Installation of lammps-5Nov14 on Mac OS X Yosemite

8 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 -license
Then 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-5Nov14
Obtain lammps-5Nov14 from http://lammps.sandia.gov/tars/?C=M;O=D
And extract the tar fle. At lammps-5Nov14/src
$ make -yes-all (all packages are added)
Installing package asphere
Installing package body
Installing package class2
Installing package colloid
Installing package dipole
Installing package fld
Installing package gpu

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package granular
package kim
package kokkos
package kspace
package GPU
package manybody
package GPU
package mc
package meam
package misc
package molecule
package GPU
package mpiio
package opt
package peri
package poems
package qeq
package reax
package replica
package rigid
package shock
package snap
package srd
package voronoi
package xtc
package user-atc
package user-awpmd
package user-cg-cmm
package GPU
src/pair_lj_sdk_coul_long_gpu.cpp
src/pair_lj_sdk_coul_long_gpu.h
src/pair_lj_sdk_gpu.cpp
src/pair_lj_sdk_gpu.h
package user-colvars
package user-cuda
package user-eff
package user-fep
package user-intel
package user-lb
package user-misc
package GPU
src/pair_lj_sf_dipole_sf_gpu.cpp
src/pair_lj_sf_dipole_sf_gpu.h
package user-molfile
package user-omp
package user-phonon
package user-qmmm
package user-reaxc
package user-sph

Deleting some packages not used

MacBookProMid2012-2:src chibaf$ make

Uninstalling package gpu
MacBookProMid2012-2:src chibaf$ make
Uninstalling package kim
MacBookProMid2012-2:src chibaf$ make
Uninstalling package poems
MacBookProMid2012-2:src chibaf$ make
Uninstalling package reax
MacBookProMid2012-2:src chibaf$ make
Uninstalling package voronoi
MacBookProMid2012-2:src chibaf$ make
Uninstalling package meam
MacBookProMid2012-2:src chibaf$ make
Uninstalling package user-awpmd
MacBookProMid2012-2:src chibaf$ make
Uninstalling package user-cuda
MacBookProMid2012-2:src chibaf$ make
Uninstalling package kokkos
MacBookProMid2012-2:src chibaf$ make
Uninstalling package user-qmmm
MacBookProMid2012-2:src chibaf$ make
Uninstalling package user-colvars
MacBookProMid2012-2:src chibaf$ make
Uninstalling package user-atc

no-gpu
no-kim
no-poems
no-reax
no-voronoi
no-meam
no-user-awpmd
no-user-cuda
no-kokkos
no-user-qmmm
no-user-colvars
no-user-atc

Modifying src/MAKE/Makefle.mpi. We show only modifed lines:

CCFLAGS =
-g -O3 -fopenmp
LIB =
r0.2.12

-lgfortran -lgomp -lopenblas_sandybridgep-

LMP_INC =

-DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64

FFT_INC =

-DFFT_FFTW3

FFT_LIB =

-lfftw3

Then at src,
$ make mpi
If 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.lammps
where 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