Computers Basel 2016

Biozentrum

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

Opening Matlab

We will be using the Matlab release R2015b. It should be visible on the desktop, otherwise use Spotlight (the magnifying glass on the top right corner) to locate it.

Installing Dynamo

A package can be found in /Users/gast/workshop2016/dynamo

Just unpack it with this command inside a system terminal:

tar -xf  /Users/gast/workshop2016/dynamo/dynamo_temp_1.1.182.tar -C /Users/gast/workshop2016/dynamo

Note that you need to use system terminal, not a Matlab desktop. Inside a Matlab terminal, the syntax is:

!tar -xf  /Users/gast/workshop2016/dynamo/dynamo_temp_1.1.182.tar -C /Users/gast/workshop2016/dynamo

Opening Dynamo

After opening a Matlab session, you'll need to activate Dynamo in that session. Dynamo should be installed in /Users/gast/workshop2016/dynamo In order to activate your local Dynamo version, please type:

run /Users/gast/workshop2016/dynamo/dynamo_activate.m

Connecting to the instructors file share

Some files will be made available through a mounting the file system of the instructor's computer. You can mount this share by typing in Matlab

 run /Users/gast/mountData 

which will make the file share /Users/gast/mountedData visible in your workstation. You will need this in order to transfer our test data sets to your local machine.

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

   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.
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.

1. open the dynamo standalone.

dynamo x

1. create a tutorial project

dtutorial myTest -p ptest -M 128

1. tune the project to work in a GPU

dvput ptest -destination system_gpu

1. undold the project

dvunfold ptest.exe

Strubi Oxforfd

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