Installation of LAMMPS-25Jan13 - 9Mar13 on OS X 10.

8 (Mountain Lion) chibaf 5 March 2013
LAMMPS Molecular Dynamics Simulator http://lammps.sandia.gov/ Copyright (2003) Sandia Corporation.

LAMMPS is a software for molecular (and particles) dynamics. It can be installed on Mac OS X with several steps. On multi-core Mac, lammps is installed with fftw 3.x and OpenMPI. This document corresponds to lammps-25Jan13, 26Jan13, 27Jan13, 1Feb13, 3Feb13 and 18Feb13, 20Feb13, 21Feb13, 22Feb13, 5Mar13 and 9Mar13. Remark: a package voronoi was added on lammps-25Jun13. Remark: LAMMPS-19Jan13 – 24Jan13 got a compile error of msm_omp.cpp with gcc (i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)). then we employed gcc-4.8 from http://hpc.sf.net/. Remark: a package user-molfile was added on lammps-14Jun12. But this document doesn't describe installation of the package. Remark: a package USER-COLVARS was added on lammps-27May12. Remark: built without CUDA package. Remark: OS X 10.6 or later is necessary for GPU/OpenCL package. See Recent LAMMPS News for recent lammps updates. (1) OS X 10.8.x (mountain lion) is employed with MacBook Core2Duo (late 2009). (2) if you employ xcode 4.4 or later, you need to install command line tools for it. (3) downloading gcc-mlion.tar.gz from http://hpc.sf.net :

gcc-

mlion.tar.gz (4.8 / updated 2013) for os x 10.8.x
instruction: (A) $ gunzip gcc-mlion.tar.gz (B) $ sudo tar -xf gcc-mlion.tar -C / (4) downloading gfortran from http://hpc.sf.net :

gfortran-

mlion.tar.gz for os x 10.8.x
instruction: (A) $ gunzip gfortran-mlion.tar.gz (B) $ sudo tar -xf gfortrn-mlion.tar -C / (5) you can also obtain gfortran from: Tools - R for Mac OS X developer's page - GNU Fortan for Xcode (6) installation of OpenMPI 1.6.x downloading OpenMPI from http://www.open-mpi.org/software/ompi/v1.6/ extracting tar file (double clicking tar.gz file) and: $ ./configure $ make all $ make check $ sudo make install #if it passes all check.

gz file) and: $ . atc.h" #include "SparseMatrix. poem.cpp: #include "DenseMatrix.openmpi at atc: modification of Matrix. Extract the file and On Terminal $ export KIM_DIR=”the path to openkim” # ending with “/” # example: KIM_DIR = /Users/foo/openkim-api-v1.sandia.gov/download. Extract the file and on Terminal moving to the directory: voro++-0.h" // added on 28 september 2011 #include "DiagonalMatrix.h" // added on 28 september 2011 modification of Makefile.1./configure $ make all $ make check $ sudo make install (8) installing OpenKIM (Open Knowledge base Interatomic Model) download KIM API from https://openkim.4. #We employed Version 0.1/ $ cd $KIM_DIM $ make examples $ make (9) installing Voro++ (a software library for carrying out threedimensional computations of the Voronoi tessellation) download Vooro++ from http://math.lammps: user-awpmd_SYSINC = user-awpmd_SYSLIB = -framework vecLib # use apple lapack and blas user-awpmd_SYSPATH = $ make -f Makefile.sandia.gov/tars/ (11) building LAMMPS Remark: in Makefile. meam.gov/voro++/download/.5/ $ make $ sudo make install # files will be installed under /usr/local/.lammps: user-awpmd_SYSINC = user-awpmd_SYSLIB = -framework vecLib # use apple lapack and blas user-awpmd_SYSPATH = $ make -f Makefile.x # 29 February 2012 http://www.4. reax. at awpmd: modification of Makefile.fftw.1 or later.(7) installation of FFTW we employ FFTW version 3.html extracting tar file (double clicking tar.org/download. gpu.html#tar old versions are obtained from below: http://lammps. tab is used for spacing. colvars.org/kim_api#download #We employed version 1.5 or later.1. (10) Downloading Lammps the latest version is obtained from below: http://lammps.h" #include "Solver.lbl.g++ . (A) build libraries: awpmd.

