding solvent into the molecule

Energy Minimization

mdrun-openmm -v -deffnm 1TQN-md

Production Simulation

File Curcumin

grompp -np 10 -f md.mdp -c lox_pr.gro -p model.top -o topol.tpr

topol.tpr is ready to be executed

with 10 processor

dt x nsteps = …pikosecond0.002 x 100000 = 200 pikosecond

Md-job.sh#!/bin/sh

# Curcumin

#$ -N gromacs

#$ -cwd

# Jumlah prosesor

#$ -pe mpich 10

#$ -l arch=lx24-x86

#$ -o /export/home/ari/simulasi/curcumin10/stdout

#$ -e /export/home/ari/simulasi/curcumin10/stderr

#$ -i /export/home/ari/simulasi/curcumin10/stdin

#

# needs in

# $NSLOTS

# the number of tasks to be used

# $TMPDIR/machines

# a valid machine file to be passed to mpirun

echo "Got $NSLOTS slots."

/usr/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines

/export/home/nico/gromacs/bin/mdrun_mpi

-s /export/home/ari/simulasi/curcumin12/topol.tpr

-o /export/home/ari/simulasi/curcumin12/curcumin12.trr

-c /export/home/ari/simulasi/curcumin12/lox_pr.gro

-np 10 –v

qsub md-job.sh

File Curcumin (GPU)

grompp -f md.mdp -c lox_pr.gro -p model.top -o curcumin.tpr

dt x nsteps = …pikosecond0.002 x 100000 = 200 pikosecond

mdrun-openmm -v -deffnm curcumin

Production Simulation

Performance Result

File : Curcumin

Performance Time

Timesteps

1 CPU 24h:01M 200 ps

GPU 17h:01M 200 ps

InGrid 1 CPU 18h 200 ps

InGrid 2 CPU 14h 200 ps

InGrid 4 CPU 08h 200 ps

InGrid > 4 CPU Problems !!!

File : CYP3A4 Performance Time

Timesteps

1 CPU 22h :32 M 200 ps

GPU 14h : 23M 200 ps

CYP3A4 Result on InGrid is almost the same with the above result

The next targets: Improve the performance

Thank you !