Docker allows you to mount components from the host file system into a container at the time the containter is created and run (N.B. not, at the moment, after it has been created and run). We can use this facility to very painlessly access the host installation of Matlab from within a container. Let's look at a command for starting a gadgetron container to illustrate.
NV_GPU=0 nvidia-docker run --name=gt1 --publish=9002:9002 --publish=8090:8090 --publish=8002:8002 -v /:/mnt -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --rm -it gadgetron/ubuntu_1404_cuda75
Everything is the same as normal for exposing the host cuda card and the gadgetron ports (see gadgetron wiki docker page) except for the
-v /:/mnt -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY
options
This first -v /:/mnt option mounts the entire host file system to appear in the docker running image at at the /mnt mount point (which I think needs to exist in the client file system - or maybe will be automatically added / merged as part of the Docker layered file system running layer??). So, as shown below, for this example, it seems that all the (CentOS) host file systems are exported into the (Ubuntu) container. Dangerously cool for experimentation but probably better to have more specific exports for a production system!
[root@centoshost ~]# df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/centos-root 52403200 46721572 5681628 90% /
devtmpfs 16312300 0 16312300 0% /dev
tmpfs 16335808 150440 16185368 1% /dev/shm
tmpfs 16335808 107900 16227908 1% /run
tmpfs 16335808 0 16335808 0% /sys/fs/cgroup
/dev/sdb1 2928834748 64240232 2864594516 3% /scratch
/dev/sda6 505580 341236 164344 68% /boot
/dev/sda2 364544 68416 296128 19% /boot/efi
/dev/mapper/centos-home 2779703180 16215332 2763487848 1% /localhome
tmpfs 3267164 16 3267148 1% /run/user/1234
tmpfs 3267164 0 3267164 0% /run/user/0
[root@peaches ~]# docker exec -it gt1 bash
root@a445ae98b0b7:/# df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/docker-253:1-68394805-e889429230e261d7c58845bbff1fe70d067cc4de85d46f3c53515ef29062faad 10474496 3603628 6870868 35% /
tmpfs 16335808 0 16335808 0% /dev
tmpfs 16335808 0 16335808 0% /sys/fs/cgroup
/dev/mapper/centos-root 52403200 46721452 5681748 90% /mnt
devtmpfs 16312300 0 16312300 0% /mnt/dev
tmpfs 16335808 150440 16185368 1% /mnt/dev/shm
tmpfs 16335808 0 16335808 0% /mnt/sys/fs/cgroup
tmpfs 16335808 107908 16227900 1% /mnt/run
tmpfs 3267164 16 3267148 1% /mnt/run/user/1234
tmpfs 3267164 0 3267164 0% /mnt/run/user/0
/dev/sdb1 2928834748 64240232 2864594516 3% /mnt/scratch
/dev/sda6 505580 341236 164344 68% /mnt/boot
/dev/sda2 364544 68416 296128 19% /mnt/boot/efi
/dev/mapper/centos-home 2779703180 16215332 2763487848 1% /mnt/localhome
shm 65536 0 65536 0% /dev/shm
So, in particular, my host Matlab installations appear in the client docker image at
root@a445ae98b0b7:/# ls -l /mnt/usr/local/MATLAB
total 8
drwxr-xr-x. 21 root root 4096 Nov 19 2015 R2015b
drwxr-xr-x. 22 root root 4096 Mar 15 12:21 R2016a
For some of our uses of Matlab with gadgetron we want to have access to the Matlab GUI or at least images, via X11. The installation and licence management is also simplified if X11 is available. There are several methods outlined in the following
http://wiki.ros.org/docker/Tutorials/GUI
but (for now...) I am using the quickest and dirtiest I could find
http://fabiorehm.com/blog/2014/09/11/running-gui-apps-with-docker/
-v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY
The gadgetron dockerhub image seemed also to need some x cruft installed. Getting an xterm to work seems to be enough.
apt-get update && apt-get install xterm
this does throw an error - which Google says may be to do with selinux on the host machine - although error persists when I setenforce 0??
dpkg: error processing archive /var/cache/apt/archives/libelf1_0.158-0ubuntu5.2_amd64.deb (--unpack): cannot get security labeling handle: No such file or directory
UPDATE: the this error does not occur, eg., on an Ubuntu 16.04 host.
So, then you can validate matlab against the gadgetron container HWAddr via the gui
/mnt/usr/local/MATLAB/R2016a/bin/matlab
and finally run the validated matlab (with the same command). Matlab will place a new licence_XXXXX.lic file in the host's /usr/local/MATLAB/R2016a/licenses direcory for the container's use of Matlab. I don't know, yet, what happens re licensing when the container is moved.
See also
https://github.com/RenderToolbox3/VirtualScenes/wiki/Matlab-on-Docker-and-EC2