.g++ # for gfortran # use apple opencl framework (B) at src/MAKE: modification of Makefile.. -DFFT_FFTW.. OPTIONAL # see discussion in doc/Section_start.. e.. FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW3 # use fftw 3...lammps: meam_SYSINC = meam_SYSLIB = -lgfortran meam_SYSPATH = $ make -f Makefile.openmpi CC = mpic++ CCFLAGS = -O2 \ -funroll-loops -fstrict-aliasing -Wall -W -Wnouninitialized -fopenmp # use openmp DEPFLAGS = -M LINK = mpic++ LINKFLAGS = -O -lgfortran -framework vecLib -lgomp # for gfortran and openmp.g.x (C) generating makefile at src directory $ make yes-all Installing package asphere Installing package class2 Installing package colloid Installing package dipole Installing package fld Installing package gpu Installing package granular Installing package kim Installing package kspace Installing package manybody . .gfortran at poems: $ make -f Makefile.html#2_2 (step 6) # can be left blank to use provided KISS FFT library # INC = -DFFT setting.gfortran at gpu (OpenCL) modification of Makefile. use apple framework for lapack and blas .mac_opencl at colvars $ make -f Makefile....x FFT_PATH = FFT_LIB = -lfftw3 # use fftw 3.lammps: gpu_SYSINC = gpu_SYSLIB = -framework OpenCL gpu_SYSPATH = $ make -f Makefile. # FFT library.g++ at reax: $ make -f Makefile...at meam: modification of Makefile.

lammps -bash .00 0:09.01 0:14.01 UTIME 0:00.bash_profile (12) execution of Lammps as multi-process command for multi process: $ mpirun -np N lmp_openmpi < in.3 25346 20.42 0:16.lammps.11 0:00.05 0:02.1 chibaf 25346 s000 57.00 COMMAND -bash mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_openmpi lmp_openmpi -sf omp -in in.51 0:00.7 25345 18.0 -M STAT S S R S R S S PRI 31T 31T 7T 23T 4T 22T 31T STIME 0:00.29 0:00.1 chibaf 25350 s003 0. $ cp lmp_openmpi ~/bin/ $ export PATH=$PATH:~/bin # use it in .Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing Installing package package package package package package package package package package package package package package package package package package package package package package package package mc meam molecule opt peri poems reax replica rigid shock srd voronoi # voro++ employed xtc user-misc user-atc user-awpmd user-cg-cmm user-colvars user-cuda user-eff user-omp user-molfile user-reaxc user-sph $ make no-user-cuda #deleting CUDA package Uninstalling package user-cuda $ make no-user-molfile #deleting molfile package Uninstalling package user-molfile (D)at src build executable binary: lmp_openmpi $ export KIM_DIR = ”the path to openkim directory” # example: KIM_DIR = /Users/foo/openkim-api-v1.script #N is a number of MPI process #see Lammps manual for details.1 $ make openmpi (E) setting up example suppose that a directory ~/bin exists.0 chibaf 25344 s000 0.01 0:00.01 0:00.01 0:03. command for multi threads with OpenMP: $ mpirun -x OMP_NUM_THREADS=M -np N lmp_openmpi -sf omp -in in.lammps # N mpi process and M openmp threads per one mpi process MacBook2009:~ chibaf$ ps USER PID TT %CPU chibaf 25330 s000 0.1.lammps lmp_openmpi -sf omp -in in.06 0:00.0 chibaf 25345 s000 45.66 0:08.

digi2.lammps-9Mar13 running as two openmp threads x two mpi process on macbook (core2duo) via "a big tree of black honey and a spring of hot water" / illustration by poko [pixiv] (in japanese) lammps mailing list: SourceForge.net: LAMMPS: lammps-users My web site: http://math.scribd.digi2.com/chibaf mail: .chibaf http://www.jp/ http://math.jp/math/lammps/ : lammps Scribd .