== drbl-mpi shell script ==

Abstract [[br]]
I.Introduction [[br]]
II.LAMMPS simulation [[br]]
III.DRBL AND ONEMPI archtiecture [[br]]
IV.LAMMPS Benchmark [[br]]
V.Conclusions [[br]]

Abstract― [[br]]
The LAMMPS is classical molecular dynamics software which supports also large scale atomic massively parallel simulation. [[br]]
The code has been run on a PC cluster with using DRBL (Diskless Remote Boot in Linux)-ONEMPI. MPICH2 provide an MPI [[br]]
implementation that supports different computing and communication platform. How-ever, MPICH2 has still many installation [[br]]
steps that are complicate. Therefore, the paper provides DRBL-ONEMPI free software to deploy desktop clusters. It can [[br]]
construct quickly a multicores architecture environment and a convenient management for your environment. The DRBL-ONEMPI [[br]]
gives user some useful installation process and assists system administrators to deploy their own private cluster environment. [[br]]
We build a PC cluster environment, and runs in parallel using MPICH2 on our PC cluster with diskless nodes. We will introduce [[br]]
the basic architecture of DRBL-ONEMPI and present some design. [[br]]

Keywords―LAMMPS, molecular dynamics, MPICH2, DRBL-ONEMPI. [[br]]

I.Introduction [[br]]

LAMMPS is created by Sandia National La-boratories, a US Department of Energy laboratory. LAMMPS is classical molecular dynamics  [[br]]
simulation software, integrates Newton`s equation of motion, is an open source code, and runs on single processors or parallel  [[br]]
programming with using message-passing interface. The LAMMPS source is widely applied in the semiconductors, biomolecular, polymers,  [[br]]
coarse-grained and microscopic, etc. It has been used to simulate in the chemistry and semiconductor research. The LAMMPS has lots  [[br]]
of library to use, modify, or extended LAMMPS in your choose.  [[br]]
In past few years, PC cluster are more and more popular in high performance computing be-cause of computing ability. However,  [[br]]
it is difficult for the administrator manage lots of computers, to deploy the system environmental and to configure the installation  [[br]]
of the cluster. The DRBL-ONEMPI provides a way to manage the pc cluster environ-ment, such as the installation of the cluster, the  [[br]]
deployment system environment, the user man-agement, the system monitor and easy to use it.  [[br]]
The DRBL-ONEMPI has two components package, including DRBL and ONEMPI.  The DRBL is a diskless or systemless environment for client  [[br]]
machines and an open source solution to managing the deployment of the GNU/Linux oper-ating system across many clients. Hence, we  [[br]]
have an ideal plan for running MPI programming on the diskless environment and so to exploit ONEMPI. The ONEMPI make user avoid complicated  [[br]]
the MPICH2 installation process. However, we combine DRBL with ONEMPI which rename DRBL-ONEMPI. In general, the pc cluster is difficult  [[br]]
to manage and deploy environment. However, we use DRBL-ONEMPI to manage and execute mpich2 on our computing environment. The user just  [[br]]
enters some instructions on command-line that accomplish diskless environment.  [[br]]
In section.2, we will introduce LAMMPS simulation software. In section.3, the DRBL and ONEMPI system are presented in detail. In sec-tion.4,  [[br]]
the simulation and benchmark results are discussed.  [[br]]


II.	LAMMPS Simulation [[br]]
The LAMMPS has been used wildly in ma-terial processing, such as etching, deposition, sput-tering and surface cleaning, etc. some people also use [[br]]
LAMMPS to apply mechanical engineering, such as computational fluid dynamics (CFD), Fracture Mechanics, Micro and Nano Mechanics, etc. The LAMMPS [[br]]
is popular one of molecular dynamics software and lots of library. [[br]]
The LAMMPS applied process as follows: [[br]]
(1)	To input a script file for LAMMPS the initial configuration. [[br]]
(2)	To create a particle and model types, such as atoms, coarse-grained particles, all-atom poly-mers, organic molecules, proteins, DNA, etc. [[br]]
(3)	To choose force fields, the potential has Len-nard-Jones, Morse, Tersoff and EAM, etc. [[br]]
(4)	To construct boundary and constraints conditions. [[br]]
(5)	To choose integrators, such as velocity-Verlet integrator, Brownian dynamics, rigid body in-tegration, etc. [[br]]
(6)	To run program and Output file. [[br]]

