GPUs EMBO 2016
CSCS in Lugano is the Swiss Nacional Supercomputing Centre. CSCS kindly provides the EMBO course with 20 accounts. Each account should be able to submit jobs to a single node connected to a K20 GPU and four CPU cores.
Connecting with CSCS
First you need to connect to the gate node ela using your cscs credentials from the credentials handout.
ssh -Y firstname.lastname@example.org
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
An installation is ready in the account course27. Just copy it onto your own account. scp -r /users/course27/dynamo ~
Afterwards you will be able to activate Dynamo in your linux session by: source /users/courseXX/dynamo/dynamo_activate_linux_shippedMCR.sh
We are using a slightly older version of Dynamo on the supercomputer GPUs for compatibility reasons.
In a remote machine, things run differently: computing power is orders of magnitude higher, at the price of interfaces running slower and Matlab normally not being available. This makes the way you interact with Dynamo slightly more complicated. Commandline management of projects is often a more efficient way than using GUIs.
We recommend to use two shells in the remote machine.
- One remote shell is used to open a Dynamo console.
In this shell, we can create and manage projects, inspect files, even show moderately complex graphics. We call this the console shell. In this console shell, we don't have don't need to have access to a GPU.
- Another the shell is used for number crunching, we call it a computing shell.
In this example, we show how to transfer a project from a local machine into the remote system, by Dynamo-tarring a project in a local machine, copying it into a remote machine and untarring it there.
- On the local machine
- tar your project in Dynamo (in Dynamo wizard >> Tools >> Create a tarball
- rsync -avr my_project.tar email@example.com:~/
- Also rsync your data to CSCS
- Untar your Dynamo project
- You will need the Dynamo terminal for this:
- dynamo &
- dvuntar myProject
- On CSCS,
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:
to activate Dynamo in your shell.
- 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)
- 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
- run your alignment by typing srun my_project.exe
Creating tutorial projects
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:
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 matlab_gpu
- unfold the project
- dvunfold ptest inside the Dynamo console
- run the project with srun in a computing shell
- 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.