Computers Basel 2019

WLAN connection

The credentials are:

unibas-event
User :  dynamo-2019
Password : workshop@KLB50

Biozentrum

Use the credentials from your credential handout to log into the Linux workstations.

Opening a terminal

Auxiliary click on the Ubuntu screen and choose the Open terminal option.

Checking the Dynamo installation

Dynamo should be already installed in your local directory ~/dynamo. Check in with:

ls ~/dynamo

You should see something like this:

C
MCRforMac
MacOS
README_dynamo_installation.txt
cuda
ddemos
doc
dynamo_activate.m
dynamo_activate_linux.sh
dynamo_activate_linux_shipped_MCR.sh
dynamo_activate_mac.sh
dynamo_activate_mac.sh~
dynamo_activate_mac_shipped_MCR.sh
dynamo_activate_windows.bat
dynamo_compile_mpi.sh
dynamo_setup_cluster.sh
dynamo_setup_linux.sh
dynamo_setup_mac.sh
examples
licenses
matlab
mex
mpi

Installing Dynamo

If Dynamo is not installed: 'To install Dynamo locally, just open a Linux terminal (not a matlab terminal ) and write:

/clab-share/installDynamo.sh

It should take around a minute.

Opening Matlab

We will be using the Matlab release R2019a. To open it, type in the shell:

/usr/local/matlab/R2019a/bin/matlab &

Opening Dynamo in Matlab

After opening a Matlab session, you'll need to activate Dynamo in that session. Dynamo should be installed locally in ~/dynamo. In order to activate your local Dynamo version, please type in the Matlab shell:

run ~/dynamo/dynamo_activate.m

As a fallback, we have a centrally installed version in /clab-share/dynamo

Opening Dynamo as standalone

If you want to use Dynamo from a Linux terminal:

source ~/dynamo/dynamo_activate_linux_shipped_MCR.sh

To follow the workshop, we recommend to use the Matlab version.

Activate Chimera UCSF

If you want to use Chimera UCSF during a Dynamo session inside Matlab, you need to tell Dynamo where Chimera is:

run  ~/data/activateChimera.m