Installation of LAMMPS-14Feb14 - 2Apr14 on OS X 10.

9 chibaf 4 April 2014

LAMMPS Molecular Dynamics Simulator http://lammps.sandia.gov/ Copyright (2 !" Sandia Corporation.

LAMMPS is a so#t$are #or molecular (and particles" dynamics. %t can &e installed on Mac 'S ( $ith several steps. 'n multi)core Mac* lammps is installed $ith ##t$ !.+ and 'penMP%. ,his document corresponds to lammps)-./e&-.* 20/e&-.* .Mar-.* 0Mar-.* - Mar-. and -.Mar-.* 2 Mar-.* !-Mar-. and 2Apr-.. old versions are o&tained #rom &elo$: http://lammps.sandia.gov/tars/ 1emar2: the pac2age atc $as not employed #or lammps)20/e&-.* .Mar-.* 0Mar-.* - Mar-.* -.Mar-.* !-Mar-. and 2Apr-. &ecause o# lin2age errors. 1emar2: the pac2ages atc gpu $as not employed #or lammps)2 Mar-.. 1emar2: the pac2age omp* cuda* mol#ile and atc $as not employed #or lammps)-./e&-. &ecause o# lin2age errors or compile errors. 1emar2: the pac2age user)mol#ile $as added on lammps)-.3un-2. 4ut this document doesn5t descri&e installation o# the pac2age. 1emar2: &uilt $ithout C6DA pac2age. 1emar2: 'S ( - .0 or later is necessary #or 7P6/'penCL pac2age. See 1ecent LAMMPS 8e$s #or recent lammps updates. (-" 'S ( - .9.+ (mountain lion" is employed $ith Mac&oo2 Pro -!5 mid 2 -2 Core i: 2.:7;<. (2" i# you employ +code :. 2 or later* you need to install command line tools #or it. = +code)select ))install (!" do$nloading gcc)..>)&in.tar.g< #rom http://hpc.s#.net : ..>)&in.tar.g< #or os + - .9.+ instruction: (A" = gun<ip gcc)..>)&in.tar.g< (4" = sudo tar )+# gcc)..>)&in.tar )C / gcc)

(." installation o# 'penMP% -.0.: do$nloading 'penMP% #rom http://$$$.open)mpi.org/so#t$are/ompi/v-.0/ e+tracting tar #ile (dou&le clic2ing tar.g< #ile" and: = ./con#igure = ma2e all = ma2e chec2 = sudo ma2e install ? $hen it passes all chec2s. (:" installation o# //,@ $e employ //,@ version !.!.! http://$$$.##t$.org/do$nload.html e+tracting tar #ile (dou&le clic2ing tar.g< #ile" and:

= ./con#igure i# your cpu supports av+* = ./con#igure )Aena&le)av+ = ma2e all = ma2e chec2 = sudo ma2e install (0" installing 'penB%M ('pen Bno$ledge &ase %nteratomic Model" --- Option: if you don't employ OpenKIM, skip this step. do$nload B%M AP% #rom https://open2im.org/2imCapi?do$nload ?@e employed version -.!.- or later. D+tract the #ile at your home directory and 'n ,erminal = cp Ma2e#ile.B%MCCon#ig.e+ample Ma2e#ile.B%MCCon#ig modi#yng EMa2e#ile.B%MCCon#igF as #ollo$s:
!elease" #his file is part of the open$i%-api-&1.2.1 pac$a'e. this %a$e file b(il)s*cleans e&er+thin' ,IM-.I! / ,IM-.I!/=;'MD/open$i%-api-&1.0.1 ,IM-MO.2L-.!I32!S-.I! / ,IM-MO.2LS-.I! / ,IM-#2S#S-.I! / ,IM-4OMPIL2!S5I#2 / 644 ,IM-S7S#2MLI8,2! / )ar9in ,IM-S7S#2MA!4: / ;4bit ,IM-LI8, / )+na%ic-loa)

e1a%ple

'n ,erminal = e+port B%MCD%1GFthe path to open2imF ? ending $ith E/F ? e+ample: =;'MD/open$i%-api-&1.0.1 = cd =B%MCD%M = ma2e e+amples = ma2e = sudo ma2e install ? /usr/local/li&/open2im)v-.!.(H" installing IoroJJ (a so#t$are li&rary #or carrying out three) dimensional computations o# the Ioronoi tessellation" --- Option: if you don't employ Voro++, skip this step. do$nload IooroJJ #rom http://math.l&l.gov/voroJJ/do$nload/. ?@e employed Iersion ...0 or later. D+tract the #ile and on ,erminal moving to the directory: voroJJ) ...0/ = ma2e = sudo ma2e install ? #iles $ill &e installed under /usr/local/. (>" Do$nloading Lammps the latest version is o&tained #rom &elo$: http://lammps.sandia.gov/do$nload.html?tar old versions are o&tained #rom &elo$: http://lammps.sandia.gov/tars/ (9" &uilding LAMMPS !e%ar$" in Ma$efile< tab is (se) for spacin'. (A" &uild li&raries: a$pmd* atc* meam* poem* rea+* gpu* colvars.