III.	DRBL and ONEMPI design architecture [[br]]
A.	DRBL Architecture [[br]]
  Diskless Remote Boot in Linux (DRBL) is an open source solution to managing the deploy-ment of the GNU/Linux operating system across many clients. [[br]]
DRBL supports lots of popular GNU/Linux distributions, and it is developed based on diskless and systemless environment for client machines. Figure 1 [[br]]
shows DRBL system architec-ture. DRBL uses PXE/Etherboot, DHCP, TFTP, NFS and NIS to provide services to client machines, so it is not necessary to [[br]]
install GNU/Linux on the client hard drives individually. Users just prepare a server machine for DRBL to be installed as a DRBL server, and follow [[br]]
the DRBL installation wizard to configure and dispose the environment for client machines step by step. It’s really an easy job to deploy a DRBL [[br]]
environment on clustering systems even for a GNU/Linux beginner, hence cross-platform and user-friendly are the key factors that make the DRBL become [[br]]
a superior clustering tool. DRBL can efficiently deploy diskless or dis-kfull cluster environment, and manage client. It configures these services [[br]]
(TFTP, NIS, DHCP, and NFS) to build a cluster environment. According to this implementation, administrator just needs two steps to deploy cluster [[br]]
environment. (1) Step 1: In-stalls DRBL packages and generates kernel and in-itrd for client; (2) Step 2: setup environment para-meters, such IP address, [[br]]
and numbers of clients. It also provides cluster management and cluster system transformation (diskfull or diskless system). The Figure 1 shows DRBL [[br]]
system architecture [[br]]


[[Image(Using DRBL on CPU Cluster.jpg)]] [[br]]
Figure 2.Using DRBL on CPU Cluster [[br]]

B.	ONEMPI Architecture
ONEMPI is a software package, and it de-pends on DRBL to deploy PC cluster environment. We are just run the ONEMPI script which is build a PC cluster [[br]]
quickly. We employ to combine DRBL with ONEMPI to build a message-passing interface system environment. At first we need to install configuration the [[br]]
DRBL software which is easy to install on operating system. Then, we run the ONEMPI script by using super user when the DRBL is installed on ours system. [[br]]
The two steps is finished, users can execute and compile mpi pro-gramming on the system environment. The ONEMPI script is automatically produce the [[br]]
“mpd.hosts” on yours home directory, and the mpd.hosts is to record all nodes hostname and Pro-cessor numbers. However, the ONEMPI is achievement to [[br]]
realize the complicate installation process. However, users can use the instruction “mpdboot -n * -f mpd.hosts” on yours home direc-tory, and the * is [[br]]
node numbers. [[br]]
The Figure 1 shows ONEMPI architecture, and the ONEMPI script has two significance files as follows: [[br]]
(1) The “mpi_install.sh” script is configuration to install software package (g++, fort77, gcc, mpich2, etc.) in the system, and create the “mpd.conf” [[br]]
file to ours home directory. [[br]]
(2)	The “drbl_mpi_patch” script is to adjust the DRBL software, including the public key, creating the mpd.hosts file and DRBL redeploy clients, etc. [[br]]

[[Image(ONEMPI design architecture.jpg)]] [[br]]
Figure 2.ONEMPI design architecture [[br]]

(3)	We can run ONEMPI script file in the terminal command as follows: [[br]]
	Step 1: sudo ./install [[br]]
	(default : /opt/drbl-mpi) [[br]]
	Step 2: cd /opt/drbl-mpi/ [[br]]
	Step 3: sudo ./drbl_mpi.sh [[br]]

C.	System Environment Architecture [[br]]
Table 1 shows the software packages about the diskless cluster. There are one server node and two client nodes in our system environment. Server and  [[br]]
clients have one Intel 2 Quad CPU Quad CPU    Q9550 @ 2.83GHz and 8 Gbytes of memory. Ours system is Ubuntu 10.10 version. [[br]]

[[Image(Hardware specifications and Software list.jpg)]] [[br]]
Figure 3.Hardware specifications and Software list [[br]]