Workstations EMBO 2016

Accessing your account

EMBL provides a set of Windows laptops. As Dynamo does not run on Windows, we need to enter a virtual linux environment in the laptop.

Instructions will be provided by EMBL personal

Using Dynamo in Matlab

We encourage our users to run Dynamo inside the Matlab environment. This gives you an enormous flexibility when it comes to design operations that fall outside of the most basic pipelines.

Open Matlab

The version of Matlab that we need is R2014b (or, preferably, higher. The higher, the faster will the interfaces of Dynamo run). In a linux shell, type:

/g/teachinglab/sources/matlab/r2015a/bin/matlab &

after some time, the Matlab window should appear.

Activate Dynamo

Dynamo is already installed, but you need to activate it inside your matlab session. To do so, type inside the Matlab shell:

run /g/teachinglab/sources/dynamo/dynamo_activate.m

Using Dynamo as standalone

It is possible to use Dynamo as a standalone system, that can be used as an alternative to the Matlab-based Dynamo. In general, we prefer the use of Dynamo inside the Matlab environment for all the tasks that have an interactive component. For the computation of projects, everything can be done in the standalone.

Installing Dynamo

Each participant can have their own Dynamo installation. The installation procedure needs to be performed only once during the workshop.

Get the tarball (i.e., .tarfile) from this [google drive location]

We first create a location to install Dynamo, for instance:

mkdir /g/embo2016/cryo06/dynamo

and then untar (expand) the file onto the chosen location

tar -xf <NAME OF THE TAR> -C /g/embo2016/cryo06/dynamo

Activation

After installing the software, you'll need to activate it on each new shell in which you want to use it. Whenever you open a fresh shell, we need to ensure we have a fresh environment. This means, we need to overrule some default settings that are used by default in the course computers.

export PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/share/bin

unalias dynamo

Before starting Dynamo, there is another environment variable that we need to tune: MCR_CACHE_ROOT

export MCR_CACHE_ROOT=~/tmp/

Now, you can activate Dynamo in the linux shell by running:

source /g/embo2016/cryo06/dynamo/tmp/dynamo_activate_linux_shipped_MCR.sh

This includes in the linux shell the paths that it needs to find both Dynamo and its libraries.

Running Dynamo

Now, you can just type in the terminal:

dynamo

which should open a standalone console, that can be used to enter Dynamo commands manually.

For this workshop, we are using a special version of Dynamo, which will request you to type:

modeltrack.format('force',1);

after the Dynamo prompt Dynamo >>