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The computer environment

You will be working in a network environment with a central server architecture, local desktop computers like the one your are sitting on, and a compute cluster.

SpecificsApplBioCluster

SpecificsApplBioCluster

There are some things that you should keep in mind

  • :!: we have a central file server, where all your data is stored at. Thus, no matter on which computer you are logged on, you will always see your data!
  • :!: The data from all users are stored on the file server, and you can access every user's home directory and the data therein, in principle
  • :!: Many of the desktop computers are not very powerful. For more compute-intensive jobs, you will need to use our compute servers which have up to 1 TB of RAM
  • :!: Only the home directories are backed up. So make sure that important data that cannot be easily reproduced, is stored there

The operating system is Linux. You will be also get in touch with quite a number of different softwares. Instead of providing you with a nice, shiny (and almost impossible to reproduce) pre-configured computer system, we will be using the Anaconda package management system to set up our working environment. Anaconda, which is a virtual environment grants you local superuser privileges that facilitates an easy installation of software used in the Life Sciences. You can also use Anaconda on your own laptop.

General set up

You will be working with Linux as the operation system. For quite some time, the various flavors of Linux have adapted to what people are used from Windows or Mac operating systems. Basically, you have a considerably intuitive window based access to your computer. However, we will make rather extensive use of the shell that facilitates a text and command line based control of the computer. Specifically we will use the bash (Fig. 1), as many tools we will be using can be called only from the command line. It is, thus, necessary to get accustomed to the way how data and directories are organized under Linux.

Figure 1: The bash represents a terminal with which you can directly interact with the computer. You can use the bash to read and write files; generate, copy, move or delete directories; as well as executing or stopping programs. There are many ways to customize the appearance of the bash. An explanation in German can be found here.

The compute cluster

In addition to the shared disc space there is also shared computation power in the form of a computer cluster, i.e. the connection of many computers to allow parallel and distributed computing. In essence, this speeds up of calculation by spreading the compute load to multiple computers, and in additions jobs can be run that are simply too large for a local desktop computer. The use of the cluster is simple and it is controlled by a queuing system, in our case SLURM.

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