drbl-mpi shell script

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

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

Keywords―LAMMPS, molecular dynamics, MPICH2, DRBL-ONEMPI.

I.Introduction

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

1. LAMMPS Simulation
   

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

1. DRBL and ONEMPI design architecture
   
2. DRBL Architecture
   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.
   

DRBL supports lots of popular GNU/Linux distributions, and it is developed based on diskless and systemless environment for client machines. Figure 1
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
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
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
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
a superior clustering tool. DRBL can efficiently deploy diskless or dis-kfull cluster environment, and manage client. It configures these services
(TFTP, NIS, DHCP, and NFS) to build a cluster environment. According to this implementation, administrator just needs two steps to deploy cluster
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,
and numbers of clients. It also provides cluster management and cluster system transformation (diskfull or diskless system). The Figure 1 shows DRBL
system architecture

Figure 2.Using DRBL on CPU Cluster

2. 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
quickly. We employ to combine DRBL with ONEMPI to build a message-passing interface system environment. At first we need to install configuration the
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.
The two steps is finished, users can execute and compile mpi pro-gramming on the system environment. The ONEMPI script is automatically produce the
“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
realize the complicate installation process. However, users can use the instruction “mpdboot -n * -f mpd.hosts” on yours home direc-tory, and the * is
node numbers.
The Figure 1 shows ONEMPI architecture, and the ONEMPI script has two significance files as follows:
(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”
file to ours home directory.
(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.

Figure 2.ONEMPI design architecture

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

3. System Environment Architecture
   

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
clients have one Intel 2 Quad CPU Quad CPU Q9550 @ 2.83GHz and 8 Gbytes of memory. Ours system is Ubuntu 10.10 version.

Figure 3.Hardware specifications and Software list