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, ,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: 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 Sun Fire X2100  AMD Opteron 2.2GHz (Dual Core) AMD Opteron  2 GB RAM  Debian GNU/Linux 3.1 “Sarge”  Worker nodes (16)  Sun Fire X2100 Sun Fire X2100  AMD Opteron 2.2GHz (Dual Core) AMD Opteron  1 GB RAM  Debian GNU/Linux 3.1 “Sarge”  Storage node  Dual Intel Xeon 2.8GHz (HT)Intel Xeon  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 Bit  Harddisk 80 Gb  Gromacs OpenMM  GeForce GTS 250 CUDA Cores128 Graphics Clock (MHz)738 MHz Processor Clock (MHz)1836 MHz Texture Fill Rate (billion/sec) 47.2 Memory Clock (MHz)1100 Standard Memory Config512MB or 1 GB GDDR3 Memory Interface Width256-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 = …pikosecond x = 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 = …pikosecond x = 200 pikosecond mdrun-openmm -v -deffnm curcumin Production Simulation

Performance Result File : Curcumin Performance Time Timesteps 1 CPU24h:01M200 ps GPU17h:01M200 ps InGrid 1 CPU18h200 ps InGrid 2 CPU14h200 ps InGrid 4 CPU08h200 ps InGrid > 4 CPUProblems !!! File : CYP3A4Performance Time Timesteps 1 CPU22h :32 M200 ps GPU14h : 23M200 ps CYP3A4 Result on InGrid is almost the same with the above result

The next targets: Improve the performance Thank you !