== 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]]