A comprehensive manual for beginners

This page is currently under construction and will be completed soon.

This manual is intended for new users who are unfamiliar with MetaCentrum NGI (National Grid Infrastructure) or any similar infrastructure. However, it isn’t easy to summarise the detailed use of the entire infrastructure in a reasonably short guide. The following tutorial aims to provide the minimum necessary knowledge to enable new users to start calculating without any crucial problems as soon as possible.

If you are confused, please let us know

Sometimes, problems can be too complicated, and error messages can be too cryptic. Please do not hesitate to contact user support as soon as possible and ask for help. We are here to help you. But this is also important for us. It is sometimes necessary to catch inconsistent system behaviour in the act, because it is not possible to detect the cause of an error from the system logs afterwards.

Available software tools

We provide access to several hundred application tools in thousands of individual modules. For this reason, we are unable to periodically monitor and update all of them, and also, our list of available tools only includes those that require some further description. We rely on our users to inform us when a tool needs updating, and we recommend simpler installations in the home directory (with our assistance if required).

Where is my data located, and why are there so many frontend servers?

The main principle of the grid infrastructure is that it connects various compute clusters that are distributed across the Czech Republic. The same scheme applies to storage servers, where data is located, and frontend servers, which are the main access points. This is to distribute the user load across multiple localities and prevent all users from losing access to all data in the event of a technical problem.

Users can, however, use any frontend server to access data on any storage server. Each frontend server is mounted on an individual storage server, and all storage servers are accessible across MetaCentrum. You can use the standard Linux command cp to move yourself (or the current working directory) between storage servers. For example, the frontend server nympha (nympha.metacentrum.cz) is mounted on the storage server storage-plzen1.metacentrum.cz, which is accessible from compute nodes and other frontend servers via the path /storage/plzen1/home/user_name. However, switching to a different storage server is simple if needed.

local_user_name@local_pc_name:~$ ssh user_name@nympha.metacentrum.cz
...
(BOOKWORM)user_name@nympha:~$ pwd
/storage/plzen1/home/user_name
(BOOKWORM)user_name@nympha:~$ cd /storage/brno2/home/user_name
(BOOKWORM)user_name@nympha:/storage/brno2/home/user_name$ pwd
/storage/brno2/home/user_name
(BOOKWORM)user_name@nympha:/storage/brno2/home/user_name$ cd /storage/brno12-cerit/home/user_name
(BOOKWORM)user_name@nympha:/storage/brno12-cerit/home/user_name$ pwd
/storage/brno12-cerit/home/user_name