Computers Basel 2017

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

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 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/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  /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.

Connecting

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

ssh -Y stud01@ela.cscs.ch

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. tar your project in Dynamo (in Dynamo wizard >> Tools >> Create a tarball
2. rsync -avr my_project.tar stud##@ela.cscs.ch:~/
3. Also rsync your data to CSCS
4. Untar your Dynamo project

You will need the Dynamo terminal for this:

dynamo &

dvuntar myProject

On CSCS,

1. type
   salloc --gres=gpu:1
   to get a node with a gpu. It can take some time till the system allocates you a node. You can allocate up to two nodes.
   you can check the GPU on your node by:
   srun nvidia-smi
2. type
   source ~/bin/dynamoFlorida/dynamo_activate_linux_shipped_MCR.sh
   to activate Dynamo in your shell.
3. open Dynamo with dynamo &
4. open your project, and re-unfold it (make sure standalone GPU is selected and make sure your data is in the same relative location as on the local machine)

   Note

   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

5. run your alignment by typing srun my_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.

• open a Dynamo console by typing:

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.

Strubi Oxforfd

We are also using some accounts from the GPU cluster in the Structural Biology department in the University of Oxford.