at a9p%)" = ma2e )# Ma2e#ile.openmpi at atc" = ma2e )# Ma2e#ile.gJJ at %ea%" = ma2e )# Ma2e#ile.g#ortran at poe%s" = ma2e )# Ma2e#ile.gJJ at rea1" = ma2e )# Ma2e#ile.g#ortran at 'p( for Open4L = ma2e )# Ma2e#ile.macCopencl at col&ars = ma2e )# Ma2e#ile.gJJ (4" at src*,IM modi#ication o# Ma2e#ile.lammps
#his file contains the hoo$s to b(il) an) lin$ LAMMPS 9ith the Open,IM librar+ so that a LAMMPS inp(t script can (se a ,IM potential< &ia the pair-st+le $i% co%%an). 7o( sho(l) first )o9nloa) ,IM fro% 999.open$i%.or'. #hen b(il) its librar+ API in ,IM-API< 9ith the %o)els =potentials> +o( 9ant to (se. 7o( sho(l) then ha&e the files" open$i%-api-&X.X.X*,IM-API*lib$i%.a open$i%-api-&X.X.X*,IM-API*lib$i%.so ?hen +o( b(il) LAMMPS 9ith the ,IM pac$a'e installe)< it 9ill (se the 0 settin's in this file. #he+ sho(l) be set as follo9s. $i%-S7SI84 / a path to the ,IM-API )irector+ that contains @.h files $i%-S7SLIA / co%piler fla' to (se the ,IM librar+ $i%-S7SPA#: / a path to the ,IM librar+ ----------------------------------------------------------Settin's that the LAMMPS b(il) 9ill i%port 9hen this pac$a'e is installe) $i%-S7SI84 / -I*(sr*local*lib*open$i%-api-&1.0.1*,IM-API $i%-S7SLIA / -l$i% $i%-S7SPA#: / -L*(sr*local*lib*open$i%-api-&1.0.1*,IM-API

(C" at src*MA,2: modi#ication o# Ma2e#ile.openmpi:

--------------------------------------------------------------------co%piler*lin$er settin's specif+ fla's an) libraries nee)e) for +o(r co%piler 44 / 44FLA6S / S:FLA6S / .2PFLA6S / %picBB -O2 C -f(nroll-loops -fstrict-aliasin' -?all -? -?no-(ninitialiDe) C -fopen%p enable OpenMP -fPI4 -M %picBB

LI8, / LI8,FLA6S / -O

LIA / -lst)cBB -l'fortran -l'o%p -fra%e9or$ &ecLib apple lapac$ SIE2 / siDe A!4:I32 / ar A!FLA6S / -rcs& S:LIAFLA6S / -share)

'fortran< OpenMP<

--------------------------------------------------------------------LAMMPS-specific settin's specif+ settin's for LAMMPS feat(res +o( 9ill (se if +o( chan'e an+ -. settin'< )o f(ll re-co%pile after F%a$e cleanF LAMMPS if)ef settin's< OP#IO8AL see possible settin's in )oc*Section-start.ht%l 2-2 =step 4> LMP-I84 / -.LAMMPS-6EIP

MPI librar+< !2G5I!2. see )isc(ssion in )oc*Section-start.ht%l 2-2 =step H> can point to )(%%+ MPI librar+ in src*S#5AS as in Ma$efile.serial I84 / path for %pi.h< MPI co%piler settin's PA#: / path for MPI librar+ LIA / na%e of MPI librar+ MPI-I84 / MPI-PA#: / MPI-LIA / FF# librar+< OP#IO8AL see )isc(ssion in )oc*Section-start.ht%l 2-2 =step ;> can be left blan$ to (se pro&i)e) ,ISS FF# librar+ I84 / -.FF# settin'< e.'. -.FF#-FF#?< FF# co%piler settin's PA#: / path for FF# librar+ LIA / na%e of FF# librar+ FF#-I84 / FF#-PA#: / FF#-LIA / -.FF#-FF#?0 -lfft90 e%plo+ fft9 0 e%plo+ fft9 0

(D" generating ma2e#ile at src directory miniImage:src chi af! make yes-all Installing package asphere Installing package ody Installing package class" Installing package colloid Installing package dipole Installing package fld Installing package gpu Installing package granular Installing package kim Installing package kspace updating package #$% Installing package many ody updating package #$% Installing package mc Installing package meam Installing package misc Installing package molecule updating package #$% Installing package mpiio Installing package opt Installing package peri Installing package poems Installing package rea&

Installing Installing Installing Installing Installing Installing Installing Installing Installing updating updating updating updating updating Installing Installing Installing Installing Installing updating updating updating Installing Installing Installing Installing Installing

package replica package rigid package shock package srd package 'oronoi package &tc package user-atc package user-a(pmd package user-cg-cmm package #$% src)pair*l+*sdk*coul*long*gpu.cpp src)pair*l+*sdk*coul*long*gpu.h src)pair*l+*sdk*gpu.cpp src)pair*l+*sdk*gpu.h package user-col'ars package user-cuda package user-eff package user-l package user-misc package #$% src)pair*l+*sf*dipole*sf*gpu.cpp src)pair*l+*sf*dipole*sf*gpu.h package user-omp package user-molfile package user-phonon package user-rea&c package user-sph

= ma2e no)user)cuda ?deleting C6DA pac2age %ninstalling package user-cuda = ma2e no)user)mol#ile ?deleting mol#ile pac2age %ninstalling package user-molfile ?deleting atc pac2age #or lammps)-./e&-. = ma2e no)user)atc %ninstalling package user-atc = ma2e no)user)omp %ninstalling package user-omp ?deleting atc pac2age #or lammps)20/e&-.* .Mar-.* 0Mar-.* - Mar-. and -.Mar-.* 2 Mar-.* !-Mar-. and 2Apr-.. = ma2e no)user)atc %ninstalling package user-atc ?deleting gpu pac2age #or lammps)2 Mar-.. = ma2e no)gpu %ninstalling package gpu %# you didn5t employ 'penB%M: = ma2e no)2im ?deleting 'penB%M pac2age %ninstalling package kim %# you didn5t employ IoroJJ: = ma2e no)voronoi ?deleting IoroJJ pac2age %ninstalling package 'oronoi (D"at src

&uild e+ecuta&le &inary: lmpCopenmpi = ma2e openmpi (/" setting up e+ample suppose that a directory K/&in e+ists. = cp lmpCopenmpi K/&in/ = e+port PA,;G=PA,;:K/&in ? use it in .&ashCpro#ile (- " e+ecution o# Lammps as multi)process co%%an) for %(lti process" = mpirun )np 8 lmpCopenmpi L in.lammps.script ?8 is a num&er o# MP% process ?see Lammps manual #or details. co%%an) for %(lti threa)s 9ith OpenMP"
= mpirun )+ 'MPC86MC,;1DADSGM )np 8 lmpCopenmpi )s# omp )in in.lammps ? 8 mpi process and M openmp threads per one mpi process
Mac4oo22 9:K chi&a#= ps 6SD1 P%D ,, MCP6 chi&a# 2:!! s . chi&a# 2:!.. s . chi&a# 2:!.: s .:.H 2:!.: ->.chi&a# 2:!.0 s :H.! 2:!.0 2 .chi&a# 2:!: s ! . )M S,A, S S 1 S 1 S S P1% !-, !-, H, 2!, ., 22, !-, S,%MD : . : . : !.29 : . : : 2.-: . 0 : . 6,%MD : . : . :-..00 : >..2 :-0. : 9.:: . C'MMA8D )&ash mpirun )+ 'MPC86MC,;1DADSG2 )np 2 lmpCopenmpi lmpCopenmpi )s# omp )in in.lammps lmpCopenmpi )s# omp )in in.lammps )&ash

lammps)2Apr-. running as #our mpi processes on Mac&oo2 Pro -!5 mid 2 -2 Core i: 2.:7;< via (Planet airing"Npi+ivO (in Papanese"

Appen)i1 lammps mailing list: Source/orge.net: LAMMPS: lammps)users My $e& site: http://math.digi2.Pp/ http://math.digi2.Pp/math/lammps/ : lammps Scri&d ) chi&a# http://$$$.scri&d.com/chi&a# mail: t$itter: Qchi&a#