Installation of lammps-5Nov14 on Mac OS X Yosemite8 November 2014

In this document, lammps standard packages are emplyoed.

(0) We employ Macbook Pro 13 inch mid 2012.(1) OS X Yosemite is employed.(2) You need knowledge of UNIX.(3) Xcode.app is needed. It can be obtained from http://develope.apple.com/(4) After installation of Xcode.app, tat Termila.app:$ xcode-select -instasll$ sudo xcodebuild -licenseThen gnu tools are enable.(5) On GCC of Apple, OpenMP is not available. Then GCC 4.9.0 is obtained fron http://hpc.sf.net/ gcc-4.9-bin.tar.gz, updated Oct 2014 (Mavericks & Yosemite)$ sudo tar -zxvf gcc-4.9-bin.tar.gz -C /(6) Installation of OpenMPI:Obtain source codes of OpenMPI from http://www.open-mpi.org, and extract $ ./configure$ make$ make check$ sudo make install (if make check said no error)(7) Installation of FFTW:Obtain source codes of FFTW from http://www.fftw.org, and extract $ ./configure$ make$ make check$ sudo make install (if make check said no error)(8) Installation of OpenBLAS:$ git clone https://github.com/xianyi/OpenBLAS.git$ cd OpenBLAS$ make BINARY=64 USE_OPENMP=0$ sudo make PREFIX=/usr/local install Then /usr/local/lib/libopenblas_sandybridgep-r0.2.12.a was generated.A name of library depend on a CPU of your machine.(reference: http://dedupe.readthedocs.org/en/latest/OSX-Install-Notes.html)

Then necessary tools and libraries were installed.

(9) building of lammps-5Nov14Obtain lammps-5Nov14 from http://lammps.sandia.gov/tars/?C=M;O=DAnd extract the tar fle. At lammps-5Nov14/src$ make -yes-all (all packages are added)Installing package asphereInstalling package bodyInstalling package class2Installing package colloidInstalling package dipoleInstalling package fldInstalling package gpu

Installing package granularInstalling package kimInstalling package kokkosInstalling package kspace updating package GPUInstalling package manybody updating package GPUInstalling package mcInstalling package meamInstalling package miscInstalling package molecule updating package GPUInstalling package mpiioInstalling package optInstalling package periInstalling package poemsInstalling package qeqInstalling package reaxInstalling package replicaInstalling package rigidInstalling package shockInstalling package snapInstalling package srdInstalling package voronoiInstalling package xtcInstalling package user-atcInstalling package user-awpmdInstalling package user-cg-cmm updating package GPU updating src/pair_lj_sdk_coul_long_gpu.cpp updating src/pair_lj_sdk_coul_long_gpu.h updating src/pair_lj_sdk_gpu.cpp updating src/pair_lj_sdk_gpu.hInstalling package user-colvarsInstalling package user-cudaInstalling package user-effInstalling package user-fepInstalling package user-intelInstalling package user-lbInstalling package user-misc updating package GPU updating src/pair_lj_sf_dipole_sf_gpu.cpp updating src/pair_lj_sf_dipole_sf_gpu.hInstalling package user-molfileInstalling package user-ompInstalling package user-phononInstalling package user-qmmmInstalling package user-reaxcInstalling package user-sph

Deleting some packages not used

MacBookProMid2012-2:src chibaf$ make no-gpuUninstalling package gpuMacBookProMid2012-2:src chibaf$ make no-kimUninstalling package kimMacBookProMid2012-2:src chibaf$ make no-poemsUninstalling package poemsMacBookProMid2012-2:src chibaf$ make no-reaxUninstalling package reaxMacBookProMid2012-2:src chibaf$ make no-voronoiUninstalling package voronoiMacBookProMid2012-2:src chibaf$ make no-meamUninstalling package meamMacBookProMid2012-2:src chibaf$ make no-user-awpmdUninstalling package user-awpmdMacBookProMid2012-2:src chibaf$ make no-user-cudaUninstalling package user-cudaMacBookProMid2012-2:src chibaf$ make no-kokkosUninstalling package kokkosMacBookProMid2012-2:src chibaf$ make no-user-qmmmUninstalling package user-qmmmMacBookProMid2012-2:src chibaf$ make no-user-colvarsUninstalling package user-colvarsMacBookProMid2012-2:src chibaf$ make no-user-atcUninstalling package user-atc

Modifying src/MAKE/Makefle.mpi. We show only modifed lines:CCFLAGS = -g -O3 -fopenmp

LIB = -lgfortran -lgomp -lopenblas_sandybridgep-r0.2.12

LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64

FFT_INC = -DFFT_FFTW3

FFT_LIB = -lfftw3

Then at src, $ make mpiIf build becomes successful, lmp_mpi is generated at src.

(10) Execution of lammps(A) mpirun -np N lmp_mpi < in.lammps(B) mpirun -x OMP_NUM_THREADS=M -np N lmp_mpi -sf omp -in in.lammpswhere N is number of mpi process, M number of OpenMP, and in.lammps is lammps input.

Description of lammps input is found in lammps manual.Example of lammps inputs are also found in http://math.digi2.jp/math/lammps/or internet.

Lammps-5Nov14 on Macbook Pro 13inch mid 2012