Difference between revisions of "Computers Basel 2016"

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=== Using ''Dynamo''===
 
=== Using ''Dynamo''===
 
We are using a slightly older version of ''Dynamo'' on the supercomputer GPUs for compatibility reasons
 
We are using a slightly older version of ''Dynamo'' on the supercomputer GPUs for compatibility reasons
#On the local machine, tar your project in'' Dynamo'' (in <tt>Dynamo wizard >> Tools >> Create a tarball</tt>
+
;On the local machine
 +
#tar your project in'' Dynamo'' (in <tt>Dynamo wizard >> Tools >> Create a tarball</tt>
 
#<tt>rsync -avr my_project.tar stud##@ela.cscs.ch:~/</tt>
 
#<tt>rsync -avr my_project.tar stud##@ela.cscs.ch:~/</tt>
 
## hi
 
## hi
 
#Also rsync your data to CSCS
 
#Also rsync your data to CSCS
 
#Untar your ''Dynamo'' project (dvuntar)
 
#Untar your ''Dynamo'' project (dvuntar)
#On CSCS, after <tt>salloc --gres=gpu:1</tt>, type: <tt>source ~/bin/dynamoFlorida/dynamo_activate_linux_shipped_MCR.sh</tt>
+
;On CSCS, after <tt>salloc --gres=gpu:1</tt>, type: <tt>source ~/bin/dynamoFlorida/dynamo_activate_linux_shipped_MCR.sh</tt>
 
#Open ''Dynamo'' with <tt> ' dynamo & '</tt>, 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)
 
#Open ''Dynamo'' with <tt> ' dynamo & '</tt>, 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)
 
#Run your alignment by typing  <tt>srun my_project.exe</tt>
 
#Run your alignment by typing  <tt>srun my_project.exe</tt>

Revision as of 07:31, 18 August 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:~/
    1. hi
  3. Also rsync your data to CSCS
  4. Untar your Dynamo project (dvuntar)
On CSCS, after salloc --gres=gpu:1, type
source ~/bin/dynamoFlorida/dynamo_activate_linux_shipped_MCR.sh
  1. Open Dynamo with ' dynamo & ', 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)
  2. Run your alignment by typing srun my_project.exe

Strubi Oxforfd

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