Since the apps require a linux environment, docker does not run natively in Mac and PC. Rather, it sets up a linux virtual machine and runs docker engine inside that. Before version 1.12, docker on Mac required installation of virtualbox and docker-machine to manage this linux virtual machine inside which the containers are run. However, latest version of docker for mac uses hypervisor to run operating system as a service and thus has more native feel. Lets install it using Homebrew:

brew cask install docker

Run the app from the launcher and it will go through the initial setup process. We can now interact with the docker daemon through the shell.

Next, we will pull a debian image and install gimp and inkscape in it. Open a terminal and create a Dockerfile inside a folder called apps.

FROM debian:jessie
RUN apt-get update
RUN DEBIAN_FRONTEND=noninteractive \
  apt-get install -y -q gimp inkscape \
  ttf-dejavu --no-install-recommends
RUN rm -rf /var/lib/apt/lists/*
CMD "gimp"

Next, build the docker image called apps:

docker build -t apps .

docker commands

To run graphics inside docker containers, we will need X11 running on Mac. At the time of this writing the stable version of XQuartz (2.7.9) has a bug which prevents graphics forwarding. However, 2.7.10_beta2 works.

brew cask install xquartz-beta

The stable version of xquartz may work if it is higher than 2.7.10. Check the version in home-brew by: brew cask info quartz.

Start XQuartz and allow connections from network clients in preferences > security. Now the following commands should get gimp running:

ip=$(ifconfig | grep "inet " | grep -v 127.0.0.1 | awk '{print $2}')
xhost + $ip
docker run --rm -it -e DISPLAY=$ip:0 -v $HOME/Downloads:/root/Downloads apps

This will also share the ~/Downloads folder with the container. To run inkscape:

docker run --rm -it -e DISPLAY=$ip:0 -v $HOME/Downloads:/root/Downloads apps inkscape

Any changes made to gimp itself will be lost when the app is closed. Any additional plugins or customizations should be included in the Dockerfile to make them permanent.

The Unity desktop in Ubuntu is very slow over VNC for some reason. So, the first step is to switch to Xfce or xubuntu desktop. Also installed x11vnc while at it.

sudo apt-get install xubuntu-desktop x11vnc

For security, it better not to run VNC server all the time, but rather start it when needed. This can be accomplished by the following command at the terminal from the home computer (Macbook):

ssh -t -L 5900:localhost:5900 remote-host 'x11vnc -localhost -display :0

Where remote-host is the work PC. The above command starts x11vnc in the work PC and forwards the port to the home machine. One can now connect to it by typing in another terminal,

open vnc://localhost

It is advisable to create a VNC password for the server in the remote-host for added security. Refer to x11vnc web or man page for instructions. The above command will stop the server once the client exists, or -forever can be used to keep it alive. Then it will need to be stopped by CTRL-c.

Unfortunately, this method works only if the remote-host is logged in. When at the lock-screen in Ubuntu, the virtual terminal runs at display :1 (rather than at :0), so the x11vnc will have to be started with arguments -auth /var/run/lightdm/root/:1. But after unlocking the session, the VT falls back to :0, so x11vnc needs to be restarted with default VT. To work around this problem, I wrote the following script:

#!/bin/bash
vncpa=$HOME/.vnc/passwd
vtpath=/var/run/lightdm/root
vtuser=:0
vtlock=:1
while [ -e "$vtpath/$vtlock" ]; do
   echo "screen locked"
   x11vnc -localhost -rfbauth $vncpa -display $vtlock -auth $vtpath/$vtlock
   sleep 2
done
echo "screen unlocked"
x11vnc -localhost -rfbauth $vncpa -nevershared -forever -display $vtuser -auth $vtpath/$vtuser

Saved it as ~/bin/x11run and made it executable. Note that, access to the folder /var/run/lighdtm requires root privileges, so this script has to be run with sudo. So, to establish the tunnel, start the server and client in a single script, I use the ever-useful expect with ssh.

#!/bin/bash
echo -n "ID: "; read paD
sleep 5 && open vnc://localhost &
/usr/bin/expect << EOF
set timeout 120
spawn ssh -L 5900:localhost:5900 remote-host

expect "remote-host:~$ "
send "sudo ~/bin/x11run\r"

expect "*for user: "
send "$paD\r"

expect eof
interact
EOF

With appropriate modifications to those marked in red, it should work!

Host machineA
  Compression yes
  HostName machineA.company.org
  User UserNameA

Host machineB
  ProxyCommand ssh machineA -W %h:%p
  User UserNameB

Here, machineA is the firewall and machineB is the server behind it. Usernames can be specified if they are different from that of the local machine. Now, typing ssh machineB will tunnel the connection through machineA automatically. However, some servers may not allow tunneling.

Multiple SSH

One of the servers at work uses a secureID token for login, so password-less login with ssh-key is not an option. Opening multiple connections to this server was tedious, till I realized that SSH has a cool option to make all subsequent connections tunnel through the first connection to that server. With this enabled in ~/.ssh/config, only the first connection requires login/password:

ControlMaster auto
ControlPath ~/.ssh/control:%h:%p:%r

Below are the instruction to compile VASP version 5.3.5 with gfortran. First step is to build the vasp.5.lib. Copy the linux_gfortran makefile:

cp makefile.linux_gfortran makefile

We are going to use gfortran, so make sure it is installed. There are several package management systems for OS X; I personally like Homebrew. One point that took me a while to realize was that OS X by default has a case insensitive file system, so preclib.F and preclib.f are the same file. VASP preprocesses the .F files and creates .f files, basically overwriting the original ones. We will need to fix that. Make the following changes to the makefile:

CPP = gcc -E -P -x c $*.F >$*.f90
FFLAGS = -O1 -cpp

and compile by typing: make and ignore any warnings. It should build the library libdmy.a. Now change over to the main folder vasp.5.3 and copy over makefile.linux_gfortran and make the following changes to the file.

FC=gfortran
CPP_ = ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional -w >$*$(SUFFIX)
FFLAGS = -ffree-form -ffree-line-length-0
BLAS= -framework vecLib

Save the file and type make. Unfortunately, the code is not fully compatible with gfortran, so we will need to make several fixes. One of them is a space between a function call and (. Run the following command to fix files with errors.

for file in dfast.F choleski2.F dos.F broyden.F fock.F force.F rot.F main.F; do
  sed -i.bak s/CALLMPI\ \(/CALLMPI\(/g $file; rm $file.bak 
done
sed -i.bak s/CALLMPI_C\ \(/CALLMPI_C\(/g main.F; rm main.F.bak

Replace the USE us lines in us.F so that it looks like

1462 USE constant
1463 USE us, only : setdij_
1464 IMPLICIT NONE
2695 USE wave
2696 USE us, only : augmentation_charge
2697
2698 IMPLICIT NONE

Now, running make should hopefully compile it.

Most publishers have a “download citation” button on the article pages, but not all of them export in bib format. Looking for an alternative, I learned that Crossref now has a nice feature with which one can get the bibliography entry from the DOI. More info here. Use the following code at the commandline (needs curl installed)

curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/10.1103/PhysRevLett.112.086802

which returns:

@article{Shanavas_Satpathy_2014, 
title={Electric Field Tuning of the Rashba Effect in the Polar Perovskite Structures},
volume={112}, ISSN={1079-7114}, 
url={http://dx.doi.org/10.1103/PhysRevLett.112.086802}, DOI={10.1103/physrevlett.112.086802}, 
number={8}, 
journal={Physical Review Letters}, 
publisher={American Physical Society (APS)}, author={Shanavas, K. V. and Satpathy, S.}, 
year={2014}, 
month={Feb}}

I wrote a function which can be put in the .bashrc file. It will seperate the entry into multiple lines for readability

doi2bib() { curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/"$@" | awk '{sub(",",",\n"); gsub("},","},\n"); print $0}'; }

To use it, simply run doi2bib 10.1103/PhysRevLett.112.086802 from the command line.

At this stage there are three problems with this method:

1. The journal abbreviations are not always used
2. The author list is truncated if it is too long
3. For many APS articles page numbers are not returned