| | 1 | == drbl-mpi shell script == |
| | 2 | |
| | 3 | Abstract [[br]] |
| | 4 | I.Introduction [[br]] |
| | 5 | II.LAMMPS simulation [[br]] |
| | 6 | III.DRBL AND ONEMPI archtiecture [[br]] |
| | 7 | IV.LAMMPS Benchmark [[br]] |
| | 8 | V.Conclusions [[br]] |
| | 9 | |
| | 10 | Abstract― [[br]] |
| | 11 | The LAMMPS is classical molecular dynamics software which supports also large scale atomic massively parallel simulation. [[br]] |
| | 12 | The code has been run on a PC cluster with using DRBL (Diskless Remote Boot in Linux)-ONEMPI. MPICH2 provide an MPI [[br]] |
| | 13 | implementation that supports different computing and communication platform. How-ever, MPICH2 has still many installation [[br]] |
| | 14 | steps that are complicate. Therefore, the paper provides DRBL-ONEMPI free software to deploy desktop clusters. It can [[br]] |
| | 15 | construct quickly a multicores architecture environment and a convenient management for your environment. The DRBL-ONEMPI [[br]] |
| | 16 | gives user some useful installation process and assists system administrators to deploy their own private cluster environment. [[br]] |
| | 17 | We build a PC cluster environment, and runs in parallel using MPICH2 on our PC cluster with diskless nodes. We will introduce [[br]] |
| | 18 | the basic architecture of DRBL-ONEMPI and present some design. [[br]] |
| | 19 | |
| | 20 | Keywords―LAMMPS, molecular dynamics, MPICH2, DRBL-ONEMPI. [[br]] |
| | 21 | |
| | 22 | I.Introduction [[br]] |
| | 23 | |
| | 24 | LAMMPS is created by Sandia National La-boratories, a US Department of Energy laboratory. LAMMPS is classical molecular dynamics simula-tion software [[br]] |
| | 25 | , integrates Newton`s equation of mo-tion, is an open source code, and runs on single processors or parallel programming with using message-passing [[br]] |
| | 26 | interface. The LAMMPS source is widely applied in the semiconductors, biomolecular, polymers, coarse-grained and microscopic, etc. It has been used [[br]] |
| | 27 | to simulate in the chemistry and semiconductor research. The LAMMPS has lots of library to use, modify, or extended LAMMPS in your choose. [[br]] |
| | 28 | 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 [[br]] |
| | 29 | the administrator manage lots of computers, to deploy the system environmental and to configure the installation of the cluster. The DRBL-ONEMPI provides [[br]] |
| | 30 | 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 [[br]] |
| | 31 | monitor and easy to use it. [[br]] |
| | 32 | |
| | 33 | 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 com-bine DRBL with ONEMPI which rename DRBL-ONEMPI. In general, the pc cluster is diffi-cult 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. |
| | 34 | In section.2, we will introduce LAMMPS si-mulation software. In section.3, the DRBL and ONEMPI system are presented in detail. In sec-tion.4, the simulation and benchmark results are discussed. |
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