Every few years, I give my laptop a fresh start and remove all the debris (applications, libraries, updates) that have built up. This time I started with a clean install of Mac OS 10.11 (El Capitan).
The first step is to install the essentials including Dropbox, Evernote, Todoist, Xcode (with
xcode-select --install), Slack, Mendeley, MS Office, gcc/gfortran, Python superpack, VESTA, Transmission, Mactex, Texmaker, Unrar, VLC, Adobe Creative Suite, iTerm, Textmate, XQuartz.
While it is possible to survive using gfortan and freely available maths libraries, Intel Fortran and MKL tend to be faster and better tested (easier to compile) in my experience. For non-commericial purposes Intel Composer is now free for OS X. The package installs in a few clicks, but be sure source the variables in your
source /opt/intel/mkl/bin/mklvars.sh intel64
source /opt/intel/bin/ifortvars.sh intel64
Finally you will need to make the MKL fast fourier transforms (FFTs) for use in most solid-state simulation packages:
sudo make libintel64 CC=gcc
Arons-Air-V:~ aron$ which ifort
Arons-Air-V:~ aron$ ifort --version
ifort (IFORT) 16.0.1 20151020
To enable parallelism, I downloaded the latest source code of openmpi (1.10.1).
./configure -prefix=/usr/local/openmpi-1.10.1 CC=gcc FC=ifort F77=ifort
sudo make install
be patient… it can easily take 20 minutes. Finally add to your
Arons-Air-V:~ aron$ which mpif90
Arons-Air-V:~ aron$ mpif90 --version
ifort (IFORT) 16.0.1 20151020
We use this open-source lattice-dynamics package a lot in our research. There are a few more libraries to install first:
sudo easy_install pip
pip2 install lxml
pip2 install pyyaml
then after expanding the source code, simply type:
python setup.py install
Arons-Air-V:~ aron$ phonopy
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
If harmonic phonons are not enough for you, then Phono3py lets you calculate phonon-phonon interactions, but it gets very computationally expensive. We need to install hdf5 (for more efficient data management):
pip2 install h5py
and lapacke for faster code. Download the latest version of lapack and:
cp make.inc.example make.inc
Then you are ready to compile. Download Phono3py and modify
setup3.py to link to your compiled lapacke library.
if platform.system() == 'Darwin':
include_dirs += ['/Users/aron/Documents/progs/lapack/lapack-3.6.1/lapacke/include']
extra_link_args = ['/Users/aron/Documents/progs/lapack/lapack-3.6.1/liblapacke.a']
python setup3.py install
Arons-Air-V:~ aron$ phono3py
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
While we use a range of electronic structure packages, VASP is the old reliable. I downloaded the latest version (5.4.1), which has streamlined the install process
cp ./arch/makefile.include.linux_intel ./makefile.include
which needs to be modified to point to the correct compilers (here gcc, ifort and mpifort). We will also remove
-DscaLAPACK from the precompiler options and set
SCALAPACK = . There are now three patches/bug fixes to install:
patch -p1 < patch.5.4.1.08072015
patch -p1 < patch.22.214.171.124082015
patch -p1 < patch.5.4.1.06112015
and one fix to sort out a gcc error. To the file
./src/lib/getshmem.c add one line at the end of the include statements
#define SHM_NORESERVE 010000
Arons-Air-V:test aron$ mpirun -np 4 ../vasp_std
running on 4 total cores
distrk: each k-point on 4 cores, 1 groups
distr: one band on 1 cores, 4 groups
using from now: INCAR
vasp.5.4.1 24Jun15 (build Jan 02 2016 21:20:37) complex
The atomistic simulation environment is a useful set of Python tools and modules. It now installs, including the gui, in two lines:
brew install pygtk
pip install python-ase
I will update with more codes and tools as I find time (posted in January; revised in July).
A slow running laptop was a good excuse to play around with a fresh install of OSX 10.8 (Mountain Lion). The implementation of Xcode has been changing over the last few versions, so here are the few straight forward steps required to get command-line Fortran running on your Mac.
1. Download Xcode from the App Store
– Run application to Install
– Xcode Preferences -> Downloads -> Command Line Tools
2. GNU Compilers
– Download 10.8 gcc and gfortran binaries and libraries from http://hpc.sourceforge.net.
– In terminal run “sudo tar -xvf gcc-mlion.tar -C /”
– Ensure the line “export PATH=/usr/local/bin:$PATH” is in your .bash_profile.
$ gfortran –version
GNU Fortran (GCC) 4.8.0 20120722 (experimental)
$ gcc –version
gcc (GCC) 4.8.0 20120722 (experimental)
3. Intel Compilers (Fortran Composer 2011)
– Install package.
– For install environment choose “Command line install only”.
– If write permission issues arise, run “sudo chmod u+rwx /Users/Shared/Library/Application\ Support/”.
– source /opt/intel/bin/ifortvars.sh intel64
– source /opt/intel/mkl/bin/intel64/mklvars_intel64.sh
– Run once as “sudo ifort” to overcome some permissions issues with the libraries.
$ ifort –version
ifort (IFORT) 12.1.0 20111011
Example Makefile (FHI-AIMS):
FC = ifort
FFLAGS = -O3 -ip
F90FLAGS = $(FFLAGS)
ARCHITECTURE = Generic
LAPACKBLAS = -L/opt/intel/mkl/lib \
-I/opt/intel/mkl/include -lmkl_intel_lp64 \