== 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]]