Summary of videos
Why do we have these video summaries?
There are some important topics that you need to know.
But we can’t teach them every time (and don’t need to).
Modern tech to the rescue! We teach them occasionally and you can watch at your own pace.
Still, we want to summarize them now.
Scientific computing workflows
There are many ways to do your work, from
Your own laptop
Remote desktop system
All of these have their own role.
Days 2-3 of this course are about the cluster computing.
But many people don’t need to go so far
Or start off and it becomes difficult to go further.
Plan for the future
It is good to start simple when developing.
Eventually you need:
More computing power for a single task
To do it automatically, over and over again.
Then, you need to be able to move up this “computing ladder”
It pays to learn how to design your code/analysis workflow to grow:
Design for reusable with different parameters and data
Command line interfaces
Split the calculation from the analysis
Where to go next?
Each university hopefully has some guide to the different services
Don’t get locked into the lower levels
Slowly move up as you need
Ask for help when needed.
Basic Linux shell and scripting
Like we said above, sometimes you need to do things over and over again.
Clicking buttons is not scaleable.
The command line is the standard way of automating programs.
It is also the standard way of interacting with servers or clusters.
What’s the command line?
Current interface developed as part of UNIX in 1960-70s, now used by almost everything.
Interface includes program name and arguments
For example, you can run to copy a file:
cp source.txt destination.txt
Or you can run a program with arguments:
./your_code --argument1 input1 input2 -o output2
These can equally be done interactively (in the shell) or via a shell script.
Making a reusable program
Separating parameters from code
Connecting different programs together
Automating things for yourself
Automating things for the cluster
Where to go next?
You really need to know some basics
Watching these crash course videos and attending this course is plenty for now.
Don’t be scared, ask for help about what you need to do
You don’t need to go very deep at the start