Computers Basel 2017

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WLAN connection

The credentials are:

User     :  eventbzpz
Password : DynamoWS17!


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:


Installing Dynamo

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


It should take around a minute.

Opening Matlab

We will be using the Matlab release R2017a. To open it, type in the shell:

/usr/local/matlab/R2017a/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/

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  /clab-share/activateChimera.m

CSCS: Lugano

CSCS Lugano is the Nacional Supercomputing Center of Switzerland. Each account should be able to submit jobs to a single node connected to a K20 GPU and four cores.


First you need to connect to the gate node ela using your cscs credentials from the credentials handout.

ssh -Y

and then you can connect to the computing machine called daint, again you will be requested to type in your credentials.

stud01@ela2:~> ssh -Y daint

Using Dynamo

We are using a slightly older version of Dynamo on the supercomputer GPUs for compatibility reasons

On the local machine
  1. Create alignment project >> computational parameters >> system_gpu
  2. Dynamo Wizard >> Tools >> Create tarball
    alternatively you can use the command line
    dvtar myProject
  3. scp <project.tar>
  4. ssh -Y >> mkdir data/
  5. scp <your data folder>
  1. source /users/course42/bin/dynamoFlorida/
  2. dynamo x
  3. Untar your Dynamo project
  4. dvuntar <project.tar>
  5. dcp <project>
  6. Check >> Unfold
    if the graphical interface is too slow, you can use the command line instead:
    open a Dynamo console in your shell with dynamo x
    dvput my_project -destination system_gpu
    dvunfold my_project
  7. Make sure everything is correctly located.
    dvcheck myProject
  8. (on ela):
    ssh -Y daint
  9. source /users/course42/bin/dynamoFlorida/
  10. salloc -C gpu
  11. srun <project.exe>

Dynamo as standalone

We can use the system terminal as an equivalent of the Matlab terminal using the Dynamo standalone. This is an example on how to use it to create a phantom project like the one we did yesterday.

dynamo x

in a linux shell (you'll need to source Dynamo activation script on that shell beforehand).

  • create a tutorial project. For this, type inside the Dynamo console:
dtutorial myTest -p ptest -M 128
  • tune the project to work in a GPU
dvput ptest -destination system_gpu
  • unfold the project
dvunfold ptest.exe inside the Dynamo console
  • run the project with srun
srun ptest.exe in a terminal shell, i.e., not inside the Dynamo console
  • when it finishes, the averages can be also accessed programmatically with the database tool. For instance, to access the last computed average and view it with dview, type:
ddb ptest:a -v

Note about performance You will notice that the project stops at several points during execution. Those are the points where the project accesses the MCR libraries. This overhead is a constant, and is a very small fraction of the computing time for a real project with thousands of particles.

We are using an old Dynamo version. Modern Dynamo versions don't access the MCR library several